Starting phenix.real_space_refine
on Tue Mar  3 11:36:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jva_22497/03_2026/7jva_22497.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jva_22497/03_2026/7jva_22497.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jva_22497/03_2026/7jva_22497.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jva_22497/03_2026/7jva_22497.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jva_22497/03_2026/7jva_22497.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jva_22497/03_2026/7jva_22497.cif"
  }
  resolution = 3.6
  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=   0.021
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      15      5.16       5
     C    2068      2.51       5
     N     548      2.21       5
     O     617      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 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: 3248
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 911
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 911
          Classifications: {'peptide': 117}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 2, 'TRANS': 114}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "L"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 803
          Classifications: {'peptide': 110}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 6, 'TRANS': 103}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "A"
      Number of atoms: 1495
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1495
          Classifications: {'peptide': 193}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 11, 'TRANS': 181}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASN:plan1': 3, 'GLU:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "B"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 0.90, per 1000 atoms: 0.28
  Number of scatterers: 3248
  At special positions: 0
  Unit cell: (89.25, 75.6, 70.35, 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      15     16.00
     O     617      8.00
     N     548      7.00
     C    2068      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.09
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  91 " distance=2.04
    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=2.05
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.07

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
    NAG-ASN
      " NAG B   1 " - " ASN A 343 "
  Time building additional restraints: 0.22
  Conformation dependent library (CDL) restraints added in 87.5 milliseconds
  

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  766

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 10 sheets defined
      13.3% alpha, 35.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 62 through 65
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'L' and resid 28 through 32
      removed outlier: 4.028A  pdb=" N   ASN L  32 " --> pdb=" O   ILE L  29 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 69 through 71
      No H-bonds generated for 'chain 'L' and resid 69 through 71'
    Processing helix  chain 'A' and resid 337 through 343
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 386 through 390
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.358A  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 sheet with id=AA1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.815A  pdb=" N   MET H  34 " --> pdb=" O   ASN H  50 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   ASN H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11
      removed outlier: 3.922A  pdb=" N   TYR H 108 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 11
      removed outlier: 5.951A  pdb=" N   GLN L  38 " --> pdb=" O   THR L  47 " (cutoff:3.500A)
      removed outlier: 5.747A  pdb=" N   THR L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 11
    Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 23
    Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362
      removed outlier: 6.530A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474

    129 hydrogen bonds defined for protein.
    285 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: 0.49

  Time building geometry restraints manager: 0.30 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 586
        1.31 -     1.45: 1042
        1.45 -     1.58: 1682
        1.58 -     1.71: 4
        1.71 -     1.84: 18
  Bond restraints: 3332
  Sorted by residual:
  bond pdb=" CD  GLU H   6 "
       pdb=" OE2 GLU H   6 "
    ideal  model  delta    sigma   weight residual
    1.249  1.182  0.067 1.90e-02 2.77e+03 1.23e+01
  bond pdb=" CB  ASN A 422 "
       pdb=" CG  ASN A 422 "
    ideal  model  delta    sigma   weight residual
    1.516  1.437  0.079 2.50e-02 1.60e+03 9.92e+00
  bond pdb=" CB  ASN H  50 "
       pdb=" CG  ASN H  50 "
    ideal  model  delta    sigma   weight residual
    1.516  1.437  0.079 2.50e-02 1.60e+03 9.89e+00
  bond pdb=" C5  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.476 -0.063 2.00e-02 2.50e+03 9.85e+00
  bond pdb=" NE  ARG A 357 "
       pdb=" CZ  ARG A 357 "
    ideal  model  delta    sigma   weight residual
    1.326  1.360 -0.034 1.10e-02 8.26e+03 9.59e+00
  ... (remaining 3327 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.15: 4438
        4.15 -     8.30: 98
        8.30 -    12.45: 1
       12.45 -    16.60: 0
       16.60 -    20.75: 2
  Bond angle restraints: 4539
  Sorted by residual:
  angle pdb=" CD1 LEU H  86 "
        pdb=" CG  LEU H  86 "
        pdb=" CD2 LEU H  86 "
      ideal   model   delta    sigma   weight residual
     110.80  131.55  -20.75 2.20e+00 2.07e-01 8.89e+01
  angle pdb=" CG1 VAL H   2 "
        pdb=" CB  VAL H   2 "
        pdb=" CG2 VAL H   2 "
      ideal   model   delta    sigma   weight residual
     110.80  131.11  -20.31 2.20e+00 2.07e-01 8.52e+01
  angle pdb=" C   SER A 383 "
        pdb=" N   PRO A 384 "
        pdb=" CA  PRO A 384 "
      ideal   model   delta    sigma   weight residual
     119.56  127.19   -7.63 1.02e+00 9.61e-01 5.60e+01
  angle pdb=" C   LEU A 425 "
        pdb=" N   PRO A 426 "
        pdb=" CA  PRO A 426 "
      ideal   model   delta    sigma   weight residual
     119.85  126.34   -6.49 1.01e+00 9.80e-01 4.12e+01
  angle pdb=" C   GLN A 498 "
        pdb=" N   PRO A 499 "
        pdb=" CA  PRO A 499 "
      ideal   model   delta    sigma   weight residual
     119.56  126.05   -6.49 1.02e+00 9.61e-01 4.04e+01
  ... (remaining 4534 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.24: 1898
       21.24 -    42.49: 57
       42.49 -    63.73: 8
       63.73 -    84.98: 8
       84.98 -   106.22: 5
  Dihedral angle restraints: 1976
    sinusoidal: 767
      harmonic: 1209
  Sorted by residual:
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -36.13  -49.87     1      1.00e+01 1.00e-02 3.41e+01
  dihedral pdb=" O4  BMA B   3 "
           pdb=" C4  BMA B   3 "
           pdb=" C5  BMA B   3 "
           pdb=" O5  BMA B   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -177.51  106.22     1      3.00e+01 1.11e-03 1.36e+01
  dihedral pdb=" C3  BMA B   3 "
           pdb=" C4  BMA B   3 "
           pdb=" C5  BMA B   3 "
           pdb=" O5  BMA B   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
      47.62  -57.96  105.58     1      3.00e+01 1.11e-03 1.35e+01
  ... (remaining 1973 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.112: 422
       0.112 -    0.224: 60
       0.224 -    0.336: 9
       0.336 -    0.448: 3
       0.448 -    0.560: 2
  Chirality restraints: 496
  Sorted by residual:
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.62    0.22 2.00e-02 2.50e+03 1.25e+02
  chirality pdb=" C1  BMA B   3 "
            pdb=" O4  NAG B   2 "
            pdb=" C2  BMA B   3 "
            pdb=" O5  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.48    0.08 2.00e-02 2.50e+03 1.68e+01
  chirality pdb=" CG  LEU H  86 "
            pdb=" CB  LEU H  86 "
            pdb=" CD1 LEU H  86 "
            pdb=" CD2 LEU H  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.03   -0.56 2.00e-01 2.50e+01 7.83e+00
  ... (remaining 493 not shown)

  Planarity restraints: 586
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H 108 "    0.036 2.00e-02 2.50e+03   1.86e-02 6.92e+00
        pdb=" CG  TYR H 108 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD1 TYR H 108 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TYR H 108 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE1 TYR H 108 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TYR H 108 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR H 108 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR H 108 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 495 "   -0.035 2.00e-02 2.50e+03   1.83e-02 6.70e+00
        pdb=" CG  TYR A 495 "    0.013 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 495 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 495 "    0.016 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 495 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 495 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 495 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 495 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR L  37 "    0.027 2.00e-02 2.50e+03   1.51e-02 4.59e+00
        pdb=" CG  TYR L  37 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD1 TYR L  37 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TYR L  37 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 TYR L  37 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TYR L  37 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR L  37 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR L  37 "    0.024 2.00e-02 2.50e+03
  ... (remaining 583 not shown)

  Histogram of nonbonded interaction distances:
        2.40 -     2.90: 1320
        2.90 -     3.40: 2801
        3.40 -     3.90: 5451
        3.90 -     4.40: 6366
        4.40 -     4.90: 10508
  Nonbonded interactions: 26446
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP L  52 "
            pdb=" NZ  LYS A 378 "
     model   vdw
     2.398 3.120
  nonbonded pdb=" OE2 GLU H   6 "
            pdb=" N   GLN H 111 "
     model   vdw
     2.536 3.120
  nonbonded pdb=" N   ASN A 440 "
            pdb=" OD1 ASN A 440 "
     model   vdw
     2.551 3.120
  nonbonded pdb=" N   ASP A 428 "
            pdb=" OD1 ASP A 428 "
     model   vdw
     2.552 3.120
  nonbonded pdb=" N   CYS H  96 "
            pdb=" O   CYS H  96 "
     model   vdw
     2.557 2.496
  ... (remaining 26441 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:             2.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.740
  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:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
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      :  0.016   0.079   3341  Z= 0.861
  Angle     :  1.533  20.747   4560  Z= 0.985
  Chirality :  0.093   0.560    496
  Planarity :  0.006   0.034    585
  Dihedral  : 13.100 106.220   1192
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 0.80
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  0.97 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  1.22 %
    Favored  : 98.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.43), residues: 412
  helix: -4.22 (0.39), residues: 28
  sheet:  0.47 (0.42), residues: 154
  loop :  1.57 (0.44), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  72 
 TYR   0.036   0.006   TYR H 108 
 PHE   0.024   0.004   PHE H  29 
 TRP   0.025   0.007   TRP H  33 
 HIS   0.002   0.001   HIS L   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.01578 ( 3332)
  covalent geometry    : angle       1.51478 ( 4539)
  SS BOND              : bond        0.02855 (    6)
  SS BOND              : angle       3.67329 (   12)
  hydrogen bonds       : bond        0.19354 (  117)
  hydrogen bonds       : angle       8.62319 (  285)
  link_BETA1-4         : bond        0.07331 (    2)
  link_BETA1-4         : angle       4.68704 (    6)
  link_NAG-ASN         : bond        0.05556 (    1)
  link_NAG-ASN         : angle       2.05395 (    3)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   91 THR cc_start: 0.8641 (m) cc_final: 0.8333 (t)
REVERT: L   37 TYR cc_start: 0.9058 (m-80) cc_final: 0.8693 (m-10)
REVERT: A  375 SER cc_start: 0.8854 (m) cc_final: 0.8574 (t)
  outliers start: 1
  outliers final: 1
  residues processed: 100
  average time/residue: 0.0891
  time to fit residues: 10.3735
Evaluate side-chains
  64 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 63
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   86 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.2980
   chunk 19 optimal weight:    0.1980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.3980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
L  38 GLN
L  99 HIS
A 394 ASN
A 506 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.122270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.111329 restraints weight = 5806.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.114346 restraints weight = 2990.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.116303 restraints weight = 1824.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.117603 restraints weight = 1240.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.118520 restraints weight = 904.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3341  Z= 0.214
  Angle     :  0.741   9.072   4560  Z= 0.377
  Chirality :  0.048   0.172    496
  Planarity :  0.004   0.034    585
  Dihedral  :  9.184  60.831    525
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  0.49 %
    Favored  : 99.27 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 10.98 %
    Favored  : 86.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.62 (0.42), residues: 412
  helix: -3.56 (0.64), residues: 28
  sheet:  0.44 (0.41), residues: 149
  loop :  1.14 (0.42), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  62 
 TYR   0.022   0.002   TYR H  32 
 PHE   0.013   0.002   PHE H 106 
 TRP   0.022   0.002   TRP H  33 
 HIS   0.003   0.002   HIS L  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 3332)
  covalent geometry    : angle       0.71110 ( 4539)
  SS BOND              : bond        0.00685 (    6)
  SS BOND              : angle       1.85252 (   12)
  hydrogen bonds       : bond        0.04745 (  117)
  hydrogen bonds       : angle       6.94718 (  285)
  link_BETA1-4         : bond        0.01094 (    2)
  link_BETA1-4         : angle       4.59208 (    6)
  link_NAG-ASN         : bond        0.00101 (    1)
  link_NAG-ASN         : angle       3.82713 (    3)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   60 TYR cc_start: 0.9045 (m-80) cc_final: 0.8832 (m-80)
REVERT: H   91 THR cc_start: 0.8636 (m) cc_final: 0.8421 (t)
REVERT: L   37 TYR cc_start: 0.9061 (m-80) cc_final: 0.8839 (m-10)
REVERT: A  375 SER cc_start: 0.8891 (m) cc_final: 0.8518 (t)
REVERT: A  441 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8251 (mp)
  outliers start: 9
  outliers final: 8
  residues processed: 80
  average time/residue: 0.0641
  time to fit residues: 6.3151
Evaluate side-chains
  74 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain L residue   55 ARG
Chi-restraints excluded: chain L residue   91 CYS
Chi-restraints excluded: chain L residue  109 THR
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  443 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0050
   chunk 24 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   chunk 30 optimal weight:    0.4980
   chunk 13 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0470
   chunk 29 optimal weight:    0.1980
   chunk 39 optimal weight:    0.9980
   chunk 38 optimal weight:    0.1980
   overall best weight:    0.1892

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.123543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.112761 restraints weight = 5688.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.115757 restraints weight = 2944.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.117712 restraints weight = 1802.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.119039 restraints weight = 1218.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.119899 restraints weight = 879.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   3341  Z= 0.133
  Angle     :  0.670  10.374   4560  Z= 0.331
  Chirality :  0.045   0.146    496
  Planarity :  0.004   0.037    585
  Dihedral  :  7.221  38.910    523
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 10.06 %
    Favored  : 85.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.42), residues: 412
  helix: -3.37 (0.71), residues: 28
  sheet:  0.40 (0.43), residues: 149
  loop :  1.09 (0.42), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  55 
 TYR   0.012   0.001   TYR A 369 
 PHE   0.010   0.001   PHE H 106 
 TRP   0.016   0.001   TRP H  33 
 HIS   0.003   0.001   HIS L  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 3332)
  covalent geometry    : angle       0.65024 ( 4539)
  SS BOND              : bond        0.00286 (    6)
  SS BOND              : angle       1.24638 (   12)
  hydrogen bonds       : bond        0.04011 (  117)
  hydrogen bonds       : angle       6.61189 (  285)
  link_BETA1-4         : bond        0.00947 (    2)
  link_BETA1-4         : angle       3.87953 (    6)
  link_NAG-ASN         : bond        0.00588 (    1)
  link_NAG-ASN         : angle       2.32763 (    3)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   55 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7878 (ptt-90)
REVERT: A  375 SER cc_start: 0.8921 (m) cc_final: 0.8593 (t)
REVERT: A  441 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8266 (mp)
REVERT: A  506 GLN cc_start: 0.8220 (mp10) cc_final: 0.7831 (mp10)
  outliers start: 13
  outliers final: 6
  residues processed: 79
  average time/residue: 0.0583
  time to fit residues: 5.7539
Evaluate side-chains
  70 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain L residue   55 ARG
Chi-restraints excluded: chain L residue   86 GLU
Chi-restraints excluded: chain L residue   91 CYS
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  443 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 35 optimal weight:    0.2980
   chunk 25 optimal weight:    0.5980
   chunk 20 optimal weight:    0.2980
   chunk 17 optimal weight:    0.9980
   chunk 14 optimal weight:    0.2980
   chunk 38 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 5 optimal weight:    0.4980
   chunk 37 optimal weight:    0.2980
   chunk 11 optimal weight:    0.4980
   chunk 6 optimal weight:    0.3980
   overall best weight:    0.3180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.121584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.110650 restraints weight = 5751.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.113620 restraints weight = 3020.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.115545 restraints weight = 1861.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.116825 restraints weight = 1270.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.117735 restraints weight = 931.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.3212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3341  Z= 0.163
  Angle     :  0.662  10.152   4560  Z= 0.328
  Chirality :  0.046   0.156    496
  Planarity :  0.004   0.055    585
  Dihedral  :  5.972  33.763    523
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 11.28 %
    Favored  : 84.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.42), residues: 412
  helix: -3.23 (0.76), residues: 28
  sheet:  0.27 (0.43), residues: 148
  loop :  1.05 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  62 
 TYR   0.012   0.001   TYR A 495 
 PHE   0.011   0.001   PHE A 456 
 TRP   0.011   0.001   TRP H  33 
 HIS   0.003   0.002   HIS L  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 3332)
  covalent geometry    : angle       0.64552 ( 4539)
  SS BOND              : bond        0.00552 (    6)
  SS BOND              : angle       1.37501 (   12)
  hydrogen bonds       : bond        0.03836 (  117)
  hydrogen bonds       : angle       6.30710 (  285)
  link_BETA1-4         : bond        0.00905 (    2)
  link_BETA1-4         : angle       3.52578 (    6)
  link_NAG-ASN         : bond        0.00624 (    1)
  link_NAG-ASN         : angle       1.91465 (    3)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   55 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7906 (ptt-90)
REVERT: L  109 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8386 (p)
REVERT: A  375 SER cc_start: 0.8929 (m) cc_final: 0.8631 (t)
REVERT: A  441 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8292 (mp)
REVERT: A  506 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7920 (mp10)
  outliers start: 13
  outliers final: 6
  residues processed: 75
  average time/residue: 0.0640
  time to fit residues: 6.0035
Evaluate side-chains
  74 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain L residue   52 ASP
Chi-restraints excluded: chain L residue   55 ARG
Chi-restraints excluded: chain L residue   86 GLU
Chi-restraints excluded: chain L residue  109 THR
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  506 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 16 optimal weight:    0.4980
   chunk 2 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0980
   chunk 38 optimal weight:    0.9980
   chunk 22 optimal weight:    0.3980
   chunk 35 optimal weight:    0.0870
   chunk 30 optimal weight:    0.5980
   chunk 27 optimal weight:    0.5980
   chunk 36 optimal weight:    0.0870
   chunk 40 optimal weight:    0.4980
   overall best weight:    0.2336

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.122690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.111453 restraints weight = 5758.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.114418 restraints weight = 3066.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.116360 restraints weight = 1915.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.117651 restraints weight = 1321.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.118590 restraints weight = 978.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.3504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3341  Z= 0.133
  Angle     :  0.630  10.068   4560  Z= 0.311
  Chirality :  0.045   0.149    496
  Planarity :  0.004   0.041    585
  Dihedral  :  5.400  32.131    523
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 11.59 %
    Favored  : 83.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.43), residues: 412
  helix: -2.67 (1.02), residues: 21
  sheet:  0.21 (0.42), residues: 146
  loop :  0.99 (0.42), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L  62 
 TYR   0.011   0.001   TYR A 369 
 PHE   0.010   0.001   PHE A 456 
 TRP   0.009   0.001   TRP H  33 
 HIS   0.003   0.001   HIS L  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 3332)
  covalent geometry    : angle       0.61597 ( 4539)
  SS BOND              : bond        0.00369 (    6)
  SS BOND              : angle       1.25592 (   12)
  hydrogen bonds       : bond        0.03579 (  117)
  hydrogen bonds       : angle       6.18745 (  285)
  link_BETA1-4         : bond        0.00855 (    2)
  link_BETA1-4         : angle       3.12787 (    6)
  link_NAG-ASN         : bond        0.00562 (    1)
  link_NAG-ASN         : angle       1.63894 (    3)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   72 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8072 (ttp80)
REVERT: L   55 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7884 (ptt-90)
REVERT: L  109 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8506 (p)
REVERT: A  375 SER cc_start: 0.9017 (m) cc_final: 0.8637 (t)
REVERT: A  441 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8314 (mp)
REVERT: A  506 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8000 (mp10)
  outliers start: 15
  outliers final: 7
  residues processed: 79
  average time/residue: 0.0613
  time to fit residues: 5.9792
Evaluate side-chains
  80 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   72 ARG
Chi-restraints excluded: chain L residue   52 ASP
Chi-restraints excluded: chain L residue   55 ARG
Chi-restraints excluded: chain L residue   76 LEU
Chi-restraints excluded: chain L residue   86 GLU
Chi-restraints excluded: chain L residue  109 THR
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  506 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 14 optimal weight:    0.4980
   chunk 2 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0980
   chunk 39 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0870
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.120551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.109261 restraints weight = 5895.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.112189 restraints weight = 3105.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.114090 restraints weight = 1946.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.115377 restraints weight = 1356.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.116235 restraints weight = 1009.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.3731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3341  Z= 0.189
  Angle     :  0.665  10.115   4560  Z= 0.330
  Chirality :  0.046   0.158    496
  Planarity :  0.004   0.038    585
  Dihedral  :  5.400  33.396    523
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 13.41 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.43), residues: 412
  helix: -2.55 (1.04), residues: 21
  sheet:  0.10 (0.43), residues: 148
  loop :  0.88 (0.42), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  98 
 TYR   0.012   0.001   TYR A 369 
 PHE   0.012   0.002   PHE A 456 
 TRP   0.008   0.001   TRP H 101 
 HIS   0.003   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 3332)
  covalent geometry    : angle       0.65247 ( 4539)
  SS BOND              : bond        0.00296 (    6)
  SS BOND              : angle       1.26354 (   12)
  hydrogen bonds       : bond        0.03785 (  117)
  hydrogen bonds       : angle       6.18092 (  285)
  link_BETA1-4         : bond        0.00893 (    2)
  link_BETA1-4         : angle       3.00843 (    6)
  link_NAG-ASN         : bond        0.00558 (    1)
  link_NAG-ASN         : angle       1.67079 (    3)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   72 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8092 (ttp80)
REVERT: L   55 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7914 (ptt-90)
REVERT: L  109 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8531 (p)
REVERT: A  506 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8105 (mp10)
  outliers start: 14
  outliers final: 7
  residues processed: 78
  average time/residue: 0.0670
  time to fit residues: 6.4281
Evaluate side-chains
  79 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   72 ARG
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain L residue   52 ASP
Chi-restraints excluded: chain L residue   55 ARG
Chi-restraints excluded: chain L residue   76 LEU
Chi-restraints excluded: chain L residue   86 GLU
Chi-restraints excluded: chain L residue  109 THR
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  506 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0170
   chunk 23 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 26 optimal weight:    0.3980
   chunk 6 optimal weight:    0.3980
   chunk 5 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0050
   overall best weight:    0.3232

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

Flipped N/Q/H residues before XYZ refinement:
** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.120646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.109447 restraints weight = 5887.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.112368 restraints weight = 3077.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.114289 restraints weight = 1918.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.115531 restraints weight = 1324.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.116446 restraints weight = 996.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.3959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3341  Z= 0.160
  Angle     :  0.651  10.344   4560  Z= 0.323
  Chirality :  0.045   0.154    496
  Planarity :  0.004   0.039    585
  Dihedral  :  5.320  34.387    523
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 14.63 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.43), residues: 412
  helix: -2.55 (1.04), residues: 21
  sheet: -0.03 (0.43), residues: 148
  loop :  0.88 (0.42), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  62 
 TYR   0.011   0.001   TYR A 369 
 PHE   0.014   0.001   PHE A 456 
 TRP   0.010   0.001   TRP H  33 
 HIS   0.003   0.002   HIS L  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 3332)
  covalent geometry    : angle       0.64021 ( 4539)
  SS BOND              : bond        0.00294 (    6)
  SS BOND              : angle       1.26293 (   12)
  hydrogen bonds       : bond        0.03578 (  117)
  hydrogen bonds       : angle       6.15566 (  285)
  link_BETA1-4         : bond        0.00943 (    2)
  link_BETA1-4         : angle       2.77809 (    6)
  link_NAG-ASN         : bond        0.00473 (    1)
  link_NAG-ASN         : angle       1.65429 (    3)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.084 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   72 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8510 (ttp80)
REVERT: L   55 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7948 (ptt-90)
REVERT: L  109 THR cc_start: 0.8782 (m) cc_final: 0.8558 (p)
REVERT: A  506 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8140 (mp10)
  outliers start: 11
  outliers final: 6
  residues processed: 76
  average time/residue: 0.0623
  time to fit residues: 5.7731
Evaluate side-chains
  79 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   72 ARG
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain L residue   52 ASP
Chi-restraints excluded: chain L residue   55 ARG
Chi-restraints excluded: chain L residue   76 LEU
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  506 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 11 optimal weight:    0.4980
   chunk 29 optimal weight:    0.6980
   chunk 15 optimal weight:    0.3980
   chunk 40 optimal weight:    0.9990
   chunk 21 optimal weight:    0.3980
   chunk 17 optimal weight:    0.9990
   chunk 33 optimal weight:    0.3980
   chunk 1 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   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 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.107080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.097632 restraints weight = 5952.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.099941 restraints weight = 3391.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.101546 restraints weight = 2224.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.102612 restraints weight = 1580.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.103353 restraints weight = 1194.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.4199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   3341  Z= 0.208
  Angle     :  0.692  10.319   4560  Z= 0.347
  Chirality :  0.046   0.183    496
  Planarity :  0.004   0.038    585
  Dihedral  :  5.606  35.994    523
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 15.24 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.43), residues: 412
  helix: -2.23 (1.15), residues: 21
  sheet: -0.29 (0.43), residues: 148
  loop :  0.78 (0.42), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  62 
 TYR   0.017   0.002   TYR A 508 
 PHE   0.014   0.002   PHE A 456 
 TRP   0.009   0.001   TRP H 101 
 HIS   0.004   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 3332)
  covalent geometry    : angle       0.68112 ( 4539)
  SS BOND              : bond        0.00277 (    6)
  SS BOND              : angle       1.38576 (   12)
  hydrogen bonds       : bond        0.03757 (  117)
  hydrogen bonds       : angle       6.32622 (  285)
  link_BETA1-4         : bond        0.00732 (    2)
  link_BETA1-4         : angle       2.71673 (    6)
  link_NAG-ASN         : bond        0.00448 (    1)
  link_NAG-ASN         : angle       1.79190 (    3)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   72 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8021 (ttp80)
REVERT: L   55 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7782 (ptt-90)
  outliers start: 12
  outliers final: 6
  residues processed: 76
  average time/residue: 0.0699
  time to fit residues: 6.4547
Evaluate side-chains
  75 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   72 ARG
Chi-restraints excluded: chain L residue   52 ASP
Chi-restraints excluded: chain L residue   55 ARG
Chi-restraints excluded: chain L residue   76 LEU
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  415 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 40 optimal weight:    0.0670
   chunk 0 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 12 optimal weight:    0.2980
   chunk 22 optimal weight:    0.0470
   chunk 10 optimal weight:    0.8980
   chunk 21 optimal weight:    0.3980
   chunk 32 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.2816

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.108850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.099415 restraints weight = 5960.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.101781 restraints weight = 3430.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.103265 restraints weight = 2235.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.104387 restraints weight = 1612.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.105072 restraints weight = 1218.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.4338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087   3341  Z= 0.155
  Angle     :  0.694  16.031   4560  Z= 0.338
  Chirality :  0.045   0.195    496
  Planarity :  0.004   0.039    585
  Dihedral  :  5.511  35.743    523
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 17.38 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.42), residues: 412
  helix: -2.50 (1.04), residues: 21
  sheet: -0.24 (0.44), residues: 141
  loop :  0.73 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  55 
 TYR   0.011   0.001   TYR A 369 
 PHE   0.012   0.001   PHE A 456 
 TRP   0.010   0.001   TRP H  33 
 HIS   0.003   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 3332)
  covalent geometry    : angle       0.68533 ( 4539)
  SS BOND              : bond        0.00256 (    6)
  SS BOND              : angle       1.23982 (   12)
  hydrogen bonds       : bond        0.03504 (  117)
  hydrogen bonds       : angle       6.34293 (  285)
  link_BETA1-4         : bond        0.00708 (    2)
  link_BETA1-4         : angle       2.58651 (    6)
  link_NAG-ASN         : bond        0.00409 (    1)
  link_NAG-ASN         : angle       1.53665 (    3)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
REVERT: L  101 VAL cc_start: 0.9231 (t) cc_final: 0.9005 (m)
REVERT: A  333 THR cc_start: 0.7905 (m) cc_final: 0.7685 (p)
  outliers start: 8
  outliers final: 7
  residues processed: 75
  average time/residue: 0.0565
  time to fit residues: 5.3872
Evaluate side-chains
  71 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   99 VAL
Chi-restraints excluded: chain L residue   52 ASP
Chi-restraints excluded: chain L residue   76 LEU
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  415 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 16 optimal weight:    0.3980
   chunk 5 optimal weight:    0.0980
   chunk 21 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0570
   chunk 39 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0970
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.2696

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

Flipped N/Q/H residues before XYZ refinement:
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.111764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.102192 restraints weight = 5985.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.104607 restraints weight = 3409.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.106142 restraints weight = 2206.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.107132 restraints weight = 1563.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.107950 restraints weight = 1191.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.4447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.122   3341  Z= 0.154
  Angle     :  0.707  18.708   4560  Z= 0.335
  Chirality :  0.045   0.194    496
  Planarity :  0.004   0.046    585
  Dihedral  :  5.466  35.212    523
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 16.77 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.43), residues: 412
  helix: -2.69 (1.03), residues: 21
  sheet: -0.02 (0.44), residues: 141
  loop :  0.74 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  55 
 TYR   0.010   0.001   TYR A 369 
 PHE   0.010   0.001   PHE A 456 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.003   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 3332)
  covalent geometry    : angle       0.69796 ( 4539)
  SS BOND              : bond        0.00239 (    6)
  SS BOND              : angle       1.30082 (   12)
  hydrogen bonds       : bond        0.03444 (  117)
  hydrogen bonds       : angle       6.27015 (  285)
  link_BETA1-4         : bond        0.00801 (    2)
  link_BETA1-4         : angle       2.59772 (    6)
  link_NAG-ASN         : bond        0.00399 (    1)
  link_NAG-ASN         : angle       1.54487 (    3)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
REVERT: L  101 VAL cc_start: 0.9212 (t) cc_final: 0.8992 (m)
REVERT: A  333 THR cc_start: 0.7911 (m) cc_final: 0.7700 (p)
REVERT: A  375 SER cc_start: 0.9068 (m) cc_final: 0.8704 (t)
  outliers start: 7
  outliers final: 7
  residues processed: 69
  average time/residue: 0.0462
  time to fit residues: 4.1879
Evaluate side-chains
  71 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   99 VAL
Chi-restraints excluded: chain L residue   52 ASP
Chi-restraints excluded: chain L residue   76 LEU
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  415 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 11 optimal weight:    0.4980
   chunk 3 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0040
   chunk 14 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 17 optimal weight:    0.7980
   chunk 23 optimal weight:    0.1980
   chunk 2 optimal weight:    0.4980
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.3592

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.110985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.101395 restraints weight = 5973.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.103715 restraints weight = 3416.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.105274 restraints weight = 2236.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.106362 restraints weight = 1588.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.107136 restraints weight = 1193.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.4491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.119   3341  Z= 0.178
  Angle     :  0.709  17.315   4560  Z= 0.341
  Chirality :  0.046   0.197    496
  Planarity :  0.004   0.047    585
  Dihedral  :  5.524  35.534    523
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 16.46 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.42), residues: 412
  helix: -2.84 (1.01), residues: 21
  sheet: -0.10 (0.44), residues: 142
  loop :  0.67 (0.41), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  62 
 TYR   0.011   0.001   TYR A 453 
 PHE   0.010   0.001   PHE A 456 
 TRP   0.008   0.001   TRP H 101 
 HIS   0.004   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 3332)
  covalent geometry    : angle       0.69968 ( 4539)
  SS BOND              : bond        0.00261 (    6)
  SS BOND              : angle       1.34801 (   12)
  hydrogen bonds       : bond        0.03557 (  117)
  hydrogen bonds       : angle       6.28315 (  285)
  link_BETA1-4         : bond        0.00820 (    2)
  link_BETA1-4         : angle       2.56147 (    6)
  link_NAG-ASN         : bond        0.00387 (    1)
  link_NAG-ASN         : angle       1.62592 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 854.99 seconds
wall clock time: 15 minutes 20.37 seconds (920.37 seconds total)