Starting phenix.real_space_refine
on Fri May  9 12:43:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uoa_42432/05_2025/8uoa_42432_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uoa_42432/05_2025/8uoa_42432.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uoa_42432/05_2025/8uoa_42432.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uoa_42432/05_2025/8uoa_42432.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uoa_42432/05_2025/8uoa_42432_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uoa_42432/05_2025/8uoa_42432_neut.cif"
  }
  resolution = 3.8
  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=   0.001 sd=   0.013
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       2      5.16       5
     C     888      2.51       5
     N     251      2.21       5
     O     299      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 1440
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 758
          Classifications: {'peptide': 96}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 1, 'TRANS': 94}
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 77
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 46
    Chain: "B"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 587
          Classifications: {'peptide': 119}
          Incomplete info: {'truncation_to_alanine': 93}
          Link IDs: {'PTRANS': 4, 'TRANS': 114}
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 325
          Unresolved non-hydrogen angles: 418
          Unresolved non-hydrogen dihedrals: 271
          Unresolved non-hydrogen chiralities: 28
          Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 188
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 2.55, per 1000 atoms: 1.77
  Number of scatterers: 1440
  At special positions: 0
  Unit cell: (59.616, 57.672, 68.688, 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       2     16.00
     O     299      8.00
     N     251      7.00
     C     888      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 573 "
      " NAG D   1 " - " ASN A 548 "
      " NAG E   1 " - " ASN A 498 "
  Time building additional restraints: 0.55
  Conformation dependent library (CDL) restraints added in 209.0 milliseconds
  

  422 Ramachandran restraints generated.
    211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  396

  Finding SS restraints...
    Secondary structure from input PDB file:
      2 helices and 6 sheets defined
      3.3% alpha, 40.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'B' and resid 61 through 64
    Processing helix  chain 'B' and resid 73 through 75
      No H-bonds generated for 'chain 'B' and resid 73 through 75'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 515 through 516
    Processing sheet with id=AA2, first strand: chain 'A' and resid 525 through 532
      removed outlier: 5.786A  pdb=" N   PHE A 526 " --> pdb=" O   ARG A 547 " (cutoff:3.500A)
      removed outlier: 5.418A  pdb=" N   CYS A 549 " --> pdb=" O   PHE A 526 " (cutoff:3.500A)
      removed outlier: 7.738A  pdb=" N   ASP A 528 " --> pdb=" O   CYS A 549 " (cutoff:3.500A)
      removed outlier: 9.723A  pdb=" N   PHE A 551 " --> pdb=" O   ASP A 528 " (cutoff:3.500A)
      removed outlier: 8.634A  pdb=" N   LEU A 530 " --> pdb=" O   PHE A 551 " (cutoff:3.500A)
      removed outlier: 10.114A  pdb=" N   ASN A 553 " --> pdb=" O   LEU A 530 " (cutoff:3.500A)
      removed outlier: 5.817A  pdb=" N   GLU A 532 " --> pdb=" O   ASN A 553 " (cutoff:3.500A)
      removed outlier: 8.348A  pdb=" N   VAL A 555 " --> pdb=" O   GLU A 532 " (cutoff:3.500A)
      removed outlier: 9.159A  pdb=" N   LEU A 571 " --> pdb=" O   ASN A 548 " (cutoff:3.500A)
      removed outlier: 8.621A  pdb=" N   THR A 550 " --> pdb=" O   LEU A 571 " (cutoff:3.500A)
      removed outlier: 9.163A  pdb=" N   ASN A 573 " --> pdb=" O   THR A 550 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   ILE A 552 " --> pdb=" O   ASN A 573 " (cutoff:3.500A)
      removed outlier: 8.885A  pdb=" N   THR A 575 " --> pdb=" O   ILE A 552 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   THR A 554 " --> pdb=" O   THR A 575 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 558 through 559
      removed outlier: 3.681A  pdb=" N   THR A 559 " --> pdb=" O   HIS A 578 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 5
    Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.155A  pdb=" N   VAL B  98 " --> pdb=" O   VAL B  33 " (cutoff:3.500A)
      removed outlier: 5.393A  pdb=" N   VAL B  33 " --> pdb=" O   VAL B  98 " (cutoff:3.500A)
      removed outlier: 9.298A  pdb=" N   MET B  34 " --> pdb=" O   SER B  50 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   SER B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12

    47 hydrogen bonds defined for protein.
    105 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: 0.34

  Time building geometry restraints manager: 0.60 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 323
        1.33 -     1.45: 362
        1.45 -     1.57: 771
        1.57 -     1.69: 0
        1.69 -     1.81: 2
  Bond restraints: 1458
  Sorted by residual:
  bond pdb=" N   VAL B  63 "
       pdb=" CA  VAL B  63 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.037 1.09e-02 8.42e+03 1.16e+01
  bond pdb=" CA  LEU B  85 "
       pdb=" C   LEU B  85 "
    ideal  model  delta    sigma   weight residual
    1.526  1.487  0.039 1.20e-02 6.94e+03 1.05e+01
  bond pdb=" CA  MET B  82 "
       pdb=" C   MET B  82 "
    ideal  model  delta    sigma   weight residual
    1.523  1.486  0.037 1.24e-02 6.50e+03 8.95e+00
  bond pdb=" CA  LEU B  80 "
       pdb=" C   LEU B  80 "
    ideal  model  delta    sigma   weight residual
    1.524  1.489  0.035 1.23e-02 6.61e+03 7.95e+00
  bond pdb=" C   VAL B  12 "
       pdb=" O   VAL B  12 "
    ideal  model  delta    sigma   weight residual
    1.236  1.208  0.028 9.90e-03 1.02e+04 7.79e+00
  ... (remaining 1453 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.33: 1795
        2.33 -     4.66: 150
        4.66 -     6.99: 35
        6.99 -     9.32: 9
        9.32 -    11.65: 2
  Bond angle restraints: 1991
  Sorted by residual:
  angle pdb=" N   ARG B  32 "
        pdb=" CA  ARG B  32 "
        pdb=" C   ARG B  32 "
      ideal   model   delta    sigma   weight residual
     108.67   98.68    9.99 1.55e+00 4.16e-01 4.16e+01
  angle pdb=" C   LYS B  86 "
        pdb=" N   PRO B  87 "
        pdb=" CA  PRO B  87 "
      ideal   model   delta    sigma   weight residual
     119.47  126.72   -7.25 1.16e+00 7.43e-01 3.90e+01
  angle pdb=" N   THR B 101 "
        pdb=" CA  THR B 101 "
        pdb=" C   THR B 101 "
      ideal   model   delta    sigma   weight residual
     110.19  117.85   -7.66 1.24e+00 6.50e-01 3.82e+01
  angle pdb=" N   ALA B  52 "
        pdb=" CA  ALA B  52 "
        pdb=" C   ALA B  52 "
      ideal   model   delta    sigma   weight residual
     111.71  118.09   -6.38 1.15e+00 7.56e-01 3.08e+01
  angle pdb=" C   GLY B 104 "
        pdb=" N   PRO B 105 "
        pdb=" CA  PRO B 105 "
      ideal   model   delta    sigma   weight residual
     119.76  125.47   -5.71 1.03e+00 9.43e-01 3.08e+01
  ... (remaining 1986 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.00: 847
       21.00 -    41.99: 41
       41.99 -    62.99: 15
       62.99 -    83.98: 7
       83.98 -   104.98: 13
  Dihedral angle restraints: 923
    sinusoidal: 310
      harmonic: 613
  Sorted by residual:
  dihedral pdb=" CA  LEU A 521 "
           pdb=" C   LEU A 521 "
           pdb=" N   LYS A 522 "
           pdb=" CA  LYS A 522 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.31   28.69     0      5.00e+00 4.00e-02 3.29e+01
  dihedral pdb=" C1  NAG C   2 "
           pdb=" C2  NAG C   2 "
           pdb=" C3  NAG C   2 "
           pdb=" O3  NAG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -175.09  -70.11 -104.98     1      3.00e+01 1.11e-03 1.34e+01
  dihedral pdb=" C2  NAG C   2 "
           pdb=" C3  NAG C   2 "
           pdb=" C4  NAG C   2 "
           pdb=" O4  NAG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.11   70.32  104.79     1      3.00e+01 1.11e-03 1.34e+01
  ... (remaining 920 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 214
       0.092 -    0.184: 34
       0.184 -    0.276: 5
       0.276 -    0.369: 1
       0.369 -    0.461: 2
  Chirality restraints: 256
  Sorted by residual:
  chirality pdb=" C5  NAG E   2 "
            pdb=" C4  NAG E   2 "
            pdb=" C6  NAG E   2 "
            pdb=" O5  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.41   -1.95   -0.46 2.00e-01 2.50e+01 5.30e+00
  chirality pdb=" C1  NAG E   2 "
            pdb=" O4  NAG E   1 "
            pdb=" C2  NAG E   2 "
            pdb=" O5  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.36   -0.04 2.00e-02 2.50e+03 4.88e+00
  chirality pdb=" C4  NAG E   2 "
            pdb=" C3  NAG E   2 "
            pdb=" C5  NAG E   2 "
            pdb=" O4  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.14   -0.39 2.00e-01 2.50e+01 3.77e+00
  ... (remaining 253 not shown)

  Planarity restraints: 265
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG E   1 "   -0.044 2.00e-02 2.50e+03   3.64e-02 1.66e+01
        pdb=" C7  NAG E   1 "    0.012 2.00e-02 2.50e+03
        pdb=" C8  NAG E   1 "   -0.034 2.00e-02 2.50e+03
        pdb=" N2  NAG E   1 "    0.058 2.00e-02 2.50e+03
        pdb=" O7  NAG E   1 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG E   2 "    0.044 2.00e-02 2.50e+03   3.63e-02 1.65e+01
        pdb=" C7  NAG E   2 "   -0.012 2.00e-02 2.50e+03
        pdb=" C8  NAG E   2 "    0.033 2.00e-02 2.50e+03
        pdb=" N2  NAG E   2 "   -0.058 2.00e-02 2.50e+03
        pdb=" O7  NAG E   2 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B  94 "   -0.011 2.00e-02 2.50e+03   2.18e-02 4.74e+00
        pdb=" C   TYR B  94 "    0.038 2.00e-02 2.50e+03
        pdb=" O   TYR B  94 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   CYS B  95 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 262 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 536
        2.86 -     3.37: 1257
        3.37 -     3.88: 2074
        3.88 -     4.39: 2123
        4.39 -     4.90: 3730
  Nonbonded interactions: 9720
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 535 "
            pdb=" OE1 GLU A 537 "
     model   vdw
     2.349 3.040
  nonbonded pdb=" O   GLN A 504 "
            pdb=" N   SER A 525 "
     model   vdw
     2.400 3.120
  nonbonded pdb=" OD1 ASN A 548 "
            pdb=" O5  NAG D   1 "
     model   vdw
     2.427 3.040
  nonbonded pdb=" O3  NAG C   1 "
            pdb=" O5  NAG C   2 "
     model   vdw
     2.429 3.040
  nonbonded pdb=" O   ASN A 548 "
            pdb=" OD1 ASN A 548 "
     model   vdw
     2.430 3.040
  ... (remaining 9715 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
Found NCS groups:
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
}

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:             2.320
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     12.080
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3767
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      :  0.009   0.042   1465  Z= 0.613
  Angle     :  1.549  11.650   2012  Z= 0.993
  Chirality :  0.079   0.461    256
  Planarity :  0.006   0.036    262
  Dihedral  : 22.405 104.975    527
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 27.16 %
    Favored  : 72.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.49 (0.55), residues: 211
  helix:  None (None), residues: 0
  sheet: -0.20 (0.64), residues: 65
  loop : -1.45 (0.48), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP B  36 
 HIS   0.001   0.000   HIS A 578 
 PHE   0.003   0.001   PHE A 536 
 TYR   0.003   0.001   TYR A 564 
 ARG   0.001   0.000   ARG A 547 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00579 (    3)
  link_NAG-ASN         : angle       2.68327 (    9)
  link_BETA1-4         : bond        0.00373 (    4)
  link_BETA1-4         : angle       2.44088 (   12)
  hydrogen bonds       : bond        0.21118 (   40)
  hydrogen bonds       : angle       9.66446 (  105)
  covalent geometry    : bond        0.00854 ( 1458)
  covalent geometry    : angle       1.53474 ( 1991)

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

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

  422 Ramachandran restraints generated.
    211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  422 Ramachandran restraints generated.
    211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A  560 ASP cc_start: 0.6964 (t0) cc_final: 0.6485 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.1271
  time to fit residues: 3.4466
Evaluate side-chains
  20 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.4281 r_free = 0.4281 target = 0.180198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.165247 restraints weight = 3385.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.168160 restraints weight = 2292.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.170315 restraints weight = 1659.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.4179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5669
moved from start:          0.2208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   1465  Z= 0.236
  Angle     :  0.794   6.200   2012  Z= 0.411
  Chirality :  0.054   0.202    256
  Planarity :  0.004   0.016    262
  Dihedral  : 19.857  86.598    365
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 28.40 %
    Favored  : 70.37 %
  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: -2.05 (0.50), residues: 211
  helix:  None (None), residues: 0
  sheet: -0.73 (0.57), residues: 65
  loop : -1.77 (0.45), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP B  36 
 HIS   0.003   0.001   HIS A 506 
 PHE   0.026   0.003   PHE A 566 
 TYR   0.022   0.003   TYR A 557 
 ARG   0.001   0.000   ARG A 491 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00698 (    3)
  link_NAG-ASN         : angle       2.15439 (    9)
  link_BETA1-4         : bond        0.00278 (    4)
  link_BETA1-4         : angle       2.60326 (   12)
  hydrogen bonds       : bond        0.04920 (   40)
  hydrogen bonds       : angle       7.55170 (  105)
  covalent geometry    : bond        0.00438 ( 1458)
  covalent geometry    : angle       0.75805 ( 1991)

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

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

  422 Ramachandran restraints generated.
    211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  422 Ramachandran restraints generated.
    211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 18
  time to evaluate  : 0.137 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 19
  average time/residue: 0.0839
  time to fit residues: 2.0535
Evaluate side-chains
  18 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.4242 r_free = 0.4242 target = 0.177026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.161354 restraints weight = 3200.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.164425 restraints weight = 2172.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.166655 restraints weight = 1570.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.4126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5884
moved from start:          0.3962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   1465  Z= 0.309
  Angle     :  0.958   7.742   2012  Z= 0.477
  Chirality :  0.062   0.258    256
  Planarity :  0.004   0.023    262
  Dihedral  : 18.554  75.001    365
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 25.93 %
    Favored  : 69.14 %
  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: -2.29 (0.53), residues: 211
  helix:  None (None), residues: 0
  sheet: -1.35 (0.56), residues: 68
  loop : -1.67 (0.49), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP B  36 
 HIS   0.002   0.001   HIS A 578 
 PHE   0.051   0.004   PHE A 566 
 TYR   0.023   0.004   TYR A 511 
 ARG   0.002   0.001   ARG A 547 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00346 (    3)
  link_NAG-ASN         : angle       3.28045 (    9)
  link_BETA1-4         : bond        0.00555 (    4)
  link_BETA1-4         : angle       2.96607 (   12)
  hydrogen bonds       : bond        0.05126 (   40)
  hydrogen bonds       : angle       8.11431 (  105)
  covalent geometry    : bond        0.00625 ( 1458)
  covalent geometry    : angle       0.90902 ( 1991)

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

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

  422 Ramachandran restraints generated.
    211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  422 Ramachandran restraints generated.
    211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 20
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A  560 ASP cc_start: 0.7363 (t0) cc_final: 0.7005 (t0)
  outliers start: 4
  outliers final: 2
  residues processed: 24
  average time/residue: 0.1061
  time to fit residues: 3.0648
Evaluate side-chains
  21 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 19
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  491 ARG
Chi-restraints excluded: chain A residue  552 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0470
   chunk 12 optimal weight:    5.9990
   chunk 15 optimal weight:    0.2980
   chunk 17 optimal weight:    0.0970
   chunk 9 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 6 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.3676

-------------------------------------------------------------------------------
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 = 0.4280 r_free = 0.4280 target = 0.180976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.165219 restraints weight = 3228.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.168308 restraints weight = 2176.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.170684 restraints weight = 1566.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.4178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5784
moved from start:          0.4058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   1465  Z= 0.144
  Angle     :  0.738   8.326   2012  Z= 0.356
  Chirality :  0.054   0.261    256
  Planarity :  0.002   0.012    262
  Dihedral  : 15.200  63.030    365
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 27.16 %
    Favored  : 70.37 %
  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: -2.19 (0.54), residues: 211
  helix:  None (None), residues: 0
  sheet: -1.11 (0.58), residues: 71
  loop : -1.71 (0.49), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP B  36 
 HIS   0.000   0.000   HIS A 494 
 PHE   0.013   0.002   PHE A 566 
 TYR   0.008   0.001   TYR A 557 
 ARG   0.001   0.000   ARG A 547 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00562 (    3)
  link_NAG-ASN         : angle       2.07226 (    9)
  link_BETA1-4         : bond        0.00471 (    4)
  link_BETA1-4         : angle       2.97990 (   12)
  hydrogen bonds       : bond        0.02876 (   40)
  hydrogen bonds       : angle       6.55715 (  105)
  covalent geometry    : bond        0.00283 ( 1458)
  covalent geometry    : angle       0.69131 ( 1991)

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

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

  422 Ramachandran restraints generated.
    211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  422 Ramachandran restraints generated.
    211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 19
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A  560 ASP cc_start: 0.7269 (t0) cc_final: 0.6916 (t0)
  outliers start: 2
  outliers final: 2
  residues processed: 21
  average time/residue: 0.1124
  time to fit residues: 2.8450
Evaluate side-chains
  21 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 19
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  491 ARG
Chi-restraints excluded: chain A residue  552 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 1 optimal weight:    0.4980
   chunk 19 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.4226 r_free = 0.4226 target = 0.175497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.160542 restraints weight = 3215.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.163704 restraints weight = 2151.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.165846 restraints weight = 1530.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.4124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5955
moved from start:          0.5246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   1465  Z= 0.253
  Angle     :  0.874   8.137   2012  Z= 0.434
  Chirality :  0.058   0.284    256
  Planarity :  0.003   0.015    262
  Dihedral  : 12.950  62.556    365
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.37 %
    Favored  : 88.63 %
  Rotamer:
    Outliers :  8.64 %
    Allowed  : 28.40 %
    Favored  : 62.96 %
  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: -2.20 (0.54), residues: 211
  helix:  None (None), residues: 0
  sheet: -1.16 (0.62), residues: 65
  loop : -1.68 (0.49), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP B  36 
 HIS   0.003   0.001   HIS A 494 
 PHE   0.033   0.003   PHE A 566 
 TYR   0.027   0.003   TYR A 511 
 ARG   0.000   0.000   ARG A 491 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00518 (    3)
  link_NAG-ASN         : angle       1.91334 (    9)
  link_BETA1-4         : bond        0.00595 (    4)
  link_BETA1-4         : angle       2.68008 (   12)
  hydrogen bonds       : bond        0.04109 (   40)
  hydrogen bonds       : angle       7.75292 (  105)
  covalent geometry    : bond        0.00502 ( 1458)
  covalent geometry    : angle       0.84404 ( 1991)

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

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

  422 Ramachandran restraints generated.
    211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  422 Ramachandran restraints generated.
    211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 19
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A  560 ASP cc_start: 0.7255 (t0) cc_final: 0.6913 (t0)
  outliers start: 7
  outliers final: 7
  residues processed: 23
  average time/residue: 0.1117
  time to fit residues: 3.0951
Evaluate side-chains
  26 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 19
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  487 PHE
Chi-restraints excluded: chain A residue  491 ARG
Chi-restraints excluded: chain A residue  503 ASN
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  543 ASN
Chi-restraints excluded: chain A residue  552 ILE
Chi-restraints excluded: chain A residue  567 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0010
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.6990

-------------------------------------------------------------------------------
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 = 0.4228 r_free = 0.4228 target = 0.176168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.161811 restraints weight = 3255.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.164487 restraints weight = 2232.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.166398 restraints weight = 1630.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.4118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5930
moved from start:          0.5516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   1465  Z= 0.187
  Angle     :  0.749   7.830   2012  Z= 0.367
  Chirality :  0.053   0.283    256
  Planarity :  0.003   0.015    262
  Dihedral  : 10.766  49.626    365
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.95 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 33.33 %
    Favored  : 62.96 %
  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: -2.15 (0.54), residues: 211
  helix:  None (None), residues: 0
  sheet: -1.13 (0.64), residues: 59
  loop : -1.64 (0.48), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP B  36 
 HIS   0.002   0.001   HIS A 506 
 PHE   0.021   0.002   PHE A 566 
 TYR   0.012   0.002   TYR A 511 
 ARG   0.002   0.000   ARG A 547 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00547 (    3)
  link_NAG-ASN         : angle       2.00829 (    9)
  link_BETA1-4         : bond        0.00549 (    4)
  link_BETA1-4         : angle       2.63240 (   12)
  hydrogen bonds       : bond        0.03015 (   40)
  hydrogen bonds       : angle       7.08705 (  105)
  covalent geometry    : bond        0.00374 ( 1458)
  covalent geometry    : angle       0.71192 ( 1991)

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

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

  422 Ramachandran restraints generated.
    211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  422 Ramachandran restraints generated.
    211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 20
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A  560 ASP cc_start: 0.7159 (t0) cc_final: 0.6891 (t0)
  outliers start: 3
  outliers final: 2
  residues processed: 23
  average time/residue: 0.1128
  time to fit residues: 3.1190
Evaluate side-chains
  21 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 19
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  491 ARG
Chi-restraints excluded: chain A residue  552 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   chunk 0 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 12 optimal weight:    4.9990
   chunk 11 optimal weight:    6.9990
   chunk 3 optimal weight:    0.8980
   chunk 10 optimal weight:    0.1980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4226 r_free = 0.4226 target = 0.177373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.166891 restraints weight = 3487.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.168672 restraints weight = 2496.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.170000 restraints weight = 1894.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.4142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5878
moved from start:          0.5846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   1465  Z= 0.203
  Angle     :  0.789   6.790   2012  Z= 0.385
  Chirality :  0.054   0.309    256
  Planarity :  0.003   0.017    262
  Dihedral  :  9.928  45.773    365
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.85 %
    Favored  : 88.15 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 30.86 %
    Favored  : 64.20 %
  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: -2.17 (0.54), residues: 211
  helix:  None (None), residues: 0
  sheet: -1.07 (0.63), residues: 59
  loop : -1.69 (0.48), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP B  36 
 HIS   0.001   0.001   HIS A 494 
 PHE   0.023   0.002   PHE A 566 
 TYR   0.016   0.002   TYR A 511 
 ARG   0.001   0.000   ARG A 570 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00587 (    3)
  link_NAG-ASN         : angle       2.22024 (    9)
  link_BETA1-4         : bond        0.00422 (    4)
  link_BETA1-4         : angle       2.84204 (   12)
  hydrogen bonds       : bond        0.03173 (   40)
  hydrogen bonds       : angle       7.15392 (  105)
  covalent geometry    : bond        0.00408 ( 1458)
  covalent geometry    : angle       0.74681 ( 1991)

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

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

  422 Ramachandran restraints generated.
    211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  422 Ramachandran restraints generated.
    211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.152 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 22
  average time/residue: 0.1167
  time to fit residues: 3.0829
Evaluate side-chains
  22 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 19
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  487 PHE
Chi-restraints excluded: chain A residue  552 ILE
Chi-restraints excluded: chain A residue  567 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 12 optimal weight:    8.9990
   chunk 9 optimal weight:    4.9990
   chunk 1 optimal weight:    0.2980
   chunk 17 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   overall best weight:    1.1786

-------------------------------------------------------------------------------
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 = 0.4144 r_free = 0.4144 target = 0.169659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.156172 restraints weight = 3158.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.158776 restraints weight = 2148.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.160456 restraints weight = 1568.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.4043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6096
moved from start:          0.6731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   1465  Z= 0.317
  Angle     :  1.001   8.101   2012  Z= 0.493
  Chirality :  0.062   0.377    256
  Planarity :  0.005   0.037    262
  Dihedral  : 10.318  44.221    365
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 16.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.69 %
    Favored  : 85.31 %
  Rotamer:
    Outliers :  6.17 %
    Allowed  : 28.40 %
    Favored  : 65.43 %
  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: -2.36 (0.54), residues: 211
  helix:  None (None), residues: 0
  sheet: -1.19 (0.66), residues: 59
  loop : -1.84 (0.48), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP B  36 
 HIS   0.004   0.002   HIS A 578 
 PHE   0.039   0.004   PHE A 566 
 TYR   0.037   0.004   TYR A 511 
 ARG   0.006   0.001   ARG A 491 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00583 (    3)
  link_NAG-ASN         : angle       3.44662 (    9)
  link_BETA1-4         : bond        0.00572 (    4)
  link_BETA1-4         : angle       3.32317 (   12)
  hydrogen bonds       : bond        0.03955 (   40)
  hydrogen bonds       : angle       8.68623 (  105)
  covalent geometry    : bond        0.00650 ( 1458)
  covalent geometry    : angle       0.94430 ( 1991)

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

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

  422 Ramachandran restraints generated.
    211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  422 Ramachandran restraints generated.
    211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 17
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A  560 ASP cc_start: 0.7259 (t0) cc_final: 0.7045 (t0)
  outliers start: 5
  outliers final: 4
  residues processed: 20
  average time/residue: 0.0563
  time to fit residues: 1.6012
Evaluate side-chains
  21 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 17
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  487 PHE
Chi-restraints excluded: chain A residue  503 ASN
Chi-restraints excluded: chain A residue  552 ILE
Chi-restraints excluded: chain A residue  567 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 14 optimal weight:    4.9990
   chunk 1 optimal weight:    0.2980
   chunk 0 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0670
   chunk 13 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.7120

-------------------------------------------------------------------------------
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 = 0.4159 r_free = 0.4159 target = 0.171126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.157802 restraints weight = 3164.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.160348 restraints weight = 2148.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.162165 restraints weight = 1570.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.4065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6032
moved from start:          0.6730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   1465  Z= 0.201
  Angle     :  0.801   5.139   2012  Z= 0.398
  Chirality :  0.054   0.305    256
  Planarity :  0.003   0.027    262
  Dihedral  :  9.341  38.721    365
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.95 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 29.63 %
    Favored  : 66.67 %
  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: -2.33 (0.54), residues: 211
  helix:  None (None), residues: 0
  sheet: -1.02 (0.66), residues: 59
  loop : -1.89 (0.47), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP B  36 
 HIS   0.004   0.001   HIS A 494 
 PHE   0.021   0.002   PHE A 566 
 TYR   0.015   0.002   TYR A 511 
 ARG   0.002   0.001   ARG A 491 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00607 (    3)
  link_NAG-ASN         : angle       2.65084 (    9)
  link_BETA1-4         : bond        0.00275 (    4)
  link_BETA1-4         : angle       2.74281 (   12)
  hydrogen bonds       : bond        0.03091 (   40)
  hydrogen bonds       : angle       7.77057 (  105)
  covalent geometry    : bond        0.00409 ( 1458)
  covalent geometry    : angle       0.75621 ( 1991)

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

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

  422 Ramachandran restraints generated.
    211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  422 Ramachandran restraints generated.
    211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 18
  time to evaluate  : 0.166 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 20
  average time/residue: 0.0612
  time to fit residues: 1.7138
Evaluate side-chains
  21 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 18
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  487 PHE
Chi-restraints excluded: chain A residue  552 ILE
Chi-restraints excluded: chain A residue  567 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 19 optimal weight:    0.3980
   chunk 9 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0370
   chunk 1 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 17 optimal weight:    0.4980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.7860

-------------------------------------------------------------------------------
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 = 0.4136 r_free = 0.4136 target = 0.169476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.156192 restraints weight = 3283.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.158759 restraints weight = 2232.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.160609 restraints weight = 1616.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.4039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6054
moved from start:          0.6962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   1465  Z= 0.224
  Angle     :  0.848   6.164   2012  Z= 0.424
  Chirality :  0.054   0.315    256
  Planarity :  0.003   0.025    262
  Dihedral  :  9.449  33.958    365
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.64 %
    Favored  : 84.36 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 28.40 %
    Favored  : 67.90 %
  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: -2.09 (0.55), residues: 211
  helix:  None (None), residues: 0
  sheet: -0.73 (0.69), residues: 56
  loop : -1.77 (0.47), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP B  36 
 HIS   0.004   0.002   HIS A 494 
 PHE   0.028   0.003   PHE A 566 
 TYR   0.018   0.002   TYR A 511 
 ARG   0.001   0.000   ARG A 491 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00656 (    3)
  link_NAG-ASN         : angle       3.05501 (    9)
  link_BETA1-4         : bond        0.00327 (    4)
  link_BETA1-4         : angle       2.66377 (   12)
  hydrogen bonds       : bond        0.03133 (   40)
  hydrogen bonds       : angle       7.69918 (  105)
  covalent geometry    : bond        0.00459 ( 1458)
  covalent geometry    : angle       0.80079 ( 1991)

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

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

  422 Ramachandran restraints generated.
    211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  422 Ramachandran restraints generated.
    211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 17
  time to evaluate  : 0.163 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 19
  average time/residue: 0.0638
  time to fit residues: 1.7339
Evaluate side-chains
  20 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 17
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  487 PHE
Chi-restraints excluded: chain A residue  552 ILE
Chi-restraints excluded: chain A residue  567 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 8 optimal weight:    0.2980
   chunk 12 optimal weight:   10.0000
   chunk 15 optimal weight:    0.0870
   chunk 14 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0370
   chunk 1 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.4236

-------------------------------------------------------------------------------
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 = 0.4178 r_free = 0.4178 target = 0.171764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.156482 restraints weight = 3317.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.159590 restraints weight = 2207.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.161533 restraints weight = 1578.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.4057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6021
moved from start:          0.6949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   1465  Z= 0.154
  Angle     :  0.745   5.415   2012  Z= 0.382
  Chirality :  0.050   0.287    256
  Planarity :  0.003   0.025    262
  Dihedral  :  8.382  28.445    365
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 30.86 %
    Favored  : 67.90 %
  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: -1.97 (0.55), residues: 211
  helix:  None (None), residues: 0
  sheet: -0.25 (0.75), residues: 47
  loop : -1.78 (0.46), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP B  36 
 HIS   0.003   0.001   HIS A 494 
 PHE   0.014   0.002   PHE A 566 
 TYR   0.009   0.001   TYR A 511 
 ARG   0.001   0.000   ARG A 570 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00498 (    3)
  link_NAG-ASN         : angle       2.13623 (    9)
  link_BETA1-4         : bond        0.00238 (    4)
  link_BETA1-4         : angle       2.40159 (   12)
  hydrogen bonds       : bond        0.02659 (   40)
  hydrogen bonds       : angle       7.07521 (  105)
  covalent geometry    : bond        0.00304 ( 1458)
  covalent geometry    : angle       0.71125 ( 1991)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1113.75 seconds
wall clock time: 19 minutes 58.04 seconds (1198.04 seconds total)