Starting phenix.real_space_refine
on Tue Mar  3 12:02:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zr8_14886/03_2026/7zr8_14886.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zr8_14886/03_2026/7zr8_14886.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zr8_14886/03_2026/7zr8_14886.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zr8_14886/03_2026/7zr8_14886.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zr8_14886/03_2026/7zr8_14886.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zr8_14886/03_2026/7zr8_14886.map"
  }
  resolution = 3.7
  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=   0.012
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      18      5.16       5
     C    2346      2.51       5
     N     623      2.21       5
     O     706      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3693
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1945
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1945
          Classifications: {'peptide': 245}
          Link IDs: {'PTRANS': 13, 'TRANS': 231}
    Chain: "H"
      Number of atoms: 900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 900
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 4, 'TRANS': 113}
    Chain: "L"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 0.95, per 1000 atoms: 0.26
  Number of scatterers: 3693
  At special positions: 0
  Unit cell: (68.06, 75.53, 111.22, 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      18     16.00
     O     706      8.00
     N     623      7.00
     C    2346      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 333 " - pdb=" SG  CYS A 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 376 " - pdb=" SG  CYS A 429 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 388 " - pdb=" SG  CYS A 522 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 477 " - pdb=" SG  CYS A 485 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03

  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 A1301 " - " ASN A 340 "
  Time building additional restraints: 0.31
  Conformation dependent library (CDL) restraints added in 132.8 milliseconds
  

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  866

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 12 sheets defined
      9.6% alpha, 32.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 346 through 350
      removed outlier: 3.601A  pdb=" N   TRP A 350 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 367
    Processing helix  chain 'A' and resid 381 through 386
      removed outlier: 4.017A  pdb=" N   ASN A 385 " --> pdb=" O   THR A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 407
      removed outlier: 4.371A  pdb=" N   ARG A 405 " --> pdb=" O   ASP A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 419
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 4.137A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.714A  pdb=" N   PHE L  83 " --> pdb=" O   PRO L  80 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 321 through 323
      removed outlier: 7.131A  pdb=" N   GLU A 321 " --> pdb=" O   ASN A 537 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   ASN A 539 " --> pdb=" O   GLU A 321 " (cutoff:3.500A)
      removed outlier: 7.431A  pdb=" N   ILE A 323 " --> pdb=" O   ASN A 539 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 321 through 323
      removed outlier: 7.131A  pdb=" N   GLU A 321 " --> pdb=" O   ASN A 537 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   ASN A 539 " --> pdb=" O   GLU A 321 " (cutoff:3.500A)
      removed outlier: 7.431A  pdb=" N   ILE A 323 " --> pdb=" O   ASN A 539 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 351 through 355
      removed outlier: 3.569A  pdb=" N   LYS A 353 " --> pdb=" O   ALA A 394 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   TRP A 433 " --> pdb=" O   ARG A 506 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 358 through 359
      removed outlier: 6.794A  pdb=" N   CYS A 358 " --> pdb=" O   CYS A 522 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 449 through 451
    Processing sheet with id=AA6, first strand: chain 'A' and resid 470 through 471
    Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.926A  pdb=" N   THR H 112 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   THR H  33 " --> pdb=" O   SER H  99 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   ILE H  34 " --> pdb=" O   ARG H  50 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   ARG H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   TRP H  36 " --> pdb=" O   MET H  48 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.926A  pdb=" N   THR H 112 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   VAL H 107 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   GLY H 100 " --> pdb=" O   PHE H 105 " (cutoff:3.500A)
      removed outlier: 5.996A  pdb=" N   PHE H 105 " --> pdb=" O   GLY H 100 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 7
      removed outlier: 3.530A  pdb=" N   VAL L  19 " --> pdb=" O   ILE L  75 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   GLU L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   SER L  67 " --> pdb=" O   GLU L  70 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13
    Processing sheet with id=AB3, first strand: chain 'L' and resid 35 through 37
      removed outlier: 6.339A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)

    112 hydrogen bonds defined for protein.
    252 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.45

  Time building geometry restraints manager: 0.42 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1178
        1.34 -     1.46: 930
        1.46 -     1.58: 1653
        1.58 -     1.69: 0
        1.69 -     1.81: 23
  Bond restraints: 3784
  Sorted by residual:
  bond pdb=" C1  NAG A1301 "
       pdb=" O5  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.92e+00
  bond pdb=" C5  NAG A1301 "
       pdb=" O5  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.23e+00
  bond pdb=" C3  NAG A1301 "
       pdb=" O3  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 1.03e+00
  bond pdb=" C2  NAG A1301 "
       pdb=" N2  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.439  1.455 -0.016 2.00e-02 2.50e+03 6.08e-01
  bond pdb=" C4  NAG A1301 "
       pdb=" O4  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.409  1.423 -0.014 2.00e-02 2.50e+03 4.82e-01
  ... (remaining 3779 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.15: 4994
        1.15 -     2.31: 101
        2.31 -     3.46: 37
        3.46 -     4.61: 4
        4.61 -     5.77: 1
  Bond angle restraints: 5137
  Sorted by residual:
  angle pdb=" N   ILE L  29 "
        pdb=" CA  ILE L  29 "
        pdb=" C   ILE L  29 "
      ideal   model   delta    sigma   weight residual
     111.77  109.00    2.77 1.04e+00 9.25e-01 7.10e+00
  angle pdb=" C   ALA A 517 "
        pdb=" N   PRO A 518 "
        pdb=" CA  PRO A 518 "
      ideal   model   delta    sigma   weight residual
     121.65  119.16    2.49 1.01e+00 9.80e-01 6.07e+00
  angle pdb=" N   ASP H 103 "
        pdb=" CA  ASP H 103 "
        pdb=" CB  ASP H 103 "
      ideal   model   delta    sigma   weight residual
     113.65  110.44    3.21 1.47e+00 4.63e-01 4.78e+00
  angle pdb=" N   TYR L  94 "
        pdb=" CA  TYR L  94 "
        pdb=" C   TYR L  94 "
      ideal   model   delta    sigma   weight residual
     112.97  110.97    2.00 1.06e+00 8.90e-01 3.57e+00
  angle pdb=" C   ASP L  50 "
        pdb=" N   ALA L  51 "
        pdb=" CA  ALA L  51 "
      ideal   model   delta    sigma   weight residual
     121.54  125.02   -3.48 1.91e+00 2.74e-01 3.32e+00
  ... (remaining 5132 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.18: 2044
       10.18 -    20.36: 146
       20.36 -    30.54: 47
       30.54 -    40.72: 13
       40.72 -    50.90: 5
  Dihedral angle restraints: 2255
    sinusoidal: 893
      harmonic: 1362
  Sorted by residual:
  dihedral pdb=" CA  LEU L  33 "
           pdb=" CB  LEU L  33 "
           pdb=" CG  LEU L  33 "
           pdb=" CD1 LEU L  33 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  129.10   50.90     3      1.50e+01 4.44e-03 8.95e+00
  dihedral pdb=" CA  PRO A 524 "
           pdb=" C   PRO A 524 "
           pdb=" N   LYS A 525 "
           pdb=" CA  LYS A 525 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.32   14.68     0      5.00e+00 4.00e-02 8.62e+00
  dihedral pdb=" N   TYR A 498 "
           pdb=" CA  TYR A 498 "
           pdb=" CB  TYR A 498 "
           pdb=" CG  TYR A 498 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -108.10   48.10     3      1.50e+01 4.44e-03 8.59e+00
  ... (remaining 2252 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 340
       0.030 -    0.059: 142
       0.059 -    0.089: 30
       0.089 -    0.118: 42
       0.118 -    0.148: 4
  Chirality restraints: 558
  Sorted by residual:
  chirality pdb=" CA  ILE L  48 "
            pdb=" N   ILE L  48 "
            pdb=" C   ILE L  48 "
            pdb=" CB  ILE L  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.46e-01
  chirality pdb=" CA  ILE L  21 "
            pdb=" N   ILE L  21 "
            pdb=" C   ILE L  21 "
            pdb=" CB  ILE L  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.12e-01
  chirality pdb=" CA  ILE A 399 "
            pdb=" N   ILE A 399 "
            pdb=" C   ILE A 399 "
            pdb=" CB  ILE A 399 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.88e-01
  ... (remaining 555 not shown)

  Planarity restraints: 664
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER L  95 "   -0.032 5.00e-02 4.00e+02   4.90e-02 3.83e+00
        pdb=" N   PRO L  96 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO L  96 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO L  96 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 326 "   -0.017 5.00e-02 4.00e+02   2.62e-02 1.10e+00
        pdb=" N   PRO A 327 "    0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO A 327 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 327 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 557 "   -0.017 5.00e-02 4.00e+02   2.54e-02 1.03e+00
        pdb=" N   PRO A 558 "    0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO A 558 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 558 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 661 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 174
        2.73 -     3.27: 3512
        3.27 -     3.81: 5835
        3.81 -     4.36: 7174
        4.36 -     4.90: 12818
  Nonbonded interactions: 29513
  Sorted by model distance:
  nonbonded pdb=" OH  TYR L  36 "
            pdb=" OE1 GLN L  89 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" OG1 THR H  33 "
            pdb=" OG  SER H  99 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OE1 GLN L   6 "
            pdb=" OG1 THR L 103 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   LYS H  13 "
            pdb=" OG  SER H  16 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   GLN L  90 "
            pdb=" N   GLU L  92 "
     model   vdw
     2.291 3.120
  ... (remaining 29508 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:             5.710
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.590
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3791  Z= 0.124
  Angle     :  0.466   5.767   5152  Z= 0.249
  Chirality :  0.042   0.148    558
  Planarity :  0.004   0.049    663
  Dihedral  :  8.421  50.903   1371
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  3.71 %
    Favored  : 95.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -0.94 (0.42), residues: 465
  helix: -3.12 (0.74), residues: 33
  sheet: -0.75 (0.46), residues: 156
  loop : -0.08 (0.41), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 506 
 TYR   0.009   0.001   TYR L  91 
 PHE   0.009   0.001   PHE A 426 
 TRP   0.006   0.001   TRP H  47 
 HIS   0.001   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 3784)
  covalent geometry    : angle       0.46498 ( 5137)
  SS BOND              : bond        0.00113 (    6)
  SS BOND              : angle       0.33517 (   12)
  hydrogen bonds       : bond        0.24152 (  106)
  hydrogen bonds       : angle      11.62971 (  252)
  link_NAG-ASN         : bond        0.00039 (    1)
  link_NAG-ASN         : angle       1.33788 (    3)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 86
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  329 ILE cc_start: 0.9035 (tp) cc_final: 0.8645 (pt)
REVERT: A  343 ARG cc_start: 0.9345 (mtt-85) cc_final: 0.9013 (ttm-80)
REVERT: A  511 SER cc_start: 0.9440 (m) cc_final: 0.9192 (t)
REVERT: A  532 LYS cc_start: 0.8724 (mttt) cc_final: 0.8496 (mttp)
  outliers start: 3
  outliers final: 1
  residues processed: 89
  average time/residue: 0.0952
  time to fit residues: 9.9316
Evaluate side-chains
  67 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 66
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  365 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:    0.1980
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.2980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 357 ASN
A 539 ASN
L   6 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.157178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.129897 restraints weight = 4452.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.130648 restraints weight = 4009.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.131402 restraints weight = 3725.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.132262 restraints weight = 3502.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.132341 restraints weight = 3315.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.1445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3791  Z= 0.208
  Angle     :  0.555   4.808   5152  Z= 0.301
  Chirality :  0.045   0.157    558
  Planarity :  0.005   0.045    663
  Dihedral  :  4.689  44.991    541
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 10.89 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -0.82 (0.42), residues: 465
  helix: -3.20 (0.92), residues: 28
  sheet: -0.76 (0.45), residues: 153
  loop :  0.01 (0.41), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  50 
 TYR   0.021   0.002   TYR L  91 
 PHE   0.012   0.001   PHE A 426 
 TRP   0.008   0.001   TRP H 108 
 HIS   0.002   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 ( 3784)
  covalent geometry    : angle       0.55376 ( 5137)
  SS BOND              : bond        0.00424 (    6)
  SS BOND              : angle       0.64268 (   12)
  hydrogen bonds       : bond        0.04534 (  106)
  hydrogen bonds       : angle       7.66274 (  252)
  link_NAG-ASN         : bond        0.00076 (    1)
  link_NAG-ASN         : angle       1.73946 (    3)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  329 ILE cc_start: 0.9108 (tp) cc_final: 0.8815 (pt)
REVERT: A  343 ARG cc_start: 0.9289 (mtt-85) cc_final: 0.9033 (ttm-80)
REVERT: L   38 GLN cc_start: 0.9182 (tt0) cc_final: 0.8731 (tt0)
  outliers start: 12
  outliers final: 8
  residues processed: 77
  average time/residue: 0.0900
  time to fit residues: 8.1281
Evaluate side-chains
  75 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   35 SER
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   74 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 5 optimal weight:    0.3980
   chunk 29 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 44 optimal weight:    0.2980
   chunk 35 optimal weight:    0.7980
   chunk 24 optimal weight:    0.3980
   chunk 10 optimal weight:    0.0470
   overall best weight:    0.3478

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

Flipped N/Q/H residues before XYZ refinement:
A 357 ASN
A 539 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.158535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.132099 restraints weight = 4327.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.133113 restraints weight = 3945.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.133468 restraints weight = 3665.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.134273 restraints weight = 3516.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 14)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.134420 restraints weight = 3365.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3791  Z= 0.138
  Angle     :  0.506   5.761   5152  Z= 0.269
  Chirality :  0.044   0.147    558
  Planarity :  0.004   0.042    663
  Dihedral  :  4.671  51.080    541
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 12.87 %
    Favored  : 84.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -0.82 (0.41), residues: 465
  helix: -3.23 (0.87), residues: 28
  sheet: -0.77 (0.43), residues: 153
  loop :  0.02 (0.40), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 325 
 TYR   0.014   0.001   TYR L  91 
 PHE   0.008   0.001   PHE A 540 
 TRP   0.009   0.001   TRP A 433 
 HIS   0.001   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3784)
  covalent geometry    : angle       0.50440 ( 5137)
  SS BOND              : bond        0.00485 (    6)
  SS BOND              : angle       0.71342 (   12)
  hydrogen bonds       : bond        0.03592 (  106)
  hydrogen bonds       : angle       6.76358 (  252)
  link_NAG-ASN         : bond        0.00055 (    1)
  link_NAG-ASN         : angle       1.43991 (    3)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  329 ILE cc_start: 0.9095 (tp) cc_final: 0.8793 (pt)
REVERT: L   38 GLN cc_start: 0.9159 (tt0) cc_final: 0.8734 (tt0)
  outliers start: 12
  outliers final: 8
  residues processed: 72
  average time/residue: 0.0888
  time to fit residues: 7.5527
Evaluate side-chains
  67 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  540 PHE
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   35 SER
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain L residue   10 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 0 optimal weight:    0.9990
   chunk 22 optimal weight:    0.3980
   chunk 1 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 3 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:
A 434 ASN
A 539 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.160641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.136283 restraints weight = 4365.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.136023 restraints weight = 3894.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.135794 restraints weight = 3750.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.135947 restraints weight = 3655.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.136041 restraints weight = 3542.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.1986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   3791  Z= 0.213
  Angle     :  0.547   5.637   5152  Z= 0.292
  Chirality :  0.045   0.159    558
  Planarity :  0.004   0.042    663
  Dihedral  :  4.913  56.210    541
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 14.36 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -1.05 (0.40), residues: 465
  helix: -3.23 (0.85), residues: 29
  sheet: -0.91 (0.42), residues: 153
  loop : -0.17 (0.39), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 454 
 TYR   0.016   0.002   TYR L  91 
 PHE   0.013   0.001   PHE A 426 
 TRP   0.009   0.002   TRP A 433 
 HIS   0.002   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 ( 3784)
  covalent geometry    : angle       0.54375 ( 5137)
  SS BOND              : bond        0.00221 (    6)
  SS BOND              : angle       0.92734 (   12)
  hydrogen bonds       : bond        0.03552 (  106)
  hydrogen bonds       : angle       6.70881 (  252)
  link_NAG-ASN         : bond        0.00026 (    1)
  link_NAG-ASN         : angle       1.81050 (    3)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  329 ILE cc_start: 0.9100 (tp) cc_final: 0.8816 (pt)
  outliers start: 12
  outliers final: 11
  residues processed: 71
  average time/residue: 0.0798
  time to fit residues: 6.7464
Evaluate side-chains
  72 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   35 SER
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   22 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0980
   chunk 25 optimal weight:    4.9990
   chunk 13 optimal weight:    0.3980
   chunk 19 optimal weight:    0.0980
   chunk 0 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0770
   overall best weight:    0.3138

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

Flipped N/Q/H residues before XYZ refinement:
A 539 ASN
** L  90 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 = 0.3753 r_free = 0.3753 target = 0.159074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.135113 restraints weight = 4354.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.134923 restraints weight = 3916.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.134552 restraints weight = 4032.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.134599 restraints weight = 3789.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.134676 restraints weight = 3828.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.2163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3791  Z= 0.130
  Angle     :  0.510   6.719   5152  Z= 0.272
  Chirality :  0.044   0.148    558
  Planarity :  0.004   0.040    663
  Dihedral  :  4.781  58.639    541
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 13.86 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -1.02 (0.40), residues: 465
  helix: -3.12 (0.85), residues: 29
  sheet: -0.94 (0.41), residues: 154
  loop : -0.12 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 325 
 TYR   0.013   0.001   TYR L  91 
 PHE   0.007   0.001   PHE A 540 
 TRP   0.010   0.001   TRP A 433 
 HIS   0.001   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 3784)
  covalent geometry    : angle       0.50754 ( 5137)
  SS BOND              : bond        0.00213 (    6)
  SS BOND              : angle       0.87237 (   12)
  hydrogen bonds       : bond        0.03085 (  106)
  hydrogen bonds       : angle       6.27676 (  252)
  link_NAG-ASN         : bond        0.00056 (    1)
  link_NAG-ASN         : angle       1.43929 (    3)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  564 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6210 (ptp90)
  outliers start: 17
  outliers final: 12
  residues processed: 74
  average time/residue: 0.0769
  time to fit residues: 6.9317
Evaluate side-chains
  70 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  540 PHE
Chi-restraints excluded: chain A residue  564 ARG
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   35 SER
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue   74 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 19 optimal weight:    0.1980
   chunk 31 optimal weight:    0.0570
   chunk 30 optimal weight:    0.9990
   chunk 3 optimal weight:    0.3980
   chunk 27 optimal weight:    1.9990
   chunk 34 optimal weight:    0.1980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.2898

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

Flipped N/Q/H residues before XYZ refinement:
A 539 ASN
** L  90 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 = 0.3784 r_free = 0.3784 target = 0.161806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.133107 restraints weight = 4400.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.134279 restraints weight = 3714.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.135948 restraints weight = 3334.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.136681 restraints weight = 3042.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.136681 restraints weight = 2858.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3791  Z= 0.123
  Angle     :  0.511   7.360   5152  Z= 0.269
  Chirality :  0.044   0.146    558
  Planarity :  0.004   0.041    663
  Dihedral  :  4.541  51.199    541
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 14.60 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -0.87 (0.41), residues: 465
  helix: -2.92 (0.87), residues: 29
  sheet: -0.81 (0.41), residues: 154
  loop : -0.05 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 325 
 TYR   0.013   0.001   TYR A 486 
 PHE   0.014   0.001   PHE A 540 
 TRP   0.009   0.001   TRP A 433 
 HIS   0.001   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 3784)
  covalent geometry    : angle       0.50901 ( 5137)
  SS BOND              : bond        0.00242 (    6)
  SS BOND              : angle       0.84481 (   12)
  hydrogen bonds       : bond        0.02916 (  106)
  hydrogen bonds       : angle       6.01833 (  252)
  link_NAG-ASN         : bond        0.00074 (    1)
  link_NAG-ASN         : angle       1.37655 (    3)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 57
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  564 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6248 (ptp90)
  outliers start: 17
  outliers final: 13
  residues processed: 67
  average time/residue: 0.0707
  time to fit residues: 5.9370
Evaluate side-chains
  68 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  539 ASN
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  564 ARG
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   35 SER
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue   60 SER
Chi-restraints excluded: chain L residue   74 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0870
   chunk 11 optimal weight:    0.0980
   chunk 6 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.3958

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

Flipped N/Q/H residues before XYZ refinement:
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 539 ASN
** L  90 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 = 0.3756 r_free = 0.3756 target = 0.159300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.133484 restraints weight = 4454.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.134279 restraints weight = 4019.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.135328 restraints weight = 3700.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.135723 restraints weight = 3490.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 15)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.135867 restraints weight = 3328.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3791  Z= 0.148
  Angle     :  0.521   7.761   5152  Z= 0.276
  Chirality :  0.044   0.148    558
  Planarity :  0.004   0.040    663
  Dihedral  :  4.500  47.441    541
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 13.86 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -0.87 (0.40), residues: 465
  helix: -2.85 (0.88), residues: 29
  sheet: -0.77 (0.41), residues: 154
  loop : -0.07 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 325 
 TYR   0.013   0.001   TYR A 486 
 PHE   0.008   0.001   PHE A 540 
 TRP   0.008   0.001   TRP A 433 
 HIS   0.001   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 3784)
  covalent geometry    : angle       0.51884 ( 5137)
  SS BOND              : bond        0.00225 (    6)
  SS BOND              : angle       0.91472 (   12)
  hydrogen bonds       : bond        0.02961 (  106)
  hydrogen bonds       : angle       5.99834 (  252)
  link_NAG-ASN         : bond        0.00067 (    1)
  link_NAG-ASN         : angle       1.44291 (    3)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 55
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 PHE cc_start: 0.8830 (m-80) cc_final: 0.8598 (m-80)
REVERT: A  564 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6245 (ptp90)
REVERT: H  112 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8316 (t)
  outliers start: 18
  outliers final: 13
  residues processed: 67
  average time/residue: 0.0766
  time to fit residues: 6.3500
Evaluate side-chains
  69 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 54
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  564 ARG
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   35 SER
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue   60 SER
Chi-restraints excluded: chain L residue   74 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 17 optimal weight:    0.3980
   chunk 3 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 2 optimal weight:    0.2980
   chunk 42 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0970
   chunk 0 optimal weight:    0.9990
   chunk 22 optimal weight:    0.1980
   chunk 1 optimal weight:    0.0170
   chunk 6 optimal weight:    0.9980
   chunk 38 optimal weight:    0.4980
   overall best weight:    0.2016

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

Flipped N/Q/H residues before XYZ refinement:
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 539 ASN
** L  90 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 = 0.3779 r_free = 0.3779 target = 0.161373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.136377 restraints weight = 4315.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.137135 restraints weight = 3852.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.138179 restraints weight = 3576.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.138463 restraints weight = 3351.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.138913 restraints weight = 3235.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   3791  Z= 0.105
  Angle     :  0.508   8.639   5152  Z= 0.269
  Chirality :  0.044   0.142    558
  Planarity :  0.004   0.040    663
  Dihedral  :  4.152  37.327    541
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 14.11 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -0.69 (0.41), residues: 465
  helix: -2.79 (0.88), residues: 29
  sheet: -0.58 (0.41), residues: 154
  loop :  0.00 (0.41), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 325 
 TYR   0.013   0.001   TYR A 486 
 PHE   0.010   0.001   PHE A 540 
 TRP   0.009   0.001   TRP A 433 
 HIS   0.001   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 3784)
  covalent geometry    : angle       0.50622 ( 5137)
  SS BOND              : bond        0.00265 (    6)
  SS BOND              : angle       0.83746 (   12)
  hydrogen bonds       : bond        0.02732 (  106)
  hydrogen bonds       : angle       5.70526 (  252)
  link_NAG-ASN         : bond        0.00091 (    1)
  link_NAG-ASN         : angle       1.23140 (    3)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 59
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  564 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6255 (ptp90)
REVERT: H  112 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8284 (t)
  outliers start: 16
  outliers final: 11
  residues processed: 70
  average time/residue: 0.0732
  time to fit residues: 6.2958
Evaluate side-chains
  69 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  539 ASN
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  564 ARG
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue   60 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0770
   chunk 26 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0870
   chunk 5 optimal weight:    0.3980
   chunk 12 optimal weight:    0.0980
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.2516

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

Flipped N/Q/H residues before XYZ refinement:
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 539 ASN
** L  90 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 = 0.3777 r_free = 0.3777 target = 0.161149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.135377 restraints weight = 4335.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.136628 restraints weight = 3863.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.137225 restraints weight = 3558.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.137225 restraints weight = 3338.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.137225 restraints weight = 3338.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3791  Z= 0.116
  Angle     :  0.521   8.653   5152  Z= 0.274
  Chirality :  0.044   0.152    558
  Planarity :  0.004   0.040    663
  Dihedral  :  3.794  15.502    539
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 15.10 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -0.67 (0.41), residues: 465
  helix: -2.67 (0.92), residues: 29
  sheet: -0.56 (0.41), residues: 154
  loop :  0.01 (0.41), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 325 
 TYR   0.018   0.001   TYR A 450 
 PHE   0.009   0.001   PHE A 540 
 TRP   0.008   0.001   TRP A 433 
 HIS   0.001   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 3784)
  covalent geometry    : angle       0.51939 ( 5137)
  SS BOND              : bond        0.00232 (    6)
  SS BOND              : angle       0.85426 (   12)
  hydrogen bonds       : bond        0.02784 (  106)
  hydrogen bonds       : angle       5.67345 (  252)
  link_NAG-ASN         : bond        0.00108 (    1)
  link_NAG-ASN         : angle       1.26781 (    3)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  564 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6278 (ptp90)
REVERT: H   34 ILE cc_start: 0.9080 (mm) cc_final: 0.8846 (mt)
REVERT: H  112 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8252 (t)
  outliers start: 14
  outliers final: 10
  residues processed: 66
  average time/residue: 0.0770
  time to fit residues: 6.2876
Evaluate side-chains
  68 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  564 ARG
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue   60 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0870
   chunk 8 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 35 optimal weight:    0.1980
   chunk 23 optimal weight:    0.0470
   overall best weight:    0.3656

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

Flipped N/Q/H residues before XYZ refinement:
A 328 ASN
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 539 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.158849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.133033 restraints weight = 4400.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.134023 restraints weight = 3919.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.134408 restraints weight = 3620.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.134408 restraints weight = 3464.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.134408 restraints weight = 3464.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.2652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3791  Z= 0.143
  Angle     :  0.538   8.975   5152  Z= 0.283
  Chirality :  0.044   0.146    558
  Planarity :  0.004   0.040    663
  Dihedral  :  3.881  14.749    539
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 14.36 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -0.67 (0.41), residues: 465
  helix: -2.66 (0.93), residues: 29
  sheet: -0.60 (0.42), residues: 154
  loop :  0.03 (0.41), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 325 
 TYR   0.014   0.001   TYR A 486 
 PHE   0.007   0.001   PHE A 512 
 TRP   0.009   0.001   TRP H  36 
 HIS   0.001   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 3784)
  covalent geometry    : angle       0.53567 ( 5137)
  SS BOND              : bond        0.00225 (    6)
  SS BOND              : angle       0.92640 (   12)
  hydrogen bonds       : bond        0.02798 (  106)
  hydrogen bonds       : angle       5.74568 (  252)
  link_NAG-ASN         : bond        0.00074 (    1)
  link_NAG-ASN         : angle       1.41805 (    3)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 55
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  564 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6253 (ptp90)
REVERT: H  112 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8260 (t)
  outliers start: 17
  outliers final: 14
  residues processed: 65
  average time/residue: 0.0648
  time to fit residues: 5.2691
Evaluate side-chains
  71 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  540 PHE
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  564 ARG
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue   60 SER
Chi-restraints excluded: chain L residue   74 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 8 optimal weight:    0.2980
   chunk 38 optimal weight:    0.1980
   chunk 0 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 21 optimal weight:    0.4980
   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 328 ASN
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 539 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.158871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.133222 restraints weight = 4346.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.133790 restraints weight = 3898.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.134551 restraints weight = 3654.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.135392 restraints weight = 3439.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.135392 restraints weight = 3287.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3791  Z= 0.164
  Angle     :  0.545   8.833   5152  Z= 0.288
  Chirality :  0.045   0.146    558
  Planarity :  0.004   0.040    663
  Dihedral  :  3.912  14.536    539
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 15.10 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -0.72 (0.41), residues: 465
  helix: -2.72 (0.91), residues: 29
  sheet: -0.64 (0.41), residues: 154
  loop :  0.00 (0.41), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 325 
 TYR   0.014   0.001   TYR A 486 
 PHE   0.008   0.001   PHE A 512 
 TRP   0.008   0.001   TRP H  36 
 HIS   0.001   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 3784)
  covalent geometry    : angle       0.54261 ( 5137)
  SS BOND              : bond        0.00213 (    6)
  SS BOND              : angle       0.89234 (   12)
  hydrogen bonds       : bond        0.02839 (  106)
  hydrogen bonds       : angle       5.76338 (  252)
  link_NAG-ASN         : bond        0.00067 (    1)
  link_NAG-ASN         : angle       1.42904 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 928.90 seconds
wall clock time: 16 minutes 38.48 seconds (998.48 seconds total)