Starting phenix.real_space_refine
on Thu Jul 24 18:00:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x94_33066/07_2025/7x94_33066_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x94_33066/07_2025/7x94_33066.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x94_33066/07_2025/7x94_33066.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x94_33066/07_2025/7x94_33066.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x94_33066/07_2025/7x94_33066_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x94_33066/07_2025/7x94_33066_trim.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      13      5.16       5
     C    2162      2.51       5
     N     568      2.21       5
     O     666      1.98       5
     H    3208      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6617
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3057
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 3057
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 11, 'TRANS': 186}
    Chain: "H"
      Number of atoms: 1945
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 1945
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "L"
      Number of atoms: 1576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 1576
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 6, 'TRANS': 102}
    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: 3.84, per 1000 atoms: 0.58
  Number of scatterers: 6617
  At special positions: 0
  Unit cell: (67.978, 67.978, 109.428, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      13     16.00
     O     666      8.00
     N     568      7.00
     C    2162      6.00
     H    3208      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
    NAG-ASN
      " NAG B   1 " - " ASN A 343 "
  Time building additional restraints: 1.72
  Conformation dependent library (CDL) restraints added in 685.2 milliseconds
  

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  788

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 8 sheets defined
      7.6% alpha, 23.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 343
      removed outlier: 3.549A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 371
      removed outlier: 4.131A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   SER A 371 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 390
      removed outlier: 5.238A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   LEU A 390 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.799A  pdb=" N   THR H  91 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 357
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 11
      removed outlier: 3.894A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 6.056A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 23
    Processing sheet with id=AA7, first strand: chain 'L' and resid 44 through 48
      removed outlier: 6.644A  pdb=" N   TRP L  34 " --> pdb=" O   VAL L  46 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   SER L  89 " --> pdb=" O   VAL L  99 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   VAL L  99 " --> pdb=" O   SER L  89 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 83 through 85

    88 hydrogen bonds defined for protein.
    189 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: 2.11

  Time building geometry restraints manager: 2.11 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 3206
        1.03 -     1.23: 41
        1.23 -     1.43: 1520
        1.43 -     1.62: 1924
        1.62 -     1.82: 14
  Bond restraints: 6705
  Sorted by residual:
  bond pdb=" N   GLN H   1 "
       pdb=" CA  GLN H   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.93e+00
  bond pdb=" N   SER L   1 "
       pdb=" CA  SER L   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.91e+00
  bond pdb=" C1  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.439 -0.033 2.00e-02 2.50e+03 2.67e+00
  bond pdb=" N   GLN H   1 "
       pdb=" H   GLN H   1 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.21e+00
  bond pdb=" N   SER L   1 "
       pdb=" H   SER L   1 "
    ideal  model  delta    sigma   weight residual
    0.860  0.889 -0.029 2.00e-02 2.50e+03 2.12e+00
  ... (remaining 6700 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 11681
        1.43 -     2.85: 279
        2.85 -     4.28: 29
        4.28 -     5.70: 5
        5.70 -     7.13: 3
  Bond angle restraints: 11997
  Sorted by residual:
  angle pdb=" N   VAL L  46 "
        pdb=" CA  VAL L  46 "
        pdb=" C   VAL L  46 "
      ideal   model   delta    sigma   weight residual
     113.71  110.53    3.18 9.50e-01 1.11e+00 1.12e+01
  angle pdb=" CB  LYS A 386 "
        pdb=" CG  LYS A 386 "
        pdb=" CD  LYS A 386 "
      ideal   model   delta    sigma   weight residual
     111.30  118.43   -7.13 2.30e+00 1.89e-01 9.61e+00
  angle pdb=" N   ASN A 450 "
        pdb=" CA  ASN A 450 "
        pdb=" C   ASN A 450 "
      ideal   model   delta    sigma   weight residual
     113.18  110.48    2.70 1.33e+00 5.65e-01 4.13e+00
  angle pdb=" C3  BMA B   3 "
        pdb=" C2  BMA B   3 "
        pdb=" O2  BMA B   3 "
      ideal   model   delta    sigma   weight residual
     112.95  107.01    5.94 3.00e+00 1.11e-01 3.92e+00
  angle pdb=" CG  LYS A 386 "
        pdb=" CD  LYS A 386 "
        pdb=" CE  LYS A 386 "
      ideal   model   delta    sigma   weight residual
     111.30  115.80   -4.50 2.30e+00 1.89e-01 3.82e+00
  ... (remaining 11992 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.06: 3017
       21.06 -    42.12: 198
       42.12 -    63.18: 55
       63.18 -    84.24: 12
       84.24 -   105.30: 4
  Dihedral angle restraints: 3286
    sinusoidal: 1756
      harmonic: 1530
  Sorted by residual:
  dihedral pdb=" CB  CYS A 336 "
           pdb=" SG  CYS A 336 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -131.64   45.64     1      1.00e+01 1.00e-02 2.89e+01
  dihedral pdb=" CA  ARG A 346 "
           pdb=" C   ARG A 346 "
           pdb=" N   PHE A 347 "
           pdb=" CA  PHE A 347 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.19  -26.81     0      5.00e+00 4.00e-02 2.88e+01
  dihedral pdb=" CA  CYS A 336 "
           pdb=" CB  CYS A 336 "
           pdb=" SG  CYS A 336 "
           pdb=" SG  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00   -0.49  -72.51     1      2.00e+01 2.50e-03 1.68e+01
  ... (remaining 3283 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 434
       0.057 -    0.114: 70
       0.114 -    0.171: 13
       0.171 -    0.228: 0
       0.228 -    0.285: 2
  Chirality restraints: 519
  Sorted by residual:
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN A 343 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-01 2.50e+01 2.04e+00
  chirality pdb=" C5  BMA B   3 "
            pdb=" C4  BMA B   3 "
            pdb=" C6  BMA B   3 "
            pdb=" O5  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" C2  BMA B   3 "
            pdb=" C1  BMA B   3 "
            pdb=" C3  BMA B   3 "
            pdb=" O2  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.62   -0.15 2.00e-01 2.50e+01 5.48e-01
  ... (remaining 516 not shown)

  Planarity restraints: 1026
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS H  13 "   -0.031 5.00e-02 4.00e+02   4.80e-02 3.68e+00
        pdb=" N   PRO H  14 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO H  14 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO H  14 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 462 "    0.021 5.00e-02 4.00e+02   3.16e-02 1.60e+00
        pdb=" N   PRO A 463 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO A 463 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 463 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE H  99 "   -0.020 5.00e-02 4.00e+02   3.02e-02 1.46e+00
        pdb=" N   PRO H 100 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO H 100 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO H 100 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1023 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.21: 635
        2.21 -     2.81: 13624
        2.81 -     3.41: 16452
        3.41 -     4.00: 22579
        4.00 -     4.60: 33440
  Nonbonded interactions: 86730
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP H 116 "
            pdb=" H   TYR H 117 "
     model   vdw
     1.616 2.450
  nonbonded pdb=" OD2 ASP A 398 "
            pdb=" HH  TYR A 423 "
     model   vdw
     1.618 2.450
  nonbonded pdb="HH22 ARG A 454 "
            pdb=" O   SER A 469 "
     model   vdw
     1.619 2.450
  nonbonded pdb=" OE1 GLU A 471 "
            pdb=" H   GLU A 471 "
     model   vdw
     1.645 2.450
  nonbonded pdb="HH21 ARG H  98 "
            pdb=" OD2 ASP H 116 "
     model   vdw
     1.651 2.450
  ... (remaining 86725 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.300
  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:             0.120
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     18.930
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6897
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3505  Z= 0.149
  Angle     :  0.636   7.130   4781  Z= 0.333
  Chirality :  0.047   0.285    519
  Planarity :  0.004   0.048    616
  Dihedral  : 15.697 105.302   1279
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.98 %
    Favored  : 89.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.27 (0.41), residues: 428
  helix: -4.13 (0.55), residues: 32
  sheet: -0.01 (0.45), residues: 130
  loop : -2.06 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP L  34 
 HIS   0.003   0.001   HIS A 519 
 PHE   0.020   0.001   PHE A 347 
 TYR   0.018   0.001   TYR H  60 
 ARG   0.004   0.000   ARG A 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01270 (    1)
  link_NAG-ASN         : angle       4.36631 (    3)
  link_BETA1-4         : bond        0.00569 (    2)
  link_BETA1-4         : angle       2.13419 (    6)
  hydrogen bonds       : bond        0.14462 (   88)
  hydrogen bonds       : angle       5.80480 (  189)
  SS BOND              : bond        0.00197 (    5)
  SS BOND              : angle       1.45154 (   10)
  covalent geometry    : bond        0.00312 ( 3497)
  covalent geometry    : angle       0.61963 ( 4762)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.4191
  time to fit residues: 57.2232
Evaluate side-chains
  68 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 31 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 20 optimal weight:   20.0000
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    9.9990
   chunk 12 optimal weight:    6.9990
   chunk 19 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:   30.0000
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 450 ASN
L  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.046759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.036391 restraints weight = 50165.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.038919 restraints weight = 20233.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.040732 restraints weight = 10690.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3505  Z= 0.205
  Angle     :  0.651   5.634   4781  Z= 0.337
  Chirality :  0.044   0.165    519
  Planarity :  0.005   0.049    616
  Dihedral  :  8.632  60.093    541
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 15.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.75 %
    Favored  : 89.25 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 12.88 %
    Favored  : 85.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.41 (0.41), residues: 428
  helix: -3.93 (0.64), residues: 32
  sheet:  0.02 (0.45), residues: 140
  loop : -2.36 (0.39), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  50 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.014   0.002   PHE A 347 
 TYR   0.016   0.001   TYR L  85 
 ARG   0.007   0.001   ARG L  28 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00641 (    1)
  link_NAG-ASN         : angle       3.05663 (    3)
  link_BETA1-4         : bond        0.00724 (    2)
  link_BETA1-4         : angle       2.36841 (    6)
  hydrogen bonds       : bond        0.04252 (   88)
  hydrogen bonds       : angle       5.79372 (  189)
  SS BOND              : bond        0.00562 (    5)
  SS BOND              : angle       1.88393 (   10)
  covalent geometry    : bond        0.00446 ( 3497)
  covalent geometry    : angle       0.63664 ( 4762)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  365 TYR cc_start: 0.9035 (m-80) cc_final: 0.8751 (m-80)
REVERT: H   43 GLN cc_start: 0.9568 (mm110) cc_final: 0.9291 (mp10)
REVERT: H   48 MET cc_start: 0.7583 (mmm) cc_final: 0.7359 (mmm)
REVERT: H  104 TYR cc_start: 0.8537 (m-80) cc_final: 0.8253 (m-80)
REVERT: H  117 TYR cc_start: 0.8752 (m-80) cc_final: 0.8275 (m-80)
  outliers start: 6
  outliers final: 6
  residues processed: 72
  average time/residue: 0.3881
  time to fit residues: 33.0788
Evaluate side-chains
  71 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 ASP
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain L residue    3 GLU
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   88 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 39 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 31 optimal weight:   10.0000
   chunk 30 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 40 optimal weight:    8.9990
   chunk 34 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 388 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 = 0.2928 r_free = 0.2928 target = 0.045309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2647 r_free = 0.2647 target = 0.035174 restraints weight = 51534.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.037659 restraints weight = 20720.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.039434 restraints weight = 10942.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.3582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   3505  Z= 0.206
  Angle     :  0.612   4.361   4781  Z= 0.321
  Chirality :  0.043   0.157    519
  Planarity :  0.004   0.047    616
  Dihedral  :  6.034  32.694    541
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 13.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.51 %
    Favored  : 89.49 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 12.33 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.47 (0.40), residues: 428
  helix: -3.86 (0.61), residues: 32
  sheet:  0.14 (0.46), residues: 128
  loop : -2.42 (0.37), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP L  34 
 HIS   0.006   0.002   HIS H  32 
 PHE   0.011   0.001   PHE A 347 
 TYR   0.023   0.002   TYR L  85 
 ARG   0.004   0.001   ARG L  28 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00418 (    1)
  link_NAG-ASN         : angle       2.58067 (    3)
  link_BETA1-4         : bond        0.00667 (    2)
  link_BETA1-4         : angle       2.00389 (    6)
  hydrogen bonds       : bond        0.03889 (   88)
  hydrogen bonds       : angle       5.79784 (  189)
  SS BOND              : bond        0.00471 (    5)
  SS BOND              : angle       1.34886 (   10)
  covalent geometry    : bond        0.00437 ( 3497)
  covalent geometry    : angle       0.60196 ( 4762)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  365 TYR cc_start: 0.9084 (m-80) cc_final: 0.8701 (m-80)
REVERT: H  117 TYR cc_start: 0.8794 (m-80) cc_final: 0.8321 (m-80)
REVERT: L   36 GLN cc_start: 0.9032 (pp30) cc_final: 0.8817 (pp30)
  outliers start: 10
  outliers final: 8
  residues processed: 73
  average time/residue: 0.4130
  time to fit residues: 35.4169
Evaluate side-chains
  71 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  405 ASP
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain L residue    3 GLU
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   91 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 35 optimal weight:    4.9990
   chunk 19 optimal weight:   20.0000
   chunk 26 optimal weight:   10.0000
   chunk 9 optimal weight:    1.9990
   chunk 2 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 37 optimal weight:   20.0000
   chunk 23 optimal weight:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 3 optimal weight:   10.0000
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 388 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 = 0.2922 r_free = 0.2922 target = 0.044676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2637 r_free = 0.2637 target = 0.034570 restraints weight = 52226.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.036999 restraints weight = 21157.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.038719 restraints weight = 11271.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.3739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3505  Z= 0.171
  Angle     :  0.579   4.616   4781  Z= 0.302
  Chirality :  0.042   0.164    519
  Planarity :  0.004   0.045    616
  Dihedral  :  5.306  32.504    541
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.28 %
    Favored  : 89.72 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 13.42 %
    Favored  : 84.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.44 (0.40), residues: 428
  helix: -3.76 (0.63), residues: 32
  sheet:  0.16 (0.46), residues: 129
  loop : -2.42 (0.37), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP L  34 
 HIS   0.004   0.001   HIS H  32 
 PHE   0.009   0.001   PHE A 347 
 TYR   0.010   0.001   TYR L  85 
 ARG   0.003   0.001   ARG H  98 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00448 (    1)
  link_NAG-ASN         : angle       2.37479 (    3)
  link_BETA1-4         : bond        0.00573 (    2)
  link_BETA1-4         : angle       1.91322 (    6)
  hydrogen bonds       : bond        0.03578 (   88)
  hydrogen bonds       : angle       5.69597 (  189)
  SS BOND              : bond        0.00884 (    5)
  SS BOND              : angle       1.17055 (   10)
  covalent geometry    : bond        0.00368 ( 3497)
  covalent geometry    : angle       0.57019 ( 4762)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  365 TYR cc_start: 0.9057 (m-80) cc_final: 0.8623 (m-80)
REVERT: H  117 TYR cc_start: 0.8802 (m-80) cc_final: 0.8351 (m-80)
REVERT: L   36 GLN cc_start: 0.9083 (pp30) cc_final: 0.8869 (pp30)
  outliers start: 9
  outliers final: 7
  residues processed: 71
  average time/residue: 0.4009
  time to fit residues: 33.7577
Evaluate side-chains
  67 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  405 ASP
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain L residue    3 GLU
Chi-restraints excluded: chain L residue   91 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 14 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 7 optimal weight:    8.9990
   chunk 17 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 31 optimal weight:   10.0000
   chunk 29 optimal weight:    9.9990
   chunk 32 optimal weight:    9.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 388 ASN
L  52 ASN
L  95 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.043827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2623 r_free = 0.2623 target = 0.033923 restraints weight = 51806.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.036311 restraints weight = 20927.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2735 r_free = 0.2735 target = 0.037997 restraints weight = 11138.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.4109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3505  Z= 0.199
  Angle     :  0.589   4.409   4781  Z= 0.308
  Chirality :  0.041   0.153    519
  Planarity :  0.005   0.044    616
  Dihedral  :  5.090  32.083    541
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.98 %
    Favored  : 89.02 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 14.25 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.51 (0.39), residues: 428
  helix: -3.77 (0.64), residues: 32
  sheet:  0.08 (0.45), residues: 134
  loop : -2.50 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP L  34 
 HIS   0.004   0.001   HIS H  32 
 PHE   0.011   0.001   PHE H  68 
 TYR   0.012   0.001   TYR H 112 
 ARG   0.009   0.001   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00322 (    1)
  link_NAG-ASN         : angle       1.96949 (    3)
  link_BETA1-4         : bond        0.00618 (    2)
  link_BETA1-4         : angle       1.93981 (    6)
  hydrogen bonds       : bond        0.03631 (   88)
  hydrogen bonds       : angle       5.71784 (  189)
  SS BOND              : bond        0.00608 (    5)
  SS BOND              : angle       1.25846 (   10)
  covalent geometry    : bond        0.00419 ( 3497)
  covalent geometry    : angle       0.58117 ( 4762)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  365 TYR cc_start: 0.9093 (m-80) cc_final: 0.8619 (m-80)
REVERT: H  117 TYR cc_start: 0.8807 (m-80) cc_final: 0.8360 (m-80)
  outliers start: 9
  outliers final: 9
  residues processed: 68
  average time/residue: 0.3451
  time to fit residues: 28.3842
Evaluate side-chains
  67 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  405 ASP
Chi-restraints excluded: chain A residue  442 ASP
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain H residue   99 ILE
Chi-restraints excluded: chain L residue    3 GLU
Chi-restraints excluded: chain L residue   91 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 38 optimal weight:   10.0000
   chunk 36 optimal weight:    2.9990
   chunk 1 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 26 optimal weight:    9.9990
   chunk 39 optimal weight:    9.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
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 = 0.2925 r_free = 0.2925 target = 0.044676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2646 r_free = 0.2646 target = 0.034719 restraints weight = 50417.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.037179 restraints weight = 20340.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.038913 restraints weight = 10732.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.4122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3505  Z= 0.114
  Angle     :  0.558   4.274   4781  Z= 0.290
  Chirality :  0.042   0.176    519
  Planarity :  0.004   0.041    616
  Dihedral  :  4.753  32.683    541
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.58 %
    Favored  : 90.42 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 15.07 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.31 (0.40), residues: 428
  helix: -3.66 (0.67), residues: 32
  sheet:  0.14 (0.45), residues: 134
  loop : -2.30 (0.38), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP L  34 
 HIS   0.002   0.001   HIS H  32 
 PHE   0.009   0.001   PHE A 377 
 TYR   0.011   0.001   TYR H 106 
 ARG   0.003   0.000   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00615 (    1)
  link_NAG-ASN         : angle       2.19240 (    3)
  link_BETA1-4         : bond        0.00407 (    2)
  link_BETA1-4         : angle       1.81852 (    6)
  hydrogen bonds       : bond        0.03243 (   88)
  hydrogen bonds       : angle       5.50064 (  189)
  SS BOND              : bond        0.00417 (    5)
  SS BOND              : angle       1.11897 (   10)
  covalent geometry    : bond        0.00265 ( 3497)
  covalent geometry    : angle       0.55066 ( 4762)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.787 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  365 TYR cc_start: 0.9099 (m-80) cc_final: 0.8634 (m-80)
REVERT: A  414 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8372 (mp10)
REVERT: H   43 GLN cc_start: 0.9503 (mm110) cc_final: 0.9236 (mm-40)
REVERT: H  104 TYR cc_start: 0.8442 (m-80) cc_final: 0.8159 (m-10)
REVERT: H  117 TYR cc_start: 0.8736 (m-80) cc_final: 0.8315 (m-80)
  outliers start: 8
  outliers final: 6
  residues processed: 69
  average time/residue: 0.5890
  time to fit residues: 48.7793
Evaluate side-chains
  66 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 1.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain H residue   99 ILE
Chi-restraints excluded: chain L residue   91 ASP
Chi-restraints excluded: chain L residue  106 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 39 optimal weight:   10.0000
   chunk 11 optimal weight:    4.9990
   chunk 28 optimal weight:   10.0000
   chunk 22 optimal weight:    8.9990
   chunk 26 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 7 optimal weight:    0.6980
   chunk 33 optimal weight:    8.9990
   overall best weight:    3.5388

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

Flipped N/Q/H residues before XYZ refinement:
** L  88 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 = 0.2917 r_free = 0.2917 target = 0.044302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.034479 restraints weight = 51332.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.036917 restraints weight = 20684.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.038617 restraints weight = 10939.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.4296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3505  Z= 0.151
  Angle     :  0.564   4.366   4781  Z= 0.294
  Chirality :  0.041   0.155    519
  Planarity :  0.004   0.041    616
  Dihedral  :  4.718  32.224    541
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.28 %
    Favored  : 89.72 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 15.07 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.38 (0.40), residues: 428
  helix: -3.69 (0.67), residues: 32
  sheet:  0.09 (0.45), residues: 134
  loop : -2.35 (0.38), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP L  34 
 HIS   0.002   0.001   HIS H  32 
 PHE   0.008   0.001   PHE A 377 
 TYR   0.010   0.001   TYR H 112 
 ARG   0.003   0.001   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00473 (    1)
  link_NAG-ASN         : angle       1.96717 (    3)
  link_BETA1-4         : bond        0.00586 (    2)
  link_BETA1-4         : angle       1.87861 (    6)
  hydrogen bonds       : bond        0.03284 (   88)
  hydrogen bonds       : angle       5.44459 (  189)
  SS BOND              : bond        0.00443 (    5)
  SS BOND              : angle       1.17145 (   10)
  covalent geometry    : bond        0.00329 ( 3497)
  covalent geometry    : angle       0.55649 ( 4762)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 1.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  365 TYR cc_start: 0.9155 (m-80) cc_final: 0.8717 (m-80)
REVERT: A  414 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8467 (mp10)
REVERT: A  417 LYS cc_start: 0.9403 (ptmm) cc_final: 0.9070 (pttt)
REVERT: H  117 TYR cc_start: 0.8804 (m-80) cc_final: 0.8319 (m-80)
  outliers start: 6
  outliers final: 6
  residues processed: 67
  average time/residue: 0.5413
  time to fit residues: 44.2099
Evaluate side-chains
  66 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain H residue   99 ILE
Chi-restraints excluded: chain L residue   88 ASN
Chi-restraints excluded: chain L residue   91 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 6 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 39 optimal weight:    9.9990
   chunk 30 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 32 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   overall best weight:    5.1588

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

Flipped N/Q/H residues before XYZ refinement:
** L  88 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 = 0.2888 r_free = 0.2888 target = 0.043310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2613 r_free = 0.2613 target = 0.033682 restraints weight = 52708.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.036043 restraints weight = 21152.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.037687 restraints weight = 11158.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.4449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3505  Z= 0.204
  Angle     :  0.587   4.463   4781  Z= 0.307
  Chirality :  0.041   0.137    519
  Planarity :  0.004   0.042    616
  Dihedral  :  4.819  32.106    541
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.21 %
    Favored  : 88.79 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 15.34 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.52 (0.39), residues: 428
  helix: -3.78 (0.64), residues: 32
  sheet: -0.05 (0.43), residues: 134
  loop : -2.43 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP L  34 
 HIS   0.003   0.001   HIS H  32 
 PHE   0.010   0.001   PHE A 515 
 TYR   0.014   0.001   TYR H 106 
 ARG   0.003   0.001   ARG A 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00291 (    1)
  link_NAG-ASN         : angle       1.71872 (    3)
  link_BETA1-4         : bond        0.00737 (    2)
  link_BETA1-4         : angle       2.05719 (    6)
  hydrogen bonds       : bond        0.03498 (   88)
  hydrogen bonds       : angle       5.54404 (  189)
  SS BOND              : bond        0.00505 (    5)
  SS BOND              : angle       1.16395 (   10)
  covalent geometry    : bond        0.00432 ( 3497)
  covalent geometry    : angle       0.57999 ( 4762)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  365 TYR cc_start: 0.9203 (m-80) cc_final: 0.8730 (m-80)
REVERT: A  414 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8535 (mp10)
REVERT: A  417 LYS cc_start: 0.9445 (ptmm) cc_final: 0.9140 (pttt)
REVERT: H  117 TYR cc_start: 0.8827 (m-80) cc_final: 0.8362 (m-80)
  outliers start: 7
  outliers final: 7
  residues processed: 65
  average time/residue: 0.4994
  time to fit residues: 39.8910
Evaluate side-chains
  65 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 1.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue   99 ILE
Chi-restraints excluded: chain L residue   88 ASN
Chi-restraints excluded: chain L residue   91 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 18 optimal weight:   10.0000
   chunk 9 optimal weight:    4.9990
   chunk 5 optimal weight:    7.9990
   chunk 31 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   chunk 32 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 39 optimal weight:   20.0000
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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 = 0.2895 r_free = 0.2895 target = 0.043596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.033899 restraints weight = 52750.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2685 r_free = 0.2685 target = 0.036309 restraints weight = 21142.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2730 r_free = 0.2730 target = 0.037976 restraints weight = 11096.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.4598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3505  Z= 0.173
  Angle     :  0.588   5.489   4781  Z= 0.307
  Chirality :  0.041   0.144    519
  Planarity :  0.004   0.042    616
  Dihedral  :  4.816  32.866    541
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.28 %
    Favored  : 89.72 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 15.07 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.54 (0.39), residues: 428
  helix: -3.75 (0.65), residues: 32
  sheet: -0.11 (0.43), residues: 134
  loop : -2.42 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP L  34 
 HIS   0.002   0.001   HIS H  32 
 PHE   0.009   0.001   PHE A 377 
 TYR   0.012   0.001   TYR H 106 
 ARG   0.003   0.001   ARG A 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00419 (    1)
  link_NAG-ASN         : angle       1.75395 (    3)
  link_BETA1-4         : bond        0.00561 (    2)
  link_BETA1-4         : angle       2.04173 (    6)
  hydrogen bonds       : bond        0.03413 (   88)
  hydrogen bonds       : angle       5.47090 (  189)
  SS BOND              : bond        0.00483 (    5)
  SS BOND              : angle       1.22289 (   10)
  covalent geometry    : bond        0.00371 ( 3497)
  covalent geometry    : angle       0.58023 ( 4762)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 1.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  365 TYR cc_start: 0.9183 (m-80) cc_final: 0.8720 (m-80)
REVERT: A  414 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8499 (mp10)
  outliers start: 8
  outliers final: 8
  residues processed: 65
  average time/residue: 0.7565
  time to fit residues: 64.0380
Evaluate side-chains
  64 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  405 ASP
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue   99 ILE
Chi-restraints excluded: chain L residue   88 ASN
Chi-restraints excluded: chain L residue   91 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 40 optimal weight:    8.9990
   chunk 25 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 11 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 38 optimal weight:    9.9990
   chunk 16 optimal weight:    6.9990
   chunk 20 optimal weight:    7.9990
   chunk 13 optimal weight:    5.9990
   chunk 34 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9980
   overall best weight:    4.9988

-------------------------------------------------------------------------------
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 = 0.2886 r_free = 0.2886 target = 0.043271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2612 r_free = 0.2612 target = 0.033731 restraints weight = 53791.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.036094 restraints weight = 21658.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.037739 restraints weight = 11378.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.4799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3505  Z= 0.196
  Angle     :  0.595   5.272   4781  Z= 0.311
  Chirality :  0.041   0.135    519
  Planarity :  0.004   0.043    616
  Dihedral  :  4.856  32.466    541
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.98 %
    Favored  : 89.02 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 14.79 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.60 (0.39), residues: 428
  helix: -3.79 (0.63), residues: 32
  sheet: -0.16 (0.43), residues: 134
  loop : -2.45 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP L  34 
 HIS   0.003   0.001   HIS L  96 
 PHE   0.010   0.001   PHE A 515 
 TYR   0.012   0.001   TYR L  85 
 ARG   0.003   0.001   ARG A 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00361 (    1)
  link_NAG-ASN         : angle       1.67949 (    3)
  link_BETA1-4         : bond        0.00640 (    2)
  link_BETA1-4         : angle       2.09173 (    6)
  hydrogen bonds       : bond        0.03515 (   88)
  hydrogen bonds       : angle       5.46845 (  189)
  SS BOND              : bond        0.00483 (    5)
  SS BOND              : angle       1.19984 (   10)
  covalent geometry    : bond        0.00426 ( 3497)
  covalent geometry    : angle       0.58781 ( 4762)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  365 TYR cc_start: 0.9210 (m-80) cc_final: 0.8745 (m-80)
REVERT: A  414 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8541 (mp10)
REVERT: A  417 LYS cc_start: 0.9433 (ptmm) cc_final: 0.9162 (pttt)
REVERT: H  117 TYR cc_start: 0.8754 (m-80) cc_final: 0.8251 (m-80)
  outliers start: 9
  outliers final: 9
  residues processed: 64
  average time/residue: 0.3684
  time to fit residues: 29.6937
Evaluate side-chains
  63 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 1.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  405 ASP
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue   99 ILE
Chi-restraints excluded: chain L residue   47 ILE
Chi-restraints excluded: chain L residue   88 ASN
Chi-restraints excluded: chain L residue   91 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 13 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 12 optimal weight:    6.9990
   chunk 11 optimal weight:    0.7980
   chunk 23 optimal weight:    8.9990
   chunk 24 optimal weight:    3.9990
   chunk 32 optimal weight:    8.9990
   overall best weight:    3.3588

-------------------------------------------------------------------------------
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 = 0.2897 r_free = 0.2897 target = 0.043708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.034033 restraints weight = 52232.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2685 r_free = 0.2685 target = 0.036430 restraints weight = 21014.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2730 r_free = 0.2730 target = 0.038119 restraints weight = 11016.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.4816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3505  Z= 0.144
  Angle     :  0.587   5.656   4781  Z= 0.305
  Chirality :  0.042   0.148    519
  Planarity :  0.004   0.042    616
  Dihedral  :  4.743  33.563    541
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.28 %
    Favored  : 89.72 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 14.25 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.47 (0.39), residues: 428
  helix: -3.68 (0.66), residues: 32
  sheet: -0.09 (0.43), residues: 134
  loop : -2.35 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP L  34 
 HIS   0.002   0.001   HIS H  32 
 PHE   0.009   0.001   PHE A 377 
 TYR   0.010   0.001   TYR L  85 
 ARG   0.003   0.000   ARG A 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00550 (    1)
  link_NAG-ASN         : angle       1.84339 (    3)
  link_BETA1-4         : bond        0.00451 (    2)
  link_BETA1-4         : angle       2.05381 (    6)
  hydrogen bonds       : bond        0.03317 (   88)
  hydrogen bonds       : angle       5.32448 (  189)
  SS BOND              : bond        0.00467 (    5)
  SS BOND              : angle       1.17376 (   10)
  covalent geometry    : bond        0.00322 ( 3497)
  covalent geometry    : angle       0.57894 ( 4762)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3481.88 seconds
wall clock time: 62 minutes 56.10 seconds (3776.10 seconds total)