Starting phenix.real_space_refine
on Fri Aug 22 12:37:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uoa_42432/08_2025/8uoa_42432_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uoa_42432/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uoa_42432/08_2025/8uoa_42432_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uoa_42432/08_2025/8uoa_42432_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uoa_42432/08_2025/8uoa_42432.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uoa_42432/08_2025/8uoa_42432.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 2, 'PHE:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 2, '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, 'GLU:plan': 4, 'ARG:plan': 8, 'PHE:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 2, 'TYR:plan': 5, 'ASP:plan': 5, 'HIS:plan': 1}
          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: 0.88, per 1000 atoms: 0.61
  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: 0.37
  Conformation dependent library (CDL) restraints added in 87.1 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.06
  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: 0.12

  Time building geometry restraints manager: 0.26 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:             3.000
  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:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.000
  Find NCS groups from input model:        0.000
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.070
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.001   0.000   ARG A 547 
 TYR   0.003   0.001   TYR A 564 
 PHE   0.003   0.001   PHE A 536 
 TRP   0.000   0.000   TRP B  36 
 HIS   0.001   0.000   HIS A 578 

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

*********************** 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  : 0.029 
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: 0.0305
  time to fit residues: 0.8291
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  : 0.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   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 = 0.4295 r_free = 0.4295 target = 0.181368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.166113 restraints weight = 3385.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.169099 restraints weight = 2286.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.171272 restraints weight = 1649.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.172940 restraints weight = 1248.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.174168 restraints weight = 981.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.4228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5565
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   1465  Z= 0.205
  Angle     :  0.756   6.121   2012  Z= 0.389
  Chirality :  0.053   0.220    256
  Planarity :  0.003   0.016    262
  Dihedral  : 19.570  86.747    365
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 27.16 %
    Favored  : 71.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.89 (0.52), residues: 211
  helix:  None (None), residues: 0
  sheet: -0.40 (0.59), residues: 66
  loop : -1.79 (0.46), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 491 
 TYR   0.021   0.003   TYR A 557 
 PHE   0.021   0.003   PHE A 566 
 TRP   0.000   0.000   TRP B  36 
 HIS   0.003   0.001   HIS A 506 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 1458)
  covalent geometry    : angle       0.71818 ( 1991)
  hydrogen bonds       : bond        0.04475 (   40)
  hydrogen bonds       : angle       7.37335 (  105)
  link_BETA1-4         : bond        0.00333 (    4)
  link_BETA1-4         : angle       2.65537 (   12)
  link_NAG-ASN         : bond        0.00556 (    3)
  link_NAG-ASN         : angle       2.05957 (    9)

*********************** 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  : 0.030 
Fit side-chains
REVERT: A  560 ASP cc_start: 0.7125 (t0) cc_final: 0.6925 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 19
  average time/residue: 0.0307
  time to fit residues: 0.6970
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  : 0.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  491 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 8 optimal weight:    0.2980
   chunk 18 optimal weight:   10.0000
   chunk 9 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 = 0.4240 r_free = 0.4240 target = 0.176972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.160957 restraints weight = 3261.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.164135 restraints weight = 2213.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.166551 restraints weight = 1598.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.168155 restraints weight = 1205.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.169430 restraints weight = 956.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.4156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5813
moved from start:          0.3710

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= 0.319
  Angle     :  0.944   7.985   2012  Z= 0.467
  Chirality :  0.063   0.261    256
  Planarity :  0.004   0.023    262
  Dihedral  : 18.869  75.806    365
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  7.41 %
    Allowed  : 24.69 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.32 (0.52), residues: 211
  helix:  None (None), residues: 0
  sheet: -1.20 (0.55), residues: 71
  loop : -1.80 (0.49), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 570 
 TYR   0.024   0.004   TYR A 511 
 PHE   0.053   0.004   PHE A 566 
 TRP   0.000   0.000   TRP B  36 
 HIS   0.003   0.001   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00631 ( 1458)
  covalent geometry    : angle       0.89920 ( 1991)
  hydrogen bonds       : bond        0.05201 (   40)
  hydrogen bonds       : angle       8.10925 (  105)
  link_BETA1-4         : bond        0.00524 (    4)
  link_BETA1-4         : angle       2.87438 (   12)
  link_NAG-ASN         : bond        0.00488 (    3)
  link_NAG-ASN         : angle       3.05819 (    9)

*********************** 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
  27 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 21
  time to evaluate  : 0.031 
Fit side-chains
REVERT: A  560 ASP cc_start: 0.7322 (t0) cc_final: 0.7043 (t0)
  outliers start: 6
  outliers final: 3
  residues processed: 25
  average time/residue: 0.0305
  time to fit residues: 0.8979
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  : 0.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  491 ARG
Chi-restraints excluded: chain A residue  527 GLU
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 16 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 8 optimal weight:    0.4980
   chunk 5 optimal weight:    0.7980
   chunk 4 optimal weight:    0.5980
   chunk 19 optimal weight:    0.0970
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.5378

-------------------------------------------------------------------------------
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 = 0.4277 r_free = 0.4277 target = 0.180041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.163781 restraints weight = 3332.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.167122 restraints weight = 2232.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.169578 restraints weight = 1595.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.171271 restraints weight = 1195.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.172687 restraints weight = 940.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.4199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5729
moved from start:          0.3984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   1465  Z= 0.168
  Angle     :  0.755   8.082   2012  Z= 0.367
  Chirality :  0.055   0.271    256
  Planarity :  0.003   0.013    262
  Dihedral  : 15.897  65.565    365
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 10.47
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.25 (0.53), residues: 211
  helix:  None (None), residues: 0
  sheet: -1.13 (0.58), residues: 71
  loop : -1.76 (0.49), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 547 
 TYR   0.011   0.002   TYR A 557 
 PHE   0.019   0.002   PHE A 566 
 TRP   0.000   0.000   TRP B  36 
 HIS   0.001   0.000   HIS A 506 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 1458)
  covalent geometry    : angle       0.71289 ( 1991)
  hydrogen bonds       : bond        0.03164 (   40)
  hydrogen bonds       : angle       6.78504 (  105)
  link_BETA1-4         : bond        0.00444 (    4)
  link_BETA1-4         : angle       2.86791 (   12)
  link_NAG-ASN         : bond        0.00513 (    3)
  link_NAG-ASN         : angle       2.04805 (    9)

*********************** 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  : 0.054 
Fit side-chains
REVERT: A  560 ASP cc_start: 0.7201 (t0) cc_final: 0.6916 (t0)
  outliers start: 2
  outliers final: 2
  residues processed: 21
  average time/residue: 0.0521
  time to fit residues: 1.3049
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  : 0.060 
-------------------------------------------------------------------------------
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 1 optimal weight:    0.4980
   chunk 17 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 13 optimal weight:    0.2980
   overall best weight:    1.1586

-------------------------------------------------------------------------------
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 = 0.4189 r_free = 0.4189 target = 0.172607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.158521 restraints weight = 3274.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.161276 restraints weight = 2231.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.163260 restraints weight = 1619.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.164534 restraints weight = 1239.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.165639 restraints weight = 1004.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.4119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5975
moved from start:          0.5552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   1465  Z= 0.321
  Angle     :  1.036   8.248   2012  Z= 0.508
  Chirality :  0.065   0.322    256
  Planarity :  0.004   0.022    262
  Dihedral  : 14.855  70.734    365
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 15.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.37 %
    Favored  : 88.63 %
  Rotamer:
    Outliers :  8.64 %
    Allowed  : 27.16 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.29 (0.56), residues: 211
  helix:  None (None), residues: 0
  sheet: -1.25 (0.63), residues: 65
  loop : -1.73 (0.51), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 547 
 TYR   0.039   0.005   TYR A 511 
 PHE   0.045   0.004   PHE A 566 
 TRP   0.000   0.000   TRP B  36 
 HIS   0.004   0.001   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00644 ( 1458)
  covalent geometry    : angle       1.00217 ( 1991)
  hydrogen bonds       : bond        0.04841 (   40)
  hydrogen bonds       : angle       8.84298 (  105)
  link_BETA1-4         : bond        0.00651 (    4)
  link_BETA1-4         : angle       3.01547 (   12)
  link_NAG-ASN         : bond        0.00623 (    3)
  link_NAG-ASN         : angle       2.35754 (    9)

*********************** 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
  27 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 20
  time to evaluate  : 0.052 
Fit side-chains
  outliers start: 7
  outliers final: 6
  residues processed: 24
  average time/residue: 0.0494
  time to fit residues: 1.4127
Evaluate side-chains
  25 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 19
  time to evaluate  : 0.052 
-------------------------------------------------------------------------------
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  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 10 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 12 optimal weight:    6.9990
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.4980
   chunk 3 optimal weight:    0.5980
   chunk 4 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4229 r_free = 0.4229 target = 0.176272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.161583 restraints weight = 3309.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.164349 restraints weight = 2263.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.166234 restraints weight = 1656.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.167576 restraints weight = 1291.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.168624 restraints weight = 1053.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.4142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5881
moved from start:          0.5574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   1465  Z= 0.181
  Angle     :  0.793   8.218   2012  Z= 0.385
  Chirality :  0.054   0.285    256
  Planarity :  0.003   0.015    262
  Dihedral  : 11.990  55.786    365
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.22 (0.54), residues: 211
  helix:  None (None), residues: 0
  sheet: -1.12 (0.64), residues: 59
  loop : -1.72 (0.47), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 547 
 TYR   0.008   0.002   TYR A 557 
 PHE   0.021   0.002   PHE A 566 
 TRP   0.000   0.000   TRP B  36 
 HIS   0.002   0.001   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 1458)
  covalent geometry    : angle       0.75691 ( 1991)
  hydrogen bonds       : bond        0.02874 (   40)
  hydrogen bonds       : angle       7.43848 (  105)
  link_BETA1-4         : bond        0.00532 (    4)
  link_BETA1-4         : angle       2.66868 (   12)
  link_NAG-ASN         : bond        0.00837 (    3)
  link_NAG-ASN         : angle       2.12573 (    9)

*********************** 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
  21 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 18
  time to evaluate  : 0.050 
Fit side-chains
REVERT: A  560 ASP cc_start: 0.7141 (t0) cc_final: 0.6917 (t0)
  outliers start: 3
  outliers final: 1
  residues processed: 21
  average time/residue: 0.0541
  time to fit residues: 1.3410
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  : 0.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 3 optimal weight:    3.9990
   chunk 8 optimal weight:    0.4980
   chunk 13 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 2 optimal weight:    0.4980
   chunk 10 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.4160 r_free = 0.4160 target = 0.170878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.156740 restraints weight = 3197.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.159547 restraints weight = 2158.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.161491 restraints weight = 1560.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.162896 restraints weight = 1198.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.163561 restraints weight = 956.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6021
moved from start:          0.6353

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= 0.303
  Angle     :  0.957   6.963   2012  Z= 0.472
  Chirality :  0.060   0.330    256
  Planarity :  0.004   0.027    262
  Dihedral  : 11.612  54.524    365
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 17.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.74 %
    Favored  : 86.26 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 28.40 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.44 (0.54), residues: 211
  helix:  None (None), residues: 0
  sheet: -1.36 (0.64), residues: 59
  loop : -1.84 (0.48), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.002   ARG A 491 
 TYR   0.038   0.004   TYR A 511 
 PHE   0.036   0.004   PHE A 566 
 TRP   0.000   0.000   TRP B  36 
 HIS   0.002   0.001   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00616 ( 1458)
  covalent geometry    : angle       0.90425 ( 1991)
  hydrogen bonds       : bond        0.04191 (   40)
  hydrogen bonds       : angle       8.62337 (  105)
  link_BETA1-4         : bond        0.00661 (    4)
  link_BETA1-4         : angle       3.56442 (   12)
  link_NAG-ASN         : bond        0.00658 (    3)
  link_NAG-ASN         : angle       2.64151 (    9)

*********************** 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
  21 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 17
  time to evaluate  : 0.074 
Fit side-chains
REVERT: A  560 ASP cc_start: 0.7347 (t0) cc_final: 0.7067 (t0)
  outliers start: 4
  outliers final: 4
  residues processed: 19
  average time/residue: 0.0317
  time to fit residues: 0.8487
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  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  487 PHE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 7 optimal weight:    0.1980
   chunk 19 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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 = 0.4127 r_free = 0.4127 target = 0.168731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.155280 restraints weight = 3230.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.157684 restraints weight = 2232.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.159378 restraints weight = 1661.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.160683 restraints weight = 1304.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.161563 restraints weight = 1058.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.4053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6040
moved from start:          0.6749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   1465  Z= 0.293
  Angle     :  0.916   7.047   2012  Z= 0.445
  Chirality :  0.058   0.325    256
  Planarity :  0.004   0.026    262
  Dihedral  : 10.921  47.520    365
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 18.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.32 %
    Favored  : 87.68 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.63 (0.55), residues: 211
  helix:  None (None), residues: 0
  sheet: -1.40 (0.64), residues: 65
  loop : -2.02 (0.48), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.001   ARG A 570 
 TYR   0.019   0.003   TYR A 511 
 PHE   0.035   0.003   PHE A 566 
 TRP   0.000   0.000   TRP B  36 
 HIS   0.006   0.002   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00594 ( 1458)
  covalent geometry    : angle       0.86053 ( 1991)
  hydrogen bonds       : bond        0.03596 (   40)
  hydrogen bonds       : angle       8.70945 (  105)
  link_BETA1-4         : bond        0.00521 (    4)
  link_BETA1-4         : angle       3.14848 (   12)
  link_NAG-ASN         : bond        0.00942 (    3)
  link_NAG-ASN         : angle       3.22863 (    9)

*********************** 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
  20 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 17
  time to evaluate  : 0.053 
Fit side-chains
REVERT: A  560 ASP cc_start: 0.7320 (t0) cc_final: 0.7070 (t0)
  outliers start: 3
  outliers final: 3
  residues processed: 19
  average time/residue: 0.0264
  time to fit residues: 0.6976
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  : 0.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  487 PHE
Chi-restraints excluded: chain A residue  543 ASN
Chi-restraints excluded: chain A residue  552 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0980
   chunk 10 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 18 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4189 r_free = 0.4189 target = 0.173736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.163927 restraints weight = 3440.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.165605 restraints weight = 2434.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.166856 restraints weight = 1838.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.167630 restraints weight = 1455.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.168266 restraints weight = 1216.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.4103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5940
moved from start:          0.6776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   1465  Z= 0.176
  Angle     :  0.764   5.172   2012  Z= 0.374
  Chirality :  0.052   0.294    256
  Planarity :  0.003   0.026    262
  Dihedral  :  9.515  41.813    365
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.90 %
    Favored  : 89.10 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.43 (0.54), residues: 211
  helix:  None (None), residues: 0
  sheet: -1.17 (0.64), residues: 59
  loop : -1.92 (0.48), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 547 
 TYR   0.012   0.002   TYR A 511 
 PHE   0.018   0.002   PHE A 566 
 TRP   0.000   0.000   TRP B  36 
 HIS   0.003   0.001   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 1458)
  covalent geometry    : angle       0.71281 ( 1991)
  hydrogen bonds       : bond        0.02934 (   40)
  hydrogen bonds       : angle       7.59839 (  105)
  link_BETA1-4         : bond        0.00343 (    4)
  link_BETA1-4         : angle       2.98939 (   12)
  link_NAG-ASN         : bond        0.00636 (    3)
  link_NAG-ASN         : angle       2.45867 (    9)

*********************** 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
  19 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 18
  time to evaluate  : 0.053 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 19
  average time/residue: 0.0237
  time to fit residues: 0.6545
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  : 0.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  552 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 4 optimal weight:    0.3980
   chunk 5 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0870
   chunk 13 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0770
   overall best weight:    0.3916

-------------------------------------------------------------------------------
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 = 0.4183 r_free = 0.4183 target = 0.172406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.157882 restraints weight = 3271.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.160721 restraints weight = 2196.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.162527 restraints weight = 1592.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.163901 restraints weight = 1233.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.164903 restraints weight = 993.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.4104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5925
moved from start:          0.6798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   1465  Z= 0.145
  Angle     :  0.728   5.508   2012  Z= 0.367
  Chirality :  0.050   0.284    256
  Planarity :  0.003   0.024    262
  Dihedral  :  8.479  40.733    365
  Min Nonbonded Distance : 2.348

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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.99 (0.55), residues: 211
  helix:  None (None), residues: 0
  sheet: -0.62 (0.69), residues: 56
  loop : -1.71 (0.47), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 547 
 TYR   0.007   0.001   TYR A 511 
 PHE   0.015   0.002   PHE A 566 
 TRP   0.000   0.000   TRP B  36 
 HIS   0.003   0.001   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 1458)
  covalent geometry    : angle       0.68869 ( 1991)
  hydrogen bonds       : bond        0.02484 (   40)
  hydrogen bonds       : angle       6.89976 (  105)
  link_BETA1-4         : bond        0.00307 (    4)
  link_BETA1-4         : angle       2.72276 (   12)
  link_NAG-ASN         : bond        0.00482 (    3)
  link_NAG-ASN         : angle       1.91312 (    9)

********************** 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
  19 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 18
  time to evaluate  : 0.052 
Fit side-chains
REVERT: A  560 ASP cc_start: 0.7107 (t0) cc_final: 0.6845 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 19
  average time/residue: 0.0356
  time to fit residues: 0.8740
Evaluate side-chains
  18 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 17
  time to evaluate  : 0.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  552 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 12 optimal weight:    0.0670
   chunk 6 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0470
   chunk 16 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    0.6020

-------------------------------------------------------------------------------
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 = 0.4166 r_free = 0.4166 target = 0.170955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.157243 restraints weight = 3314.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.159864 restraints weight = 2252.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.161464 restraints weight = 1643.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.162760 restraints weight = 1282.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.163726 restraints weight = 1039.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.4084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5967
moved from start:          0.6952

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     :  0.803   5.858   2012  Z= 0.393
  Chirality :  0.051   0.266    256
  Planarity :  0.003   0.026    262
  Dihedral  :  8.701  29.703    365
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.90 %
    Favored  : 89.10 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.97 (0.54), residues: 211
  helix:  None (None), residues: 0
  sheet: -0.64 (0.69), residues: 56
  loop : -1.68 (0.46), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 547 
 TYR   0.011   0.002   TYR A 511 
 PHE   0.020   0.002   PHE A 566 
 TRP   0.000   0.000   TRP B  36 
 HIS   0.003   0.001   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 1458)
  covalent geometry    : angle       0.74691 ( 1991)
  hydrogen bonds       : bond        0.02948 (   40)
  hydrogen bonds       : angle       7.04079 (  105)
  link_BETA1-4         : bond        0.00224 (    4)
  link_BETA1-4         : angle       2.61003 (   12)
  link_NAG-ASN         : bond        0.00762 (    3)
  link_NAG-ASN         : angle       3.41877 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 592.48 seconds
wall clock time: 11 minutes 10.48 seconds (670.48 seconds total)