Starting phenix.real_space_refine
on Fri Aug 22 16:58:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ug7_42216/08_2025/8ug7_42216.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ug7_42216/08_2025/8ug7_42216.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ug7_42216/08_2025/8ug7_42216.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ug7_42216/08_2025/8ug7_42216.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ug7_42216/08_2025/8ug7_42216.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ug7_42216/08_2025/8ug7_42216.cif"
  }
  resolution = 2.95
  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: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    4156      2.51       5
     N    1006      2.21       5
     O    1038      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  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: 6242
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 393, 3121
          Classifications: {'peptide': 393}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 383}
          Chain breaks: 7
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.16, per 1000 atoms: 0.35
  Number of scatterers: 6242
  At special positions: 0
  Unit cell: (87.15, 98.77, 70.55, 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      42     16.00
     O    1038      8.00
     N    1006      7.00
     C    4156      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
  Time building additional restraints: 0.49
  Conformation dependent library (CDL) restraints added in 346.9 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1468

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 0 sheets defined
      85.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 53
      removed outlier: 3.540A  pdb=" N   ASN A  53 " --> pdb=" O   GLY A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 85
    Processing helix  chain 'A' and resid 101 through 128
      removed outlier: 4.304A  pdb=" N   GLY A 105 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   SER A 127 " --> pdb=" O   GLY A 123 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   PHE A 128 " --> pdb=" O   TYR A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 156
      Proline residue:  A 140  - end of helix
    Processing helix  chain 'A' and resid 165 through 194
    Processing helix  chain 'A' and resid 247 through 265
    Processing helix  chain 'A' and resid 292 through 312
    Processing helix  chain 'A' and resid 322 through 353
      removed outlier: 3.562A  pdb=" N   PHE A 353 " --> pdb=" O   VAL A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 393
      removed outlier: 4.506A  pdb=" N   GLY A 379 " --> pdb=" O   GLY A 375 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   GLN A 380 " --> pdb=" O   ALA A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 429
      removed outlier: 3.564A  pdb=" N   GLY A 429 " --> pdb=" O   SER A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 508
      removed outlier: 3.572A  pdb=" N   ASP A 496 " --> pdb=" O   ARG A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 515
    Processing helix  chain 'A' and resid 522 through 530
    Processing helix  chain 'A' and resid 530 through 563
      Proline residue:  A 543  - end of helix
      removed outlier: 3.500A  pdb=" N   ILE A 546 " --> pdb=" O   LEU A 542 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   PHE A 547 " --> pdb=" O   PRO A 543 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 53
      removed outlier: 3.539A  pdb=" N   ASN B  53 " --> pdb=" O   GLY B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 85
    Processing helix  chain 'B' and resid 101 through 128
      removed outlier: 4.304A  pdb=" N   GLY B 105 " --> pdb=" O   ILE B 101 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   SER B 127 " --> pdb=" O   GLY B 123 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   PHE B 128 " --> pdb=" O   TYR B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 156
      Proline residue:  B 140  - end of helix
    Processing helix  chain 'B' and resid 165 through 194
    Processing helix  chain 'B' and resid 247 through 265
    Processing helix  chain 'B' and resid 292 through 312
    Processing helix  chain 'B' and resid 322 through 353
      removed outlier: 3.562A  pdb=" N   PHE B 353 " --> pdb=" O   VAL B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 393
      removed outlier: 4.505A  pdb=" N   GLY B 379 " --> pdb=" O   GLY B 375 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   GLN B 380 " --> pdb=" O   ALA B 376 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 398 through 429
      removed outlier: 3.564A  pdb=" N   GLY B 429 " --> pdb=" O   SER B 425 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 488 through 508
      removed outlier: 3.573A  pdb=" N   ASP B 496 " --> pdb=" O   ARG B 492 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 509 through 515
    Processing helix  chain 'B' and resid 522 through 530
    Processing helix  chain 'B' and resid 530 through 563
      Proline residue:  B 543  - end of helix
      removed outlier: 3.500A  pdb=" N   ILE B 546 " --> pdb=" O   LEU B 542 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   PHE B 547 " --> pdb=" O   PRO B 543 " (cutoff:3.500A)

    528 hydrogen bonds defined for protein.
    1584 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: 1.07

  Time building geometry restraints manager: 0.65 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: 1267
        1.33 -     1.45: 1564
        1.45 -     1.57: 3499
        1.57 -     1.69: 0
        1.69 -     1.81: 66
  Bond restraints: 6396
  Sorted by residual:
  bond pdb=" CA  SER B 256 "
       pdb=" CB  SER B 256 "
    ideal  model  delta    sigma   weight residual
    1.528  1.467  0.061 1.56e-02 4.11e+03 1.54e+01
  bond pdb=" CA  SER A 256 "
       pdb=" CB  SER A 256 "
    ideal  model  delta    sigma   weight residual
    1.528  1.468  0.060 1.56e-02 4.11e+03 1.50e+01
  bond pdb=" CA  SER B 346 "
       pdb=" CB  SER B 346 "
    ideal  model  delta    sigma   weight residual
    1.528  1.479  0.049 1.56e-02 4.11e+03 9.99e+00
  bond pdb=" CA  SER A 346 "
       pdb=" CB  SER A 346 "
    ideal  model  delta    sigma   weight residual
    1.528  1.480  0.049 1.56e-02 4.11e+03 9.85e+00
  bond pdb=" N   VAL A 307 "
       pdb=" CA  VAL A 307 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.30e-02 5.92e+03 8.78e+00
  ... (remaining 6391 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 8335
        1.53 -     3.06: 290
        3.06 -     4.60: 57
        4.60 -     6.13: 12
        6.13 -     7.66: 4
  Bond angle restraints: 8698
  Sorted by residual:
  angle pdb=" N   TYR B 124 "
        pdb=" CA  TYR B 124 "
        pdb=" C   TYR B 124 "
      ideal   model   delta    sigma   weight residual
     111.40  106.84    4.56 1.22e+00 6.72e-01 1.40e+01
  angle pdb=" N   TYR A 124 "
        pdb=" CA  TYR A 124 "
        pdb=" C   TYR A 124 "
      ideal   model   delta    sigma   weight residual
     111.40  106.86    4.54 1.22e+00 6.72e-01 1.39e+01
  angle pdb=" C   GLN A 238 "
        pdb=" N   GLN A 239 "
        pdb=" CA  GLN A 239 "
      ideal   model   delta    sigma   weight residual
     120.71  114.71    6.00 1.67e+00 3.59e-01 1.29e+01
  angle pdb=" C   GLN B 238 "
        pdb=" N   GLN B 239 "
        pdb=" CA  GLN B 239 "
      ideal   model   delta    sigma   weight residual
     120.71  114.73    5.98 1.67e+00 3.59e-01 1.28e+01
  angle pdb=" CA  ARG B 366 "
        pdb=" C   ARG B 366 "
        pdb=" O   ARG B 366 "
      ideal   model   delta    sigma   weight residual
     122.41  118.12    4.29 1.21e+00 6.83e-01 1.26e+01
  ... (remaining 8693 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.55: 2886
       12.55 -    25.10: 454
       25.10 -    37.66: 198
       37.66 -    50.21: 78
       50.21 -    62.76: 22
  Dihedral angle restraints: 3638
    sinusoidal: 1358
      harmonic: 2280
  Sorted by residual:
  dihedral pdb=" CD  ARG B 366 "
           pdb=" NE  ARG B 366 "
           pdb=" CZ  ARG B 366 "
           pdb=" NH1 ARG B 366 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -30.55   30.55     1      1.00e+01 1.00e-02 1.33e+01
  dihedral pdb=" CD  ARG A 366 "
           pdb=" NE  ARG A 366 "
           pdb=" CZ  ARG A 366 "
           pdb=" NH1 ARG A 366 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -30.49   30.49     1      1.00e+01 1.00e-02 1.33e+01
  dihedral pdb=" CG  ARG B 104 "
           pdb=" CD  ARG B 104 "
           pdb=" NE  ARG B 104 "
           pdb=" CZ  ARG B 104 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.89  -44.89     2      1.50e+01 4.44e-03 1.06e+01
  ... (remaining 3635 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 995
       0.090 -    0.179: 28
       0.179 -    0.269: 7
       0.269 -    0.359: 0
       0.359 -    0.448: 2
  Chirality restraints: 1032
  Sorted by residual:
  chirality pdb=" CB  VAL B 389 "
            pdb=" CA  VAL B 389 "
            pdb=" CG1 VAL B 389 "
            pdb=" CG2 VAL B 389 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.18   -0.45 2.00e-01 2.50e+01 5.02e+00
  chirality pdb=" CB  VAL A 389 "
            pdb=" CA  VAL A 389 "
            pdb=" CG1 VAL A 389 "
            pdb=" CG2 VAL A 389 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.18   -0.45 2.00e-01 2.50e+01 5.02e+00
  chirality pdb=" CA  ILE A 546 "
            pdb=" N   ILE A 546 "
            pdb=" C   ILE A 546 "
            pdb=" CB  ILE A 546 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.23 2.00e-01 2.50e+01 1.35e+00
  ... (remaining 1029 not shown)

  Planarity restraints: 1042
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 366 "    0.544 9.50e-02 1.11e+02   2.44e-01 3.64e+01
        pdb=" NE  ARG B 366 "   -0.033 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 366 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 366 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 366 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 366 "   -0.544 9.50e-02 1.11e+02   2.44e-01 3.63e+01
        pdb=" NE  ARG A 366 "    0.033 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 366 "    0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 366 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 366 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 293 "   -0.038 5.00e-02 4.00e+02   5.79e-02 5.36e+00
        pdb=" N   PRO A 294 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 294 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 294 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 1039 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 964
        2.75 -     3.29: 6261
        3.29 -     3.83: 11054
        3.83 -     4.36: 12647
        4.36 -     4.90: 22100
  Nonbonded interactions: 53026
  Sorted by model distance:
  nonbonded pdb=" O   PHE B 421 "
            pdb=" OG  SER B 425 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   PHE A 421 "
            pdb=" OG  SER A 425 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   ASN A 248 "
            pdb=" OG  SER A 252 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   ASN B 248 "
            pdb=" OG  SER B 252 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   VAL A 147 "
            pdb=" OG1 THR A 151 "
     model   vdw
     2.272 3.040
  ... (remaining 53021 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.840
  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:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.950
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8824
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      :  0.005   0.073   6396  Z= 0.304
  Angle     :  0.664   7.660   8698  Z= 0.436
  Chirality :  0.046   0.448   1032
  Planarity :  0.012   0.244   1042
  Dihedral  : 16.571  62.762   2170
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 29.55 %
    Favored  : 70.45 %
  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 (0.30), residues: 754
  helix:  1.80 (0.19), residues: 652
  sheet:  None (None), residues: 0
  loop : -1.92 (0.63), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 490 
 TYR   0.024   0.002   TYR B 560 
 PHE   0.009   0.001   PHE A 110 
 TRP   0.013   0.001   TRP A 509 
 HIS   0.003   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 6396)
  covalent geometry    : angle       0.66365 ( 8698)
  hydrogen bonds       : bond        0.19409 (  528)
  hydrogen bonds       : angle       6.18270 ( 1584)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A  124 TYR cc_start: 0.7932 (t80) cc_final: 0.7683 (t80)
REVERT: A  366 ARG cc_start: 0.8153 (mtt-85) cc_final: 0.7949 (mtp180)
REVERT: A  563 SER cc_start: 0.7427 (t) cc_final: 0.7200 (m)
REVERT: B  124 TYR cc_start: 0.7934 (t80) cc_final: 0.7691 (t80)
REVERT: B  366 ARG cc_start: 0.8152 (mtt-85) cc_final: 0.7948 (mtp180)
REVERT: B  563 SER cc_start: 0.7396 (t) cc_final: 0.7164 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.4268
  time to fit residues: 40.4403
Evaluate side-chains
  80 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    8.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A  53 ASN
A 404 ASN
B  53 ASN
B 404 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.117356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.088449 restraints weight = 10121.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 2.05
r_work: 0.2915 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2779 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8842
moved from start:          0.1602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6396  Z= 0.135
  Angle     :  0.497   6.472   8698  Z= 0.267
  Chirality :  0.037   0.122   1032
  Planarity :  0.005   0.057   1042
  Dihedral  :  3.494  27.644    846
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 24.33 %
    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:  3.25 (0.30), residues: 754
  helix:  2.75 (0.19), residues: 652
  sheet:  None (None), residues: 0
  loop : -2.26 (0.54), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 366 
 TYR   0.009   0.001   TYR B 548 
 PHE   0.012   0.001   PHE B 332 
 TRP   0.012   0.001   TRP A 489 
 HIS   0.004   0.001   HIS B 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6396)
  covalent geometry    : angle       0.49740 ( 8698)
  hydrogen bonds       : bond        0.04448 (  528)
  hydrogen bonds       : angle       3.94554 ( 1584)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A  124 TYR cc_start: 0.8295 (t80) cc_final: 0.7933 (t80)
REVERT: B  124 TYR cc_start: 0.8259 (t80) cc_final: 0.7903 (t80)
  outliers start: 19
  outliers final: 6
  residues processed: 114
  average time/residue: 0.3877
  time to fit residues: 47.4465
Evaluate side-chains
  90 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  389 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:    0.9980
   chunk 69 optimal weight:    3.9990
   chunk 62 optimal weight:    0.5980
   chunk 14 optimal weight:    0.5980
   chunk 30 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 44 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 39 optimal weight:    5.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 404 ASN
B 404 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.117713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.088761 restraints weight = 10015.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 2.08
r_work: 0.2915 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2782 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8836
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6396  Z= 0.119
  Angle     :  0.464   5.334   8698  Z= 0.248
  Chirality :  0.036   0.116   1032
  Planarity :  0.004   0.055   1042
  Dihedral  :  3.443  24.496    846
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 24.78 %
    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:  3.61 (0.30), residues: 754
  helix:  3.06 (0.19), residues: 642
  sheet:  None (None), residues: 0
  loop : -2.10 (0.55), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 490 
 TYR   0.009   0.001   TYR B 548 
 PHE   0.013   0.001   PHE B 153 
 TRP   0.012   0.001   TRP B 489 
 HIS   0.003   0.001   HIS B 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 6396)
  covalent geometry    : angle       0.46442 ( 8698)
  hydrogen bonds       : bond        0.04065 (  528)
  hydrogen bonds       : angle       3.74000 ( 1584)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A  124 TYR cc_start: 0.8274 (t80) cc_final: 0.7850 (t80)
REVERT: B  124 TYR cc_start: 0.8247 (t80) cc_final: 0.7771 (t80)
  outliers start: 16
  outliers final: 3
  residues processed: 98
  average time/residue: 0.3824
  time to fit residues: 40.2829
Evaluate side-chains
  84 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain B residue  289 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 20 optimal weight:    8.9990
   chunk 16 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 24 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 404 ASN
B 404 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.116151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.086836 restraints weight = 10053.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 2.08
r_work: 0.2883 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2750 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8864
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6396  Z= 0.146
  Angle     :  0.488   5.564   8698  Z= 0.258
  Chirality :  0.037   0.135   1032
  Planarity :  0.004   0.054   1042
  Dihedral  :  3.473  22.287    846
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 25.07 %
    Favored  : 72.24 %
  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:  3.55 (0.30), residues: 754
  helix:  3.01 (0.19), residues: 642
  sheet:  None (None), residues: 0
  loop : -2.00 (0.56), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 490 
 TYR   0.009   0.001   TYR B 548 
 PHE   0.014   0.001   PHE A 332 
 TRP   0.012   0.001   TRP A 489 
 HIS   0.003   0.001   HIS B 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 6396)
  covalent geometry    : angle       0.48750 ( 8698)
  hydrogen bonds       : bond        0.04094 (  528)
  hydrogen bonds       : angle       3.74394 ( 1584)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A  124 TYR cc_start: 0.8300 (t80) cc_final: 0.7943 (t80)
REVERT: B  124 TYR cc_start: 0.8271 (t80) cc_final: 0.7967 (t80)
REVERT: B  424 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7359 (mm-30)
  outliers start: 18
  outliers final: 8
  residues processed: 98
  average time/residue: 0.3607
  time to fit residues: 38.2458
Evaluate side-chains
  88 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  299 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.0470
   chunk 18 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 6 optimal weight:    7.9990
   chunk 23 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.7480

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

Flipped N/Q/H residues before XYZ refinement:
A 404 ASN
B 132 GLN
B 404 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.117788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.088564 restraints weight = 10269.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 2.11
r_work: 0.2909 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2775 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8837
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6396  Z= 0.113
  Angle     :  0.471   8.088   8698  Z= 0.242
  Chirality :  0.036   0.116   1032
  Planarity :  0.004   0.052   1042
  Dihedral  :  3.375  20.703    846
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 23.88 %
    Favored  : 71.94 %
  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:  3.78 (0.30), residues: 754
  helix:  3.10 (0.19), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.69 (0.58), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 490 
 TYR   0.010   0.001   TYR B 125 
 PHE   0.011   0.001   PHE B 332 
 TRP   0.011   0.001   TRP A 489 
 HIS   0.003   0.001   HIS B 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 6396)
  covalent geometry    : angle       0.47140 ( 8698)
  hydrogen bonds       : bond        0.03776 (  528)
  hydrogen bonds       : angle       3.61450 ( 1584)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 93
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A  124 TYR cc_start: 0.8256 (t80) cc_final: 0.7973 (t80)
REVERT: A  128 PHE cc_start: 0.7867 (p90) cc_final: 0.7130 (p90)
REVERT: A  239 GLN cc_start: 0.6882 (OUTLIER) cc_final: 0.6659 (pm20)
REVERT: A  241 TYR cc_start: 0.4007 (OUTLIER) cc_final: 0.3544 (t80)
REVERT: A  264 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8877 (tttt)
REVERT: B  128 PHE cc_start: 0.7901 (p90) cc_final: 0.7287 (p90)
REVERT: B  239 GLN cc_start: 0.6837 (OUTLIER) cc_final: 0.6618 (pm20)
REVERT: B  241 TYR cc_start: 0.4048 (OUTLIER) cc_final: 0.3569 (t80)
REVERT: B  264 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8871 (tttt)
  outliers start: 28
  outliers final: 11
  residues processed: 112
  average time/residue: 0.3957
  time to fit residues: 47.4832
Evaluate side-chains
  101 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  165 HIS
Chi-restraints excluded: chain A residue  239 GLN
Chi-restraints excluded: chain A residue  241 TYR
Chi-restraints excluded: chain A residue  264 LYS
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  404 ASN
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  165 HIS
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  239 GLN
Chi-restraints excluded: chain B residue  241 TYR
Chi-restraints excluded: chain B residue  264 LYS
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  404 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 39 optimal weight:    0.4980
   chunk 75 optimal weight:    1.9990
   chunk 71 optimal weight:    7.9990
   chunk 70 optimal weight:    8.9990
   chunk 19 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 38 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 132 GLN
A 404 ASN
B 404 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.117253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.088000 restraints weight = 10083.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 2.09
r_work: 0.2899 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2766 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8847
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6396  Z= 0.126
  Angle     :  0.481   6.995   8698  Z= 0.248
  Chirality :  0.036   0.118   1032
  Planarity :  0.004   0.052   1042
  Dihedral  :  3.368  19.974    846
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 24.93 %
    Favored  : 71.79 %
  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:  3.71 (0.30), residues: 754
  helix:  3.10 (0.19), residues: 642
  sheet:  None (None), residues: 0
  loop : -1.89 (0.56), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 490 
 TYR   0.009   0.001   TYR A 548 
 PHE   0.012   0.001   PHE A 332 
 TRP   0.012   0.001   TRP A 489 
 HIS   0.003   0.001   HIS B 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6396)
  covalent geometry    : angle       0.48076 ( 8698)
  hydrogen bonds       : bond        0.03852 (  528)
  hydrogen bonds       : angle       3.63705 ( 1584)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A  128 PHE cc_start: 0.7850 (p90) cc_final: 0.7211 (p90)
REVERT: A  264 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8874 (tttt)
REVERT: B  128 PHE cc_start: 0.7888 (p90) cc_final: 0.7239 (p90)
REVERT: B  239 GLN cc_start: 0.6855 (OUTLIER) cc_final: 0.6653 (pm20)
REVERT: B  264 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8865 (tttt)
  outliers start: 22
  outliers final: 11
  residues processed: 103
  average time/residue: 0.3817
  time to fit residues: 42.3191
Evaluate side-chains
  99 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  165 HIS
Chi-restraints excluded: chain A residue  264 LYS
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  165 HIS
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  239 GLN
Chi-restraints excluded: chain B residue  264 LYS
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  557 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 76 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 404 ASN
B 404 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.115589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.086118 restraints weight = 10087.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 2.08
r_work: 0.2868 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2734 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8871
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6396  Z= 0.159
  Angle     :  0.511   6.539   8698  Z= 0.266
  Chirality :  0.038   0.123   1032
  Planarity :  0.004   0.053   1042
  Dihedral  :  3.462  17.790    846
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 24.48 %
    Favored  : 71.49 %
  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:  3.55 (0.30), residues: 754
  helix:  3.00 (0.19), residues: 642
  sheet:  None (None), residues: 0
  loop : -1.95 (0.56), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 517 
 TYR   0.011   0.002   TYR A 125 
 PHE   0.014   0.001   PHE A 332 
 TRP   0.012   0.001   TRP A 489 
 HIS   0.004   0.001   HIS B 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 6396)
  covalent geometry    : angle       0.51131 ( 8698)
  hydrogen bonds       : bond        0.04114 (  528)
  hydrogen bonds       : angle       3.72849 ( 1584)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 82
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A  128 PHE cc_start: 0.7848 (p90) cc_final: 0.7296 (p90)
REVERT: A  241 TYR cc_start: 0.4133 (OUTLIER) cc_final: 0.3666 (t80)
REVERT: A  264 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8860 (tttt)
REVERT: B  128 PHE cc_start: 0.7881 (p90) cc_final: 0.7290 (p90)
REVERT: B  241 TYR cc_start: 0.4203 (OUTLIER) cc_final: 0.3716 (t80)
REVERT: B  264 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8866 (tttt)
  outliers start: 27
  outliers final: 10
  residues processed: 103
  average time/residue: 0.3883
  time to fit residues: 43.0775
Evaluate side-chains
  94 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  241 TYR
Chi-restraints excluded: chain A residue  264 LYS
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  241 TYR
Chi-restraints excluded: chain B residue  264 LYS
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  557 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 28 optimal weight:    7.9990
   chunk 76 optimal weight:    0.6980
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 404 ASN
B 404 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.117427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.087979 restraints weight = 10230.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 2.10
r_work: 0.2896 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2762 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8846
moved from start:          0.2401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6396  Z= 0.121
  Angle     :  0.478   7.156   8698  Z= 0.248
  Chirality :  0.036   0.116   1032
  Planarity :  0.004   0.051   1042
  Dihedral  :  3.355  17.241    846
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 25.37 %
    Favored  : 71.04 %
  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:  3.71 (0.30), residues: 754
  helix:  3.11 (0.19), residues: 642
  sheet:  None (None), residues: 0
  loop : -1.93 (0.54), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 490 
 TYR   0.010   0.001   TYR A 548 
 PHE   0.012   0.001   PHE B 332 
 TRP   0.011   0.001   TRP A  76 
 HIS   0.003   0.001   HIS B 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 6396)
  covalent geometry    : angle       0.47820 ( 8698)
  hydrogen bonds       : bond        0.03808 (  528)
  hydrogen bonds       : angle       3.62773 ( 1584)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  128 PHE cc_start: 0.7834 (p90) cc_final: 0.7325 (p90)
REVERT: A  241 TYR cc_start: 0.4096 (OUTLIER) cc_final: 0.3680 (t80)
REVERT: A  264 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8866 (tttt)
REVERT: B  128 PHE cc_start: 0.7880 (p90) cc_final: 0.7260 (p90)
REVERT: B  241 TYR cc_start: 0.4049 (OUTLIER) cc_final: 0.3645 (t80)
REVERT: B  264 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8863 (tttt)
  outliers start: 24
  outliers final: 13
  residues processed: 103
  average time/residue: 0.3551
  time to fit residues: 39.5578
Evaluate side-chains
  102 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  165 HIS
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  241 TYR
Chi-restraints excluded: chain A residue  264 LYS
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  404 ASN
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  165 HIS
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  241 TYR
Chi-restraints excluded: chain B residue  264 LYS
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  404 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 70 optimal weight:   10.0000
   chunk 76 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 9 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 404 ASN
B 404 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.116697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.087112 restraints weight = 10165.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 2.10
r_work: 0.2882 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2748 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8860
moved from start:          0.2373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6396  Z= 0.145
  Angle     :  0.504   7.369   8698  Z= 0.261
  Chirality :  0.037   0.120   1032
  Planarity :  0.004   0.052   1042
  Dihedral  :  3.385  16.781    846
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 25.37 %
    Favored  : 70.90 %
  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:  3.63 (0.30), residues: 754
  helix:  3.05 (0.19), residues: 642
  sheet:  None (None), residues: 0
  loop : -1.91 (0.54), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 517 
 TYR   0.010   0.001   TYR A 548 
 PHE   0.013   0.001   PHE A 332 
 TRP   0.010   0.001   TRP A 489 
 HIS   0.004   0.001   HIS B 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 6396)
  covalent geometry    : angle       0.50426 ( 8698)
  hydrogen bonds       : bond        0.03949 (  528)
  hydrogen bonds       : angle       3.66555 ( 1584)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 85
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A  128 PHE cc_start: 0.7828 (p90) cc_final: 0.7313 (p90)
REVERT: A  239 GLN cc_start: 0.6933 (OUTLIER) cc_final: 0.6623 (pm20)
REVERT: A  264 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8877 (tttt)
REVERT: B  128 PHE cc_start: 0.7882 (p90) cc_final: 0.7327 (p90)
REVERT: B  239 GLN cc_start: 0.6945 (OUTLIER) cc_final: 0.6682 (pm20)
REVERT: B  241 TYR cc_start: 0.4131 (OUTLIER) cc_final: 0.3696 (t80)
REVERT: B  264 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8865 (tttt)
  outliers start: 25
  outliers final: 12
  residues processed: 105
  average time/residue: 0.3747
  time to fit residues: 42.3767
Evaluate side-chains
  102 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  239 GLN
Chi-restraints excluded: chain A residue  264 LYS
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  404 ASN
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  239 GLN
Chi-restraints excluded: chain B residue  241 TYR
Chi-restraints excluded: chain B residue  264 LYS
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  404 ASN
Chi-restraints excluded: chain B residue  557 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 66 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0050
   chunk 6 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   overall best weight:    0.9598

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

Flipped N/Q/H residues before XYZ refinement:
A 404 ASN
B 404 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.116969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.087654 restraints weight = 10055.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3029 rms_B_bonded: 2.08
r_work: 0.2894 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2760 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8851
moved from start:          0.2456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6396  Z= 0.126
  Angle     :  0.503   9.413   8698  Z= 0.257
  Chirality :  0.036   0.117   1032
  Planarity :  0.004   0.051   1042
  Dihedral  :  3.373  16.494    846
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 26.72 %
    Favored  : 70.60 %
  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:  3.65 (0.30), residues: 754
  helix:  3.06 (0.19), residues: 642
  sheet:  None (None), residues: 0
  loop : -1.87 (0.54), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 490 
 TYR   0.009   0.001   TYR A 548 
 PHE   0.012   0.001   PHE A 332 
 TRP   0.011   0.001   TRP A  76 
 HIS   0.003   0.001   HIS B 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6396)
  covalent geometry    : angle       0.50272 ( 8698)
  hydrogen bonds       : bond        0.03860 (  528)
  hydrogen bonds       : angle       3.63974 ( 1584)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.224 
Fit side-chains
REVERT: A  128 PHE cc_start: 0.7837 (p90) cc_final: 0.7337 (p90)
REVERT: A  239 GLN cc_start: 0.6839 (OUTLIER) cc_final: 0.6621 (pm20)
REVERT: A  264 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8867 (tttt)
REVERT: B  128 PHE cc_start: 0.7884 (p90) cc_final: 0.7336 (p90)
REVERT: B  241 TYR cc_start: 0.4089 (OUTLIER) cc_final: 0.3651 (t80)
REVERT: B  264 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8864 (tttt)
  outliers start: 18
  outliers final: 12
  residues processed: 101
  average time/residue: 0.3753
  time to fit residues: 40.7896
Evaluate side-chains
  101 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  239 GLN
Chi-restraints excluded: chain A residue  264 LYS
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  404 ASN
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  241 TYR
Chi-restraints excluded: chain B residue  264 LYS
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  404 ASN
Chi-restraints excluded: chain B residue  557 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    0.2980
   chunk 41 optimal weight:    4.9990
   chunk 26 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 404 ASN
B 404 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.117526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.088226 restraints weight = 10145.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 2.10
r_work: 0.2902 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2768 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8843
moved from start:          0.2511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6396  Z= 0.119
  Angle     :  0.496   9.201   8698  Z= 0.254
  Chirality :  0.036   0.116   1032
  Planarity :  0.004   0.051   1042
  Dihedral  :  3.351  16.704    846
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 27.46 %
    Favored  : 70.15 %
  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:  3.73 (0.30), residues: 754
  helix:  3.06 (0.19), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.64 (0.56), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 490 
 TYR   0.009   0.001   TYR A 548 
 PHE   0.013   0.001   PHE A  63 
 TRP   0.011   0.001   TRP A  76 
 HIS   0.003   0.001   HIS B 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 6396)
  covalent geometry    : angle       0.49639 ( 8698)
  hydrogen bonds       : bond        0.03782 (  528)
  hydrogen bonds       : angle       3.61354 ( 1584)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2042.21 seconds
wall clock time: 35 minutes 47.19 seconds (2147.19 seconds total)