Starting phenix.real_space_refine
on Fri Aug 22 13:18:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ju0_36658/08_2025/8ju0_36658.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ju0_36658/08_2025/8ju0_36658.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ju0_36658/08_2025/8ju0_36658.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ju0_36658/08_2025/8ju0_36658.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ju0_36658/08_2025/8ju0_36658.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ju0_36658/08_2025/8ju0_36658.cif"
  }
  resolution = 2.98
  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=  -0.003 sd=   0.171
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      31      5.16       5
     C    2117      2.51       5
     N     519      2.21       5
     O     532      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3199
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3170
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 431, 3170
          Classifications: {'peptide': 431}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'PTRANS': 20, 'TRANS': 410}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 162
          Unresolved non-hydrogen angles: 209
          Unresolved non-hydrogen dihedrals: 124
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 2, 'ARG:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 109
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'SNL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.25, per 1000 atoms: 0.39
  Number of scatterers: 3199
  At special positions: 0
  Unit cell: (58.455, 90.93, 68.1975, 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      31     16.00
     O     532      8.00
     N     519      7.00
     C    2117      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A 121 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  62 " - pdb=" SG  CYS A 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  88 " - pdb=" SG  CYS A 142 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.23
  Conformation dependent library (CDL) restraints added in 116.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  788

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 0 sheets defined
      82.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 37
      removed outlier: 3.573A  pdb=" N   LEU A  27 " --> pdb=" O   LEU A  23 " (cutoff:3.500A)
      Proline residue:  A  34  - end of helix
    Processing helix  chain 'A' and resid 38 through 43
    Processing helix  chain 'A' and resid 54 through 62
    Processing helix  chain 'A' and resid 65 through 73
    Processing helix  chain 'A' and resid 83 through 88
    Processing helix  chain 'A' and resid 104 through 110
      removed outlier: 3.683A  pdb=" N   SER A 108 " --> pdb=" O   ASP A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 116
    Processing helix  chain 'A' and resid 133 through 139
    Processing helix  chain 'A' and resid 141 through 143
      No H-bonds generated for 'chain 'A' and resid 141 through 143'
    Processing helix  chain 'A' and resid 144 through 194
      removed outlier: 4.073A  pdb=" N   LEU A 148 " --> pdb=" O   ASP A 144 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ASP A 149 " --> pdb=" O   SER A 145 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   GLN A 152 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LEU A 155 " --> pdb=" O   PHE A 151 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   GLY A 167 " --> pdb=" O   SER A 163 " (cutoff:3.500A)
      removed outlier: 4.909A  pdb=" N   ASP A 171 " --> pdb=" O   GLY A 167 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   ARG A 172 " --> pdb=" O   TYR A 168 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   PHE A 173 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   ARG A 175 " --> pdb=" O   ASP A 171 " (cutoff:3.500A)
      removed outlier: 9.416A  pdb=" N   LYS A 176 " --> pdb=" O   ARG A 172 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LEU A 177 " --> pdb=" O   PHE A 173 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   CYS A 178 " --> pdb=" O   GLY A 174 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   LEU A 179 " --> pdb=" O   ARG A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 227
      removed outlier: 3.942A  pdb=" N   LYS A 214 " --> pdb=" O   GLY A 210 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   GLY A 215 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 258
    Processing helix  chain 'A' and resid 260 through 275
      Proline residue:  A 271  - end of helix
    Processing helix  chain 'A' and resid 334 through 338
      removed outlier: 3.835A  pdb=" N   LEU A 337 " --> pdb=" O   PHE A 334 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   PHE A 338 " --> pdb=" O   ALA A 335 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 334 through 338'
    Processing helix  chain 'A' and resid 340 through 372
    Processing helix  chain 'A' and resid 374 through 400
      Proline residue:  A 388  - end of helix
      removed outlier: 4.174A  pdb=" N   PHE A 391 " --> pdb=" O   ILE A 387 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASP A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ARG A 399 " --> pdb=" O   ILE A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 423
      removed outlier: 3.674A  pdb=" N   ILE A 421 " --> pdb=" O   CYS A 417 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   PHE A 422 " --> pdb=" O   LEU A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 456
      removed outlier: 3.623A  pdb=" N   LEU A 451 " --> pdb=" O   GLN A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 488
      Proline residue:  A 481  - end of helix
      removed outlier: 4.396A  pdb=" N   ARG A 486 " --> pdb=" O   PHE A 482 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ARG A 488 " --> pdb=" O   VAL A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 510
    Processing helix  chain 'A' and resid 511 through 513
      No H-bonds generated for 'chain 'A' and resid 511 through 513'

    235 hydrogen bonds defined for protein.
    699 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.44

  Time building geometry restraints manager: 0.31 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 478
        1.31 -     1.43: 893
        1.43 -     1.56: 1865
        1.56 -     1.69: 2
        1.69 -     1.81: 45
  Bond restraints: 3283
  Sorted by residual:
  bond pdb=" C15 SNL A 601 "
       pdb=" O58 SNL A 601 "
    ideal  model  delta    sigma   weight residual
    1.332  1.545 -0.213 2.00e-02 2.50e+03 1.14e+02
  bond pdb=" C22 SNL A 601 "
       pdb=" S61 SNL A 601 "
    ideal  model  delta    sigma   weight residual
    1.829  1.651  0.178 2.00e-02 2.50e+03 7.89e+01
  bond pdb=" C16 SNL A 601 "
       pdb=" S61 SNL A 601 "
    ideal  model  delta    sigma   weight residual
    1.767  1.677  0.090 2.00e-02 2.50e+03 2.04e+01
  bond pdb=" C9  SNL A 601 "
       pdb=" O58 SNL A 601 "
    ideal  model  delta    sigma   weight residual
    1.443  1.518 -0.075 2.00e-02 2.50e+03 1.42e+01
  bond pdb=" C18 SNL A 601 "
       pdb=" C19 SNL A 601 "
    ideal  model  delta    sigma   weight residual
    1.463  1.537 -0.074 2.00e-02 2.50e+03 1.35e+01
  ... (remaining 3278 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.48: 4455
        3.48 -     6.96: 28
        6.96 -    10.44: 8
       10.44 -    13.91: 1
       13.91 -    17.39: 2
  Bond angle restraints: 4494
  Sorted by residual:
  angle pdb=" C13 SNL A 601 "
        pdb=" C9  SNL A 601 "
        pdb=" C5  SNL A 601 "
      ideal   model   delta    sigma   weight residual
     116.85  134.24  -17.39 3.00e+00 1.11e-01 3.36e+01
  angle pdb=" C8  SNL A 601 "
        pdb=" C9  SNL A 601 "
        pdb=" O58 SNL A 601 "
      ideal   model   delta    sigma   weight residual
     111.01   96.07   14.94 3.00e+00 1.11e-01 2.48e+01
  angle pdb=" C16 SNL A 601 "
        pdb=" S61 SNL A 601 "
        pdb=" C22 SNL A 601 "
      ideal   model   delta    sigma   weight residual
     101.80  115.41  -13.61 3.00e+00 1.11e-01 2.06e+01
  angle pdb=" C1  SNL A 601 "
        pdb=" C2  SNL A 601 "
        pdb=" C24 SNL A 601 "
      ideal   model   delta    sigma   weight residual
     108.42  117.77   -9.35 3.00e+00 1.11e-01 9.71e+00
  angle pdb=" C5  SNL A 601 "
        pdb=" C9  SNL A 601 "
        pdb=" O58 SNL A 601 "
      ideal   model   delta    sigma   weight residual
     111.22  102.15    9.07 3.00e+00 1.11e-01 9.15e+00
  ... (remaining 4489 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.26: 1722
       14.26 -    28.52: 156
       28.52 -    42.77: 52
       42.77 -    57.03: 15
       57.03 -    71.29: 5
  Dihedral angle restraints: 1950
    sinusoidal: 721
      harmonic: 1229
  Sorted by residual:
  dihedral pdb=" SG  CYS A  50 "
           pdb=" CB  CYS A 121 "
           pdb=" SG  CYS A 121 "
           pdb=" CA  CYS A 121 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00    9.30   69.70     1      2.00e+01 2.50e-03 1.57e+01
  dihedral pdb=" CA  CYS A  50 "
           pdb=" CB  CYS A  50 "
           pdb=" SG  CYS A  50 "
           pdb=" SG  CYS A 121 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00  -11.22  -61.78     1      2.00e+01 2.50e-03 1.27e+01
  dihedral pdb=" CA  ASN A 453 "
           pdb=" CB  ASN A 453 "
           pdb=" CG  ASN A 453 "
           pdb=" OD1 ASN A 453 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -172.00  -68.00     2      2.00e+01 2.50e-03 1.03e+01
  ... (remaining 1947 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.181: 531
       0.181 -    0.362: 3
       0.362 -    0.542: 0
       0.542 -    0.723: 1
       0.723 -    0.904: 1
  Chirality restraints: 536
  Sorted by residual:
  chirality pdb=" C9  SNL A 601 "
            pdb=" C13 SNL A 601 "
            pdb=" C5  SNL A 601 "
            pdb=" C8  SNL A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.67   -1.77   -0.90 2.00e-01 2.50e+01 2.04e+01
  chirality pdb=" C2  SNL A 601 "
            pdb=" C1  SNL A 601 "
            pdb=" C20 SNL A 601 "
            pdb=" C24 SNL A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.82   -2.20   -0.62 2.00e-01 2.50e+01 9.56e+00
  chirality pdb=" C6  SNL A 601 "
            pdb=" C23 SNL A 601 "
            pdb=" C5  SNL A 601 "
            pdb=" C7  SNL A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.43   -2.71    0.28 2.00e-01 2.50e+01 1.96e+00
  ... (remaining 533 not shown)

  Planarity restraints: 551
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 340 "   -0.032 5.00e-02 4.00e+02   4.96e-02 3.93e+00
        pdb=" N   PRO A 341 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 341 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 341 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 270 "   -0.025 5.00e-02 4.00e+02   3.87e-02 2.39e+00
        pdb=" N   PRO A 271 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 271 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 271 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 158 "    0.008 2.00e-02 2.50e+03   1.54e-02 2.37e+00
        pdb=" C   GLY A 158 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   GLY A 158 "    0.010 2.00e-02 2.50e+03
        pdb=" N   PHE A 159 "    0.009 2.00e-02 2.50e+03
  ... (remaining 548 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 489
        2.76 -     3.29: 3209
        3.29 -     3.83: 5529
        3.83 -     4.36: 6174
        4.36 -     4.90: 10891
  Nonbonded interactions: 26292
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 147 "
            pdb=" OH  TYR A 199 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   GLY A 476 "
            pdb=" OG1 THR A 480 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   HIS A 367 "
            pdb=" OG1 THR A 371 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O   MET A 368 "
            pdb=" OG  SER A 372 "
     model   vdw
     2.374 3.040
  nonbonded pdb=" O   ASN A  71 "
            pdb=" NH2 ARG A 113 "
     model   vdw
     2.375 3.120
  ... (remaining 26287 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.000
  Set scattering table:                    0.020
  Process input model:                     5.370
  Find NCS groups from input model:        0.030
  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:11.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6925
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      :  0.006   0.213   3286  Z= 0.312
  Angle     :  0.811  17.392   4500  Z= 0.350
  Chirality :  0.063   0.904    536
  Planarity :  0.004   0.050    551
  Dihedral  : 13.409  71.290   1153
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  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:  1.57 (0.42), residues: 425
  helix:  1.50 (0.30), residues: 313
  sheet:  None (None), residues: 0
  loop : -0.12 (0.62), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 206 
 TYR   0.016   0.001   TYR A 240 
 PHE   0.010   0.001   PHE A  44 
 TRP   0.014   0.001   TRP A  64 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00630 ( 3283)
  covalent geometry    : angle       0.81124 ( 4494)
  SS BOND              : bond        0.00352 (    3)
  SS BOND              : angle       0.69732 (    6)
  hydrogen bonds       : bond        0.12065 (  235)
  hydrogen bonds       : angle       5.22257 (  699)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.126 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.2912
  time to fit residues: 13.1974
Evaluate side-chains
  33 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0170
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
A 265 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.203680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.161865 restraints weight = 2982.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3772 rms_B_bonded: 1.67
r_work: 0.3550 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3401 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6934
moved from start:          0.0915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3286  Z= 0.148
  Angle     :  0.541   5.382   4500  Z= 0.273
  Chirality :  0.037   0.131    536
  Planarity :  0.004   0.049    551
  Dihedral  :  5.345  28.996    529
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  :  9.62 %
    Favored  : 88.46 %
  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:  1.73 (0.43), residues: 425
  helix:  1.60 (0.30), residues: 320
  sheet:  None (None), residues: 0
  loop : -0.12 (0.66), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 206 
 TYR   0.014   0.001   TYR A 240 
 PHE   0.010   0.001   PHE A  44 
 TRP   0.007   0.001   TRP A  64 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 3283)
  covalent geometry    : angle       0.54033 ( 4494)
  SS BOND              : bond        0.00417 (    3)
  SS BOND              : angle       0.84943 (    6)
  hydrogen bonds       : bond        0.04714 (  235)
  hydrogen bonds       : angle       4.55474 (  699)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.085 
Fit side-chains
REVERT: A  200 MET cc_start: 0.7543 (mmm) cc_final: 0.7174 (tpp)
REVERT: A  447 GLN cc_start: 0.7409 (mm110) cc_final: 0.7015 (mm110)
  outliers start: 6
  outliers final: 1
  residues processed: 38
  average time/residue: 0.3636
  time to fit residues: 14.4594
Evaluate side-chains
  33 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 32
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 14 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 15 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 30 optimal weight:    0.1980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 410 ASN
A 453 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.200902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.159920 restraints weight = 2988.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 1.65
r_work: 0.3529 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6946
moved from start:          0.1183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3286  Z= 0.157
  Angle     :  0.548   5.774   4500  Z= 0.276
  Chirality :  0.038   0.194    536
  Planarity :  0.004   0.046    551
  Dihedral  :  5.017  28.182    529
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 11.22 %
    Favored  : 86.22 %
  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 aren not related in a simple way.
  whole:  1.78 (0.43), residues: 425
  helix:  1.61 (0.30), residues: 319
  sheet:  None (None), residues: 0
  loop :  0.00 (0.67), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 206 
 TYR   0.014   0.001   TYR A 240 
 PHE   0.010   0.001   PHE A  44 
 TRP   0.007   0.001   TRP A  64 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 3283)
  covalent geometry    : angle       0.54712 ( 4494)
  SS BOND              : bond        0.00480 (    3)
  SS BOND              : angle       0.93178 (    6)
  hydrogen bonds       : bond        0.04573 (  235)
  hydrogen bonds       : angle       4.57217 (  699)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A  200 MET cc_start: 0.7534 (mmm) cc_final: 0.7169 (tpp)
REVERT: A  420 MET cc_start: 0.7935 (mtp) cc_final: 0.7245 (mtt)
REVERT: A  447 GLN cc_start: 0.7375 (mm110) cc_final: 0.7068 (mm110)
REVERT: A  448 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8138 (mpt)
  outliers start: 8
  outliers final: 5
  residues processed: 38
  average time/residue: 0.2885
  time to fit residues: 11.5949
Evaluate side-chains
  39 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  408 MET
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  504 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:   20.0000
   chunk 33 optimal weight:    0.9990
   chunk 17 optimal weight:    0.2980
   chunk 16 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 453 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.198588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.157064 restraints weight = 2998.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3737 rms_B_bonded: 1.72
r_work: 0.3509 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3355 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6968
moved from start:          0.1318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3286  Z= 0.161
  Angle     :  0.554   6.184   4500  Z= 0.278
  Chirality :  0.039   0.155    536
  Planarity :  0.004   0.044    551
  Dihedral  :  4.854  25.733    529
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 13.14 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.78 (0.42), residues: 425
  helix:  1.61 (0.30), residues: 319
  sheet:  None (None), residues: 0
  loop :  0.02 (0.66), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 206 
 TYR   0.011   0.001   TYR A 352 
 PHE   0.011   0.001   PHE A  44 
 TRP   0.007   0.001   TRP A 354 
 HIS   0.002   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 3283)
  covalent geometry    : angle       0.55352 ( 4494)
  SS BOND              : bond        0.00508 (    3)
  SS BOND              : angle       0.92825 (    6)
  hydrogen bonds       : bond        0.04569 (  235)
  hydrogen bonds       : angle       4.57697 (  699)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 35
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A  200 MET cc_start: 0.7670 (mmm) cc_final: 0.7302 (tpp)
REVERT: A  447 GLN cc_start: 0.7277 (mm110) cc_final: 0.7006 (mm110)
REVERT: A  448 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.8090 (mpp)
  outliers start: 8
  outliers final: 5
  residues processed: 39
  average time/residue: 0.2258
  time to fit residues: 9.3436
Evaluate side-chains
  40 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 34
  time to evaluate  : 0.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  504 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 15 optimal weight:    0.4980
   chunk 25 optimal weight:    5.9990
   chunk 34 optimal weight:    0.0050
   chunk 24 optimal weight:    0.8980
   chunk 20 optimal weight:    5.9990
   chunk 21 optimal weight:    0.8980
   chunk 42 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.200217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.159471 restraints weight = 2985.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3759 rms_B_bonded: 1.69
r_work: 0.3537 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3383 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6932
moved from start:          0.1376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3286  Z= 0.136
  Angle     :  0.529   5.903   4500  Z= 0.267
  Chirality :  0.038   0.146    536
  Planarity :  0.004   0.043    551
  Dihedral  :  4.654  25.285    529
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.74 %
    Favored  : 83.01 %
  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:  1.91 (0.42), residues: 425
  helix:  1.72 (0.30), residues: 319
  sheet:  None (None), residues: 0
  loop : -0.01 (0.65), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 206 
 TYR   0.011   0.001   TYR A 352 
 PHE   0.010   0.001   PHE A  44 
 TRP   0.006   0.001   TRP A  64 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 3283)
  covalent geometry    : angle       0.52902 ( 4494)
  SS BOND              : bond        0.00400 (    3)
  SS BOND              : angle       0.74929 (    6)
  hydrogen bonds       : bond        0.04303 (  235)
  hydrogen bonds       : angle       4.46360 (  699)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 34
  time to evaluate  : 0.075 
Fit side-chains
REVERT: A  144 ASP cc_start: 0.7729 (m-30) cc_final: 0.7389 (m-30)
REVERT: A  200 MET cc_start: 0.7631 (mmm) cc_final: 0.7261 (tpp)
REVERT: A  420 MET cc_start: 0.7978 (mtp) cc_final: 0.7299 (mtt)
REVERT: A  435 MET cc_start: 0.7472 (tpp) cc_final: 0.7218 (tpp)
REVERT: A  448 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.8004 (mpp)
  outliers start: 7
  outliers final: 6
  residues processed: 38
  average time/residue: 0.3195
  time to fit residues: 12.6951
Evaluate side-chains
  40 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 36 optimal weight:    0.3980
   chunk 1 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 447 GLN
A 453 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.198761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.158309 restraints weight = 2960.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3750 rms_B_bonded: 1.62
r_work: 0.3521 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3369 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7023
moved from start:          0.1485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3286  Z= 0.156
  Angle     :  0.550   6.263   4500  Z= 0.276
  Chirality :  0.038   0.130    536
  Planarity :  0.004   0.042    551
  Dihedral  :  4.742  24.538    529
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.06 %
    Favored  : 82.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.86 (0.43), residues: 425
  helix:  1.68 (0.30), residues: 319
  sheet:  None (None), residues: 0
  loop :  0.02 (0.67), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 206 
 TYR   0.011   0.001   TYR A 352 
 PHE   0.010   0.001   PHE A  44 
 TRP   0.007   0.001   TRP A 354 
 HIS   0.003   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 3283)
  covalent geometry    : angle       0.54989 ( 4494)
  SS BOND              : bond        0.00492 (    3)
  SS BOND              : angle       0.87237 (    6)
  hydrogen bonds       : bond        0.04463 (  235)
  hydrogen bonds       : angle       4.53791 (  699)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 35
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A  200 MET cc_start: 0.7700 (mmm) cc_final: 0.7332 (tpp)
REVERT: A  435 MET cc_start: 0.7569 (tpp) cc_final: 0.7300 (tpp)
REVERT: A  447 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7237 (mm110)
REVERT: A  448 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.8029 (mpp)
  outliers start: 8
  outliers final: 5
  residues processed: 40
  average time/residue: 0.3294
  time to fit residues: 13.8466
Evaluate side-chains
  39 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 4 optimal weight:    0.2980
   chunk 40 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0970
   chunk 2 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A 453 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.200246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.159104 restraints weight = 3001.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3756 rms_B_bonded: 1.68
r_work: 0.3532 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3377 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6939
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3286  Z= 0.137
  Angle     :  0.534   6.605   4500  Z= 0.267
  Chirality :  0.038   0.124    536
  Planarity :  0.004   0.041    551
  Dihedral  :  4.633  24.469    529
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 15.06 %
    Favored  : 82.05 %
  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:  1.94 (0.43), residues: 425
  helix:  1.74 (0.30), residues: 319
  sheet:  None (None), residues: 0
  loop :  0.01 (0.67), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 206 
 TYR   0.011   0.001   TYR A 352 
 PHE   0.010   0.001   PHE A  44 
 TRP   0.006   0.001   TRP A  64 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 3283)
  covalent geometry    : angle       0.53323 ( 4494)
  SS BOND              : bond        0.00413 (    3)
  SS BOND              : angle       0.80973 (    6)
  hydrogen bonds       : bond        0.04283 (  235)
  hydrogen bonds       : angle       4.46394 (  699)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 32
  time to evaluate  : 0.111 
Fit side-chains
REVERT: A  200 MET cc_start: 0.7610 (mmm) cc_final: 0.7234 (tpp)
REVERT: A  420 MET cc_start: 0.7928 (mtp) cc_final: 0.7243 (mtt)
REVERT: A  435 MET cc_start: 0.7441 (tpp) cc_final: 0.7169 (tpp)
REVERT: A  447 GLN cc_start: 0.7655 (mm-40) cc_final: 0.7167 (mm110)
REVERT: A  448 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7955 (mpp)
  outliers start: 9
  outliers final: 5
  residues processed: 35
  average time/residue: 0.3552
  time to fit residues: 13.0457
Evaluate side-chains
  38 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 12 optimal weight:    0.0040
   chunk 2 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0670
   chunk 9 optimal weight:    9.9990
   chunk 0 optimal weight:    7.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.4330

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

Flipped N/Q/H residues before XYZ refinement:
A 453 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.203311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.162836 restraints weight = 3048.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3780 rms_B_bonded: 1.66
r_work: 0.3555 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3400 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6919
moved from start:          0.1523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3286  Z= 0.126
  Angle     :  0.524   7.020   4500  Z= 0.260
  Chirality :  0.037   0.120    536
  Planarity :  0.004   0.041    551
  Dihedral  :  4.468  25.718    529
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 14.74 %
    Favored  : 82.05 %
  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 (0.43), residues: 425
  helix:  1.79 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.09 (0.66), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 206 
 TYR   0.011   0.001   TYR A 352 
 PHE   0.009   0.001   PHE A  44 
 TRP   0.006   0.001   TRP A  64 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 3283)
  covalent geometry    : angle       0.52314 ( 4494)
  SS BOND              : bond        0.00370 (    3)
  SS BOND              : angle       0.75550 (    6)
  hydrogen bonds       : bond        0.04106 (  235)
  hydrogen bonds       : angle       4.32992 (  699)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 33
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A  144 ASP cc_start: 0.7717 (m-30) cc_final: 0.7365 (m-30)
REVERT: A  200 MET cc_start: 0.7551 (mmm) cc_final: 0.7189 (tpp)
REVERT: A  435 MET cc_start: 0.7336 (tpp) cc_final: 0.7033 (tpp)
REVERT: A  447 GLN cc_start: 0.7520 (mm-40) cc_final: 0.7030 (mm110)
REVERT: A  448 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7964 (mpp)
  outliers start: 10
  outliers final: 6
  residues processed: 37
  average time/residue: 0.3086
  time to fit residues: 12.0488
Evaluate side-chains
  39 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  408 MET
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 12 optimal weight:    0.1980
   chunk 34 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 26 optimal weight:    0.4980
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
A 453 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.200141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.158918 restraints weight = 3008.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 1.67
r_work: 0.3532 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3375 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6946
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3286  Z= 0.147
  Angle     :  0.542   7.206   4500  Z= 0.270
  Chirality :  0.038   0.121    536
  Planarity :  0.004   0.041    551
  Dihedral  :  4.582  25.741    529
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 15.06 %
    Favored  : 81.73 %
  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:  1.96 (0.43), residues: 425
  helix:  1.76 (0.30), residues: 319
  sheet:  None (None), residues: 0
  loop : -0.00 (0.66), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 206 
 TYR   0.011   0.001   TYR A 352 
 PHE   0.010   0.001   PHE A  44 
 TRP   0.007   0.001   TRP A 354 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 3283)
  covalent geometry    : angle       0.54192 ( 4494)
  SS BOND              : bond        0.00458 (    3)
  SS BOND              : angle       0.83923 (    6)
  hydrogen bonds       : bond        0.04324 (  235)
  hydrogen bonds       : angle       4.43951 (  699)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 31
  time to evaluate  : 0.091 
Fit side-chains
REVERT: A  200 MET cc_start: 0.7586 (mmm) cc_final: 0.7216 (tpp)
REVERT: A  420 MET cc_start: 0.7930 (mtp) cc_final: 0.7274 (mtt)
REVERT: A  435 MET cc_start: 0.7483 (tpp) cc_final: 0.7185 (tpp)
REVERT: A  447 GLN cc_start: 0.7539 (mm-40) cc_final: 0.7003 (mm110)
  outliers start: 10
  outliers final: 7
  residues processed: 37
  average time/residue: 0.3296
  time to fit residues: 12.7751
Evaluate side-chains
  36 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 29
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  408 MET
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0570
   chunk 40 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 36 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 42 optimal weight:    0.5980
   chunk 8 optimal weight:    6.9990
   chunk 34 optimal weight:    0.0980
   overall best weight:    0.3898

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

Flipped N/Q/H residues before XYZ refinement:
A 453 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.202724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.161980 restraints weight = 2958.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3787 rms_B_bonded: 1.64
r_work: 0.3568 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3414 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6909
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3286  Z= 0.124
  Angle     :  0.532   7.575   4500  Z= 0.263
  Chirality :  0.037   0.127    536
  Planarity :  0.004   0.041    551
  Dihedral  :  4.457  25.666    529
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 15.38 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.99 (0.43), residues: 425
  helix:  1.80 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.11 (0.67), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 206 
 TYR   0.012   0.001   TYR A 352 
 PHE   0.009   0.001   PHE A  44 
 TRP   0.006   0.001   TRP A  64 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 3283)
  covalent geometry    : angle       0.53135 ( 4494)
  SS BOND              : bond        0.00355 (    3)
  SS BOND              : angle       0.74232 (    6)
  hydrogen bonds       : bond        0.04117 (  235)
  hydrogen bonds       : angle       4.30500 (  699)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 33
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A  200 MET cc_start: 0.7525 (mmm) cc_final: 0.7165 (tpp)
REVERT: A  368 MET cc_start: 0.7940 (ttm) cc_final: 0.7591 (ttp)
REVERT: A  420 MET cc_start: 0.7957 (mtp) cc_final: 0.7313 (mtt)
REVERT: A  435 MET cc_start: 0.7480 (tpp) cc_final: 0.7169 (tpp)
REVERT: A  447 GLN cc_start: 0.7496 (mm-40) cc_final: 0.7044 (mm110)
  outliers start: 9
  outliers final: 8
  residues processed: 36
  average time/residue: 0.3302
  time to fit residues: 12.4551
Evaluate side-chains
  39 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 31
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  408 MET
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 5 optimal weight:    0.0980
   chunk 9 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 453 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.201259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.160168 restraints weight = 3030.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3754 rms_B_bonded: 1.70
r_work: 0.3528 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3372 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6948
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3286  Z= 0.149
  Angle     :  0.557   8.238   4500  Z= 0.275
  Chirality :  0.038   0.142    536
  Planarity :  0.004   0.041    551
  Dihedral  :  4.582  25.350    529
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.03 %
    Favored  : 81.09 %
  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:  1.85 (0.43), residues: 425
  helix:  1.70 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.15 (0.66), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 206 
 TYR   0.011   0.001   TYR A 352 
 PHE   0.009   0.001   PHE A  44 
 TRP   0.007   0.001   TRP A 354 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 3283)
  covalent geometry    : angle       0.55617 ( 4494)
  SS BOND              : bond        0.00452 (    3)
  SS BOND              : angle       0.85526 (    6)
  hydrogen bonds       : bond        0.04403 (  235)
  hydrogen bonds       : angle       4.43846 (  699)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1278.84 seconds
wall clock time: 22 minutes 32.59 seconds (1352.59 seconds total)