Starting phenix.real_space_refine
on Wed Mar  4 07:57:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xxb_33500/03_2026/7xxb_33500_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xxb_33500/03_2026/7xxb_33500.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xxb_33500/03_2026/7xxb_33500.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xxb_33500/03_2026/7xxb_33500.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xxb_33500/03_2026/7xxb_33500_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xxb_33500/03_2026/7xxb_33500_trim.cif"
  }
  resolution = 2.93
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    3922      2.51       5
     N     940      2.21       5
     O     996      1.98       5
     H    6138      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12038
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6006
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 377, 6006
          Classifications: {'peptide': 377}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 359}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 6006
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 377, 6006
          Classifications: {'peptide': 377}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 359}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 13
          Unusual residues: {'IAC': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 13
          Unusual residues: {'IAC': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.98, per 1000 atoms: 0.16
  Number of scatterers: 12038
  At special positions: 0
  Unit cell: (80.91, 121.83, 69.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      42     16.00
     O     996      8.00
     N     940      7.00
     C    3922      6.00
     H    6138      1.00
    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
  Time building additional restraints: 0.93
  Conformation dependent library (CDL) restraints added in 290.0 milliseconds
  

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1420

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 2 sheets defined
      79.8% alpha, 4.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 29
      Proline residue:  A  16  - end of helix
    Processing helix  chain 'A' and resid 35 through 62
      removed outlier: 4.943A  pdb=" N   VAL A  51 " --> pdb=" O   ALA A  47 " (cutoff:3.500A)
      Proline residue:  A  52  - end of helix
      removed outlier: 3.650A  pdb=" N   ASN A  62 " --> pdb=" O   PHE A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 67
    Processing helix  chain 'A' and resid 68 through 91
    Processing helix  chain 'A' and resid 97 through 110
    Processing helix  chain 'A' and resid 116 through 125
    Processing helix  chain 'A' and resid 126 through 143
    Processing helix  chain 'A' and resid 143 through 165
    Processing helix  chain 'A' and resid 168 through 170
      No H-bonds generated for 'chain 'A' and resid 168 through 170'
    Processing helix  chain 'A' and resid 475 through 492
    Processing helix  chain 'A' and resid 494 through 513
    Processing helix  chain 'A' and resid 518 through 530
      removed outlier: 4.402A  pdb=" N   LEU A 528 " --> pdb=" O   SER A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 547
    Processing helix  chain 'A' and resid 554 through 581
      removed outlier: 3.883A  pdb=" N   GLY A 569 " --> pdb=" O   ARG A 565 " (cutoff:3.500A)
      Proline residue:  A 570  - end of helix
    Processing helix  chain 'A' and resid 584 through 595
    Processing helix  chain 'A' and resid 599 through 609
      removed outlier: 4.035A  pdb=" N   PHE A 603 " --> pdb=" O   GLY A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 626
    Processing helix  chain 'A' and resid 626 through 640
      removed outlier: 3.706A  pdb=" N   ILE A 630 " --> pdb=" O   ILE A 626 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 29
      Proline residue:  B  16  - end of helix
    Processing helix  chain 'B' and resid 35 through 62
      removed outlier: 4.944A  pdb=" N   VAL B  51 " --> pdb=" O   ALA B  47 " (cutoff:3.500A)
      Proline residue:  B  52  - end of helix
      removed outlier: 3.650A  pdb=" N   ASN B  62 " --> pdb=" O   PHE B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 63 through 67
    Processing helix  chain 'B' and resid 68 through 92
    Processing helix  chain 'B' and resid 97 through 110
    Processing helix  chain 'B' and resid 116 through 125
    Processing helix  chain 'B' and resid 126 through 143
    Processing helix  chain 'B' and resid 143 through 165
    Processing helix  chain 'B' and resid 168 through 170
      No H-bonds generated for 'chain 'B' and resid 168 through 170'
    Processing helix  chain 'B' and resid 475 through 492
    Processing helix  chain 'B' and resid 494 through 513
    Processing helix  chain 'B' and resid 518 through 530
      removed outlier: 4.390A  pdb=" N   LEU B 528 " --> pdb=" O   SER B 524 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 531 through 547
    Processing helix  chain 'B' and resid 554 through 581
      removed outlier: 3.885A  pdb=" N   GLY B 569 " --> pdb=" O   ARG B 565 " (cutoff:3.500A)
      Proline residue:  B 570  - end of helix
    Processing helix  chain 'B' and resid 584 through 595
    Processing helix  chain 'B' and resid 599 through 609
      removed outlier: 4.038A  pdb=" N   PHE B 603 " --> pdb=" O   GLY B 599 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 612 through 626
    Processing helix  chain 'B' and resid 626 through 640
      removed outlier: 3.690A  pdb=" N   ILE B 630 " --> pdb=" O   ILE B 626 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 177
      removed outlier: 7.571A  pdb=" N   VAL A 204 " --> pdb=" O   VAL A 173 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   PHE A 175 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   VAL A 206 " --> pdb=" O   PHE A 175 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   VAL A 177 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 8.783A  pdb=" N   LYS A 208 " --> pdb=" O   VAL A 177 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 172 through 177
      removed outlier: 7.593A  pdb=" N   VAL B 204 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   PHE B 175 " --> pdb=" O   VAL B 204 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   VAL B 206 " --> pdb=" O   PHE B 175 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   VAL B 177 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)
      removed outlier: 8.787A  pdb=" N   LYS B 208 " --> pdb=" O   VAL B 177 " (cutoff:3.500A)

    446 hydrogen bonds defined for protein.
    1326 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.75

  Time building geometry restraints manager: 1.35 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6132
        1.03 -     1.23: 8
        1.23 -     1.42: 2460
        1.42 -     1.61: 3506
        1.61 -     1.81: 78
  Bond restraints: 12184
  Sorted by residual:
  bond pdb=" ND2 ASN A 112 "
       pdb="HD21 ASN A 112 "
    ideal  model  delta    sigma   weight residual
    0.860  0.981 -0.121 2.00e-02 2.50e+03 3.64e+01
  bond pdb=" ND2 ASN B 112 "
       pdb="HD21 ASN B 112 "
    ideal  model  delta    sigma   weight residual
    0.860  0.981 -0.121 2.00e-02 2.50e+03 3.63e+01
  bond pdb=" ND2 ASN B 112 "
       pdb="HD22 ASN B 112 "
    ideal  model  delta    sigma   weight residual
    0.860  0.980 -0.120 2.00e-02 2.50e+03 3.58e+01
  bond pdb=" ND2 ASN A 112 "
       pdb="HD22 ASN A 112 "
    ideal  model  delta    sigma   weight residual
    0.860  0.980 -0.120 2.00e-02 2.50e+03 3.58e+01
  bond pdb=" N   IAC B 701 "
       pdb=" C   IAC B 701 "
    ideal  model  delta    sigma   weight residual
    1.363  1.433 -0.070 2.00e-02 2.50e+03 1.24e+01
  ... (remaining 12179 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.95: 22089
        5.95 -    11.90: 13
       11.90 -    17.85: 0
       17.85 -    23.80: 12
       23.80 -    29.75: 18
  Bond angle restraints: 22132
  Sorted by residual:
  angle pdb=" HZ1 LYS A 158 "
        pdb=" NZ  LYS A 158 "
        pdb=" HZ3 LYS A 158 "
      ideal   model   delta    sigma   weight residual
     109.00   79.25   29.75 3.00e+00 1.11e-01 9.83e+01
  angle pdb=" CG  LEU A 504 "
        pdb=" CD2 LEU A 504 "
        pdb="HD22 LEU A 504 "
      ideal   model   delta    sigma   weight residual
     109.00   79.33   29.67 3.00e+00 1.11e-01 9.78e+01
  angle pdb=" HZ1 LYS B 158 "
        pdb=" NZ  LYS B 158 "
        pdb=" HZ3 LYS B 158 "
      ideal   model   delta    sigma   weight residual
     109.00   79.33   29.67 3.00e+00 1.11e-01 9.78e+01
  angle pdb=" CG  LEU B 504 "
        pdb=" CD2 LEU B 504 "
        pdb="HD22 LEU B 504 "
      ideal   model   delta    sigma   weight residual
     109.00   79.35   29.65 3.00e+00 1.11e-01 9.77e+01
  angle pdb=" HZ1 LYS A 158 "
        pdb=" NZ  LYS A 158 "
        pdb=" HZ2 LYS A 158 "
      ideal   model   delta    sigma   weight residual
     109.00   79.39   29.61 3.00e+00 1.11e-01 9.74e+01
  ... (remaining 22127 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.09: 5011
       14.09 -    28.17: 465
       28.17 -    42.26: 137
       42.26 -    56.35: 73
       56.35 -    70.44: 12
  Dihedral angle restraints: 5698
    sinusoidal: 3054
      harmonic: 2644
  Sorted by residual:
  dihedral pdb=" CA  LYS A 549 "
           pdb=" C   LYS A 549 "
           pdb=" N   LEU A 550 "
           pdb=" CA  LEU A 550 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.96   17.04     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CA  LYS B 549 "
           pdb=" C   LYS B 549 "
           pdb=" N   LEU B 550 "
           pdb=" CA  LEU B 550 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.31   16.69     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CA  LEU B 625 "
           pdb=" C   LEU B 625 "
           pdb=" N   ILE B 626 "
           pdb=" CA  ILE B 626 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.52   16.48     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 5695 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.350: 988
       0.350 -    0.700: 0
       0.700 -    1.050: 0
       1.050 -    1.399: 0
       1.399 -    1.749: 2
  Chirality restraints: 990
  Sorted by residual:
  chirality pdb=" CG  LEU B 550 "
            pdb=" CB  LEU B 550 "
            pdb=" CD1 LEU B 550 "
            pdb=" CD2 LEU B 550 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.84   -1.75 2.00e-01 2.50e+01 7.65e+01
  chirality pdb=" CG  LEU A 550 "
            pdb=" CB  LEU A 550 "
            pdb=" CD1 LEU A 550 "
            pdb=" CD2 LEU A 550 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.88   -1.71 2.00e-01 2.50e+01 7.28e+01
  chirality pdb=" CA  ILE A 551 "
            pdb=" N   ILE A 551 "
            pdb=" C   ILE A 551 "
            pdb=" CB  ILE A 551 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.72e-01
  ... (remaining 987 not shown)

  Planarity restraints: 1710
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 140 "   -0.156 2.00e-02 2.50e+03   1.75e-01 4.60e+02
        pdb=" CD  GLN A 140 "    0.011 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 140 "    0.150 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 140 "    0.001 2.00e-02 2.50e+03
        pdb="HE21 GLN A 140 "   -0.265 2.00e-02 2.50e+03
        pdb="HE22 GLN A 140 "    0.259 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B 140 "   -0.153 2.00e-02 2.50e+03   1.72e-01 4.42e+02
        pdb=" CD  GLN B 140 "    0.011 2.00e-02 2.50e+03
        pdb=" OE1 GLN B 140 "    0.148 2.00e-02 2.50e+03
        pdb=" NE2 GLN B 140 "   -0.002 2.00e-02 2.50e+03
        pdb="HE21 GLN B 140 "    0.254 2.00e-02 2.50e+03
        pdb="HE22 GLN B 140 "   -0.258 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 112 "   -0.137 2.00e-02 2.50e+03   1.36e-01 2.78e+02
        pdb=" CG  ASN A 112 "    0.010 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 112 "    0.131 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 112 "    0.001 2.00e-02 2.50e+03
        pdb="HD21 ASN A 112 "   -0.196 2.00e-02 2.50e+03
        pdb="HD22 ASN A 112 "    0.191 2.00e-02 2.50e+03
  ... (remaining 1707 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 714
        2.21 -     2.80: 25812
        2.80 -     3.40: 35101
        3.40 -     4.00: 45022
        4.00 -     4.60: 70411
  Nonbonded interactions: 177060
  Sorted by model distance:
  nonbonded pdb=" H   GLY B 197 "
            pdb=" O   LYS B 201 "
     model   vdw
     1.606 2.450
  nonbonded pdb=" OE1 GLU A 163 "
            pdb="HE21 GLN A 164 "
     model   vdw
     1.610 2.450
  nonbonded pdb=" OE1 GLU B 163 "
            pdb="HE21 GLN B 164 "
     model   vdw
     1.611 2.450
  nonbonded pdb=" H   GLY A 197 "
            pdb=" O   LYS A 201 "
     model   vdw
     1.615 2.450
  nonbonded pdb=" O   SER A  27 "
            pdb=" H   ILE A  33 "
     model   vdw
     1.636 2.450
  ... (remaining 177055 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.860
  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:             0.060
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.030
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
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      :  0.004   0.070   6046  Z= 0.175
  Angle     :  0.677  11.558   8238  Z= 0.343
  Chirality :  0.086   1.749    990
  Planarity :  0.005   0.053    994
  Dihedral  : 12.236  70.436   2122
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.68 (0.31), residues: 746
  helix:  0.91 (0.22), residues: 548
  sheet:  0.67 (0.75), residues: 42
  loop : -1.01 (0.50), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 583 
 TYR   0.024   0.002   TYR A  18 
 PHE   0.012   0.001   PHE A 603 
 TRP   0.014   0.001   TRP B 506 
 HIS   0.004   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 6046)
  covalent geometry    : angle       0.67710 ( 8238)
  hydrogen bonds       : bond        0.11605 (  446)
  hydrogen bonds       : angle       5.83838 ( 1326)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  551 ILE cc_start: 0.8479 (mm) cc_final: 0.8268 (mp)
REVERT: A  610 ASN cc_start: 0.8175 (t0) cc_final: 0.7956 (t0)
REVERT: B  610 ASN cc_start: 0.8117 (t0) cc_final: 0.7903 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.7644
  time to fit residues: 88.6440
Evaluate side-chains
  95 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.8184

-------------------------------------------------------------------------------
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 = 0.3914 r_free = 0.3914 target = 0.163751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.138560 restraints weight = 21223.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 1.73
r_work: 0.3535 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3429 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.0913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6046  Z= 0.153
  Angle     :  0.592  11.003   8238  Z= 0.303
  Chirality :  0.085   1.704    990
  Planarity :  0.005   0.039    994
  Dihedral  :  4.619  34.043    804
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  7.68 %
    Favored  : 91.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.30), residues: 746
  helix:  1.03 (0.22), residues: 552
  sheet:  0.74 (0.76), residues: 42
  loop : -0.98 (0.50), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 583 
 TYR   0.018   0.001   TYR A  18 
 PHE   0.012   0.001   PHE A  45 
 TRP   0.011   0.001   TRP B 506 
 HIS   0.004   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 6046)
  covalent geometry    : angle       0.59214 ( 8238)
  hydrogen bonds       : bond        0.04709 (  446)
  hydrogen bonds       : angle       5.05294 ( 1326)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ARG cc_start: 0.8208 (ttt180) cc_final: 0.8007 (ttt180)
REVERT: A  551 ILE cc_start: 0.8637 (mm) cc_final: 0.8419 (mp)
REVERT: A  610 ASN cc_start: 0.8330 (t0) cc_final: 0.8071 (t0)
REVERT: B  610 ASN cc_start: 0.8293 (t0) cc_final: 0.8014 (t0)
  outliers start: 8
  outliers final: 2
  residues processed: 113
  average time/residue: 0.7626
  time to fit residues: 92.4543
Evaluate side-chains
  99 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 97
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain B residue   61 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A  91 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.166517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.141145 restraints weight = 21583.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3655 rms_B_bonded: 1.70
r_work: 0.3563 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3462 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.1199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6046  Z= 0.189
  Angle     :  0.596  10.600   8238  Z= 0.306
  Chirality :  0.085   1.693    990
  Planarity :  0.005   0.043    994
  Dihedral  :  4.636  33.569    804
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  :  8.15 %
    Favored  : 90.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.30), residues: 746
  helix:  1.04 (0.22), residues: 552
  sheet:  0.88 (0.78), residues: 42
  loop : -1.16 (0.49), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 565 
 TYR   0.022   0.002   TYR B  18 
 PHE   0.012   0.001   PHE A  45 
 TRP   0.011   0.001   TRP A 506 
 HIS   0.005   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 6046)
  covalent geometry    : angle       0.59573 ( 8238)
  hydrogen bonds       : bond        0.04667 (  446)
  hydrogen bonds       : angle       4.99923 ( 1326)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ARG cc_start: 0.8274 (ttt180) cc_final: 0.8014 (mtp180)
REVERT: A  551 ILE cc_start: 0.8660 (mm) cc_final: 0.8434 (mp)
REVERT: A  610 ASN cc_start: 0.8330 (t0) cc_final: 0.7997 (t0)
REVERT: B  610 ASN cc_start: 0.8321 (t0) cc_final: 0.7993 (t0)
  outliers start: 10
  outliers final: 2
  residues processed: 114
  average time/residue: 0.7894
  time to fit residues: 96.3472
Evaluate side-chains
  101 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  499 SER
Chi-restraints excluded: chain B residue  499 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 57 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3962 r_free = 0.3962 target = 0.166400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.140977 restraints weight = 21409.841|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 1.71
r_work: 0.3584 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3478 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.1393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6046  Z= 0.145
  Angle     :  0.575  10.408   8238  Z= 0.291
  Chirality :  0.084   1.695    990
  Planarity :  0.005   0.043    994
  Dihedral  :  4.573  34.117    804
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  9.72 %
    Favored  : 89.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.30), residues: 746
  helix:  1.18 (0.22), residues: 552
  sheet:  0.99 (0.77), residues: 42
  loop : -1.05 (0.51), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  44 
 TYR   0.017   0.001   TYR A  18 
 PHE   0.011   0.001   PHE A  45 
 TRP   0.010   0.001   TRP A 506 
 HIS   0.004   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 6046)
  covalent geometry    : angle       0.57489 ( 8238)
  hydrogen bonds       : bond        0.04343 (  446)
  hydrogen bonds       : angle       4.79886 ( 1326)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ARG cc_start: 0.8239 (ttt180) cc_final: 0.7985 (mtp180)
REVERT: A  551 ILE cc_start: 0.8660 (mm) cc_final: 0.8432 (mp)
REVERT: A  608 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6749 (mt-10)
REVERT: A  610 ASN cc_start: 0.8339 (t0) cc_final: 0.8002 (t0)
REVERT: B  608 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6794 (mt-10)
REVERT: B  610 ASN cc_start: 0.8317 (t0) cc_final: 0.7986 (t0)
  outliers start: 8
  outliers final: 2
  residues processed: 104
  average time/residue: 0.8750
  time to fit residues: 97.3849
Evaluate side-chains
  102 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 LEU
Chi-restraints excluded: chain A residue  608 GLU
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue  608 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 6 optimal weight:    0.7980
   chunk 57 optimal weight:    7.9990
   chunk 58 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
A  91 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.162380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.136615 restraints weight = 21648.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 1.70
r_work: 0.3535 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3430 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6046  Z= 0.226
  Angle     :  0.622  10.203   8238  Z= 0.320
  Chirality :  0.085   1.696    990
  Planarity :  0.005   0.040    994
  Dihedral  :  4.716  36.225    804
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 10.66 %
    Favored  : 87.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.30), residues: 746
  helix:  1.08 (0.21), residues: 552
  sheet:  0.68 (0.78), residues: 44
  loop : -1.02 (0.51), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 565 
 TYR   0.017   0.002   TYR B 635 
 PHE   0.014   0.002   PHE B  45 
 TRP   0.012   0.001   TRP A 506 
 HIS   0.006   0.001   HIS B  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00526 ( 6046)
  covalent geometry    : angle       0.62163 ( 8238)
  hydrogen bonds       : bond        0.04762 (  446)
  hydrogen bonds       : angle       4.90550 ( 1326)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ASP cc_start: 0.7259 (t70) cc_final: 0.6688 (t0)
REVERT: A  551 ILE cc_start: 0.8716 (mm) cc_final: 0.8500 (mp)
REVERT: A  608 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6726 (mt-10)
REVERT: A  610 ASN cc_start: 0.8418 (t0) cc_final: 0.8014 (t0)
REVERT: B  608 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6728 (mt-10)
REVERT: B  610 ASN cc_start: 0.8412 (t0) cc_final: 0.8025 (t0)
  outliers start: 10
  outliers final: 2
  residues processed: 108
  average time/residue: 0.7949
  time to fit residues: 92.2827
Evaluate side-chains
  104 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  499 SER
Chi-restraints excluded: chain A residue  608 GLU
Chi-restraints excluded: chain B residue  499 SER
Chi-restraints excluded: chain B residue  608 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 57 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 14 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 547 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.158972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.134167 restraints weight = 21639.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 1.59
r_work: 0.3457 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3353 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6046  Z= 0.137
  Angle     :  0.568  10.421   8238  Z= 0.287
  Chirality :  0.085   1.701    990
  Planarity :  0.005   0.041    994
  Dihedral  :  4.590  35.245    804
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 11.60 %
    Favored  : 86.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.31), residues: 746
  helix:  1.29 (0.22), residues: 552
  sheet:  1.24 (0.79), residues: 42
  loop : -0.96 (0.53), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  44 
 TYR   0.012   0.001   TYR B 635 
 PHE   0.013   0.001   PHE B  92 
 TRP   0.010   0.001   TRP A 506 
 HIS   0.004   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6046)
  covalent geometry    : angle       0.56826 ( 8238)
  hydrogen bonds       : bond        0.04287 (  446)
  hydrogen bonds       : angle       4.72105 ( 1326)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  551 ILE cc_start: 0.8670 (mm) cc_final: 0.8465 (mp)
REVERT: A  608 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6604 (mt-10)
REVERT: A  610 ASN cc_start: 0.8407 (t0) cc_final: 0.8014 (t0)
REVERT: B  608 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6517 (mt-10)
REVERT: B  610 ASN cc_start: 0.8403 (t0) cc_final: 0.8022 (t0)
  outliers start: 9
  outliers final: 0
  residues processed: 112
  average time/residue: 0.7411
  time to fit residues: 89.6995
Evaluate side-chains
  102 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  608 GLU
Chi-restraints excluded: chain B residue  608 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 16 optimal weight:    0.4980
   chunk 21 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 59 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A  91 ASN
B 547 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.157600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.132606 restraints weight = 21631.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 1.62
r_work: 0.3438 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3335 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.1773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6046  Z= 0.177
  Angle     :  0.592  10.293   8238  Z= 0.301
  Chirality :  0.085   1.699    990
  Planarity :  0.005   0.041    994
  Dihedral  :  4.611  35.357    804
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  : 13.17 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.31), residues: 746
  helix:  1.25 (0.21), residues: 552
  sheet:  0.91 (0.79), residues: 44
  loop : -0.89 (0.53), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 565 
 TYR   0.014   0.001   TYR B 635 
 PHE   0.013   0.001   PHE A  92 
 TRP   0.010   0.001   TRP B 506 
 HIS   0.004   0.001   HIS B  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 6046)
  covalent geometry    : angle       0.59193 ( 8238)
  hydrogen bonds       : bond        0.04419 (  446)
  hydrogen bonds       : angle       4.75933 ( 1326)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 103
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  551 ILE cc_start: 0.8662 (mm) cc_final: 0.8449 (mp)
REVERT: A  608 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6607 (mt-10)
REVERT: A  610 ASN cc_start: 0.8456 (t0) cc_final: 0.8055 (t0)
REVERT: B  608 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6534 (mt-10)
REVERT: B  610 ASN cc_start: 0.8452 (t0) cc_final: 0.8066 (t0)
  outliers start: 3
  outliers final: 0
  residues processed: 103
  average time/residue: 0.7370
  time to fit residues: 81.7707
Evaluate side-chains
  101 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  608 GLU
Chi-restraints excluded: chain B residue  608 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.3797 r_free = 0.3797 target = 0.154590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.130144 restraints weight = 21600.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 1.60
r_work: 0.3435 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6046  Z= 0.142
  Angle     :  0.571  10.373   8238  Z= 0.289
  Chirality :  0.085   1.710    990
  Planarity :  0.005   0.041    994
  Dihedral  :  4.526  34.682    804
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 14.11 %
    Favored  : 85.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.30), residues: 746
  helix:  1.32 (0.21), residues: 552
  sheet:  0.92 (0.78), residues: 44
  loop : -0.90 (0.53), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 565 
 TYR   0.014   0.001   TYR B 635 
 PHE   0.011   0.001   PHE B  45 
 TRP   0.010   0.001   TRP B 506 
 HIS   0.004   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 6046)
  covalent geometry    : angle       0.57133 ( 8238)
  hydrogen bonds       : bond        0.04222 (  446)
  hydrogen bonds       : angle       4.67608 ( 1326)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 103
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  551 ILE cc_start: 0.8671 (mm) cc_final: 0.8470 (mp)
REVERT: A  608 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7128 (mm-30)
REVERT: A  610 ASN cc_start: 0.8410 (t0) cc_final: 0.8027 (t0)
REVERT: B   65 TYR cc_start: 0.9002 (m-80) cc_final: 0.8793 (m-80)
REVERT: B  608 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7138 (mp0)
REVERT: B  610 ASN cc_start: 0.8404 (t0) cc_final: 0.7998 (t0)
  outliers start: 4
  outliers final: 1
  residues processed: 106
  average time/residue: 0.7171
  time to fit residues: 82.2792
Evaluate side-chains
  100 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  608 GLU
Chi-restraints excluded: chain B residue  608 GLU
Chi-restraints excluded: chain B residue  630 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0470
   chunk 43 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0970
   chunk 31 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 67 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 57 optimal weight:    4.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.4476

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

Flipped N/Q/H residues before XYZ refinement:
A  91 ASN
B 547 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.160066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.135223 restraints weight = 21405.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 1.61
r_work: 0.3489 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.1883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6046  Z= 0.121
  Angle     :  0.572  10.212   8238  Z= 0.286
  Chirality :  0.085   1.711    990
  Planarity :  0.005   0.041    994
  Dihedral  :  4.440  33.121    804
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 14.26 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.31), residues: 746
  helix:  1.40 (0.21), residues: 552
  sheet:  1.37 (0.78), residues: 42
  loop : -0.98 (0.53), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  70 
 TYR   0.010   0.001   TYR B 635 
 PHE   0.016   0.001   PHE A  92 
 TRP   0.010   0.001   TRP A 506 
 HIS   0.002   0.000   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6046)
  covalent geometry    : angle       0.57219 ( 8238)
  hydrogen bonds       : bond        0.04027 (  446)
  hydrogen bonds       : angle       4.59843 ( 1326)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 104
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  608 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7132 (mm-30)
REVERT: A  610 ASN cc_start: 0.8420 (t0) cc_final: 0.8034 (t0)
REVERT: B  608 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7145 (mp0)
REVERT: B  610 ASN cc_start: 0.8427 (t0) cc_final: 0.8051 (t0)
  outliers start: 5
  outliers final: 1
  residues processed: 107
  average time/residue: 0.7161
  time to fit residues: 82.7901
Evaluate side-chains
  102 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 99
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  608 GLU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain B residue  608 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 57 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 53 optimal weight:    0.4980
   chunk 18 optimal weight:    5.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
B 547 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.154505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.129889 restraints weight = 21788.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 1.63
r_work: 0.3420 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3312 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6046  Z= 0.159
  Angle     :  0.592  10.218   8238  Z= 0.298
  Chirality :  0.085   1.703    990
  Planarity :  0.005   0.040    994
  Dihedral  :  4.454  33.265    804
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 14.58 %
    Favored  : 84.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.32 (0.30), residues: 746
  helix:  1.38 (0.21), residues: 552
  sheet:  1.39 (0.78), residues: 42
  loop : -1.04 (0.53), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 565 
 TYR   0.015   0.001   TYR A 635 
 PHE   0.011   0.001   PHE B  45 
 TRP   0.010   0.001   TRP B 506 
 HIS   0.004   0.001   HIS B  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 6046)
  covalent geometry    : angle       0.59240 ( 8238)
  hydrogen bonds       : bond        0.04206 (  446)
  hydrogen bonds       : angle       4.63929 ( 1326)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  608 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7091 (mm-30)
REVERT: A  610 ASN cc_start: 0.8402 (t0) cc_final: 0.8012 (t0)
REVERT: B  608 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7119 (mp0)
REVERT: B  610 ASN cc_start: 0.8412 (t0) cc_final: 0.8030 (t0)
  outliers start: 5
  outliers final: 2
  residues processed: 105
  average time/residue: 0.8053
  time to fit residues: 90.8845
Evaluate side-chains
  104 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  499 SER
Chi-restraints excluded: chain A residue  608 GLU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain B residue  608 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0870
   chunk 73 optimal weight:    0.4980
   chunk 20 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
A 547 GLN
B 547 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.160055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.135418 restraints weight = 21458.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 1.59
r_work: 0.3502 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3399 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.1998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6046  Z= 0.125
  Angle     :  0.580  10.051   8238  Z= 0.289
  Chirality :  0.085   1.715    990
  Planarity :  0.005   0.043    994
  Dihedral  :  4.382  32.501    804
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 14.58 %
    Favored  : 84.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.30), residues: 746
  helix:  1.44 (0.21), residues: 552
  sheet:  1.47 (0.79), residues: 42
  loop : -1.09 (0.53), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  70 
 TYR   0.008   0.001   TYR A 635 
 PHE   0.018   0.001   PHE B  92 
 TRP   0.010   0.001   TRP B 506 
 HIS   0.003   0.001   HIS B  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6046)
  covalent geometry    : angle       0.58003 ( 8238)
  hydrogen bonds       : bond        0.04019 (  446)
  hydrogen bonds       : angle       4.56217 ( 1326)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3869.30 seconds
wall clock time: 66 minutes 4.19 seconds (3964.19 seconds total)