Starting phenix.real_space_refine
on Wed Sep 17 03:56:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xcv_38256/09_2025/8xcv_38256_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xcv_38256/09_2025/8xcv_38256.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.83
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xcv_38256/09_2025/8xcv_38256_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xcv_38256/09_2025/8xcv_38256_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xcv_38256/09_2025/8xcv_38256.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xcv_38256/09_2025/8xcv_38256.map"
  }
  resolution = 2.83
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      14      5.16       5
     C    2101      2.51       5
     N     564      2.21       5
     O     628      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3310
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3272
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 415, 3253
          Classifications: {'peptide': 415}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 394}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
      Conformer: "B"
        Number of residues, atoms: 415, 3253
          Classifications: {'peptide': 415}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 394}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
          bond proxies already assigned to first conformer: 3303
    Chain: "A"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 38
          Unusual residues: {'NAP': 1}
          Classifications: {'undetermined': 1, 'water': 7}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 40
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'NAP:plan-2': 1, 'NAP:plan-4': 1}
          Unresolved non-hydrogen planarities: 12
  Time building chain proxies: 1.77, per 1000 atoms: 0.53
  Number of scatterers: 3310
  At special positions: 0
  Unit cell: (66.928, 72.944, 72.944, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P       3     15.00
     O     628      8.00
     N     564      7.00
     C    2101      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: 0.31
  Conformation dependent library (CDL) restraints added in 255.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  760

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 2 sheets defined
      56.1% alpha, 13.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 20
      removed outlier: 3.793A  pdb=" N   TYR A  20 " --> pdb=" O   ARG A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 24 through 32
    Processing helix  chain 'A' and resid 79 through 97
      removed outlier: 3.713A  pdb=" N   TRP A  92 " --> pdb=" O   THR A  88 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   VAL A  97 " --> pdb=" O   LYS A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 115
    Processing helix  chain 'A' and resid 116 through 132
    Processing helix  chain 'A' and resid 133 through 135
      No H-bonds generated for 'chain 'A' and resid 133 through 135'
    Processing helix  chain 'A' and resid 149 through 165
    Processing helix  chain 'A' and resid 169 through 174
      removed outlier: 3.828A  pdb=" N   ILE A 174 " --> pdb=" O   PHE A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 207
    Processing helix  chain 'A' and resid 221 through 234
    Processing helix  chain 'A' and resid 256 through 268
    Processing helix  chain 'A' and resid 280 through 285
    Processing helix  chain 'A' and resid 302 through 307
      removed outlier: 4.610A  pdb=" N   ASP A 307 " --> pdb=" O   GLU A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 333
    Processing helix  chain 'A' and resid 339 through 344
    Processing helix  chain 'A' and resid 345 through 361
    Processing helix  chain 'A' and resid 365 through 392
    Processing helix  chain 'A' and resid 394 through 414
    Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45
      removed outlier: 4.706A  pdb=" N   THR A  55 " --> pdb=" O   ILE A 109 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   GLY A 103 " --> pdb=" O   HIS A  61 " (cutoff:3.500A)
      removed outlier: 5.227A  pdb=" N   LYS A  69 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
      removed outlier: 7.485A  pdb=" N   GLY A 106 " --> pdb=" O   LYS A  69 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   GLY A  71 " --> pdb=" O   GLY A 106 " (cutoff:3.500A)
      removed outlier: 8.061A  pdb=" N   ILE A 108 " --> pdb=" O   GLY A  71 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   ARG A  73 " --> pdb=" O   ILE A 108 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   THR A  68 " --> pdb=" O   ILE A 141 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   ALA A 143 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   GLY A  70 " --> pdb=" O   ALA A 143 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 279
      removed outlier: 6.369A  pdb=" N   ILE A 215 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ALA A 241 " --> pdb=" O   ILE A 215 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   LYS A 214 " --> pdb=" O   VAL A 291 " (cutoff:3.500A)
      removed outlier: 8.363A  pdb=" N   ALA A 293 " --> pdb=" O   LYS A 214 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   ALA A 216 " --> pdb=" O   ALA A 293 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   VAL A 314 " --> pdb=" O   ILE A 338 " (cutoff:3.500A)

    185 hydrogen bonds defined for protein.
    532 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: 0.58

  Time building geometry restraints manager: 0.42 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1064
        1.34 -     1.46: 606
        1.46 -     1.57: 1682
        1.57 -     1.69: 3
        1.69 -     1.81: 27
  Bond restraints: 3382
  Sorted by residual:
  bond pdb=" C   TRP A  89 "
       pdb=" CA BTRP A  89 "
    ideal  model  delta    sigma   weight residual
    1.522  1.642 -0.119 1.39e-02 5.18e+03 7.39e+01
  bond pdb=" O2B NAP A 500 "
       pdb=" P2B NAP A 500 "
    ideal  model  delta    sigma   weight residual
    1.736  1.569  0.167 2.00e-02 2.50e+03 6.99e+01
  bond pdb=" N   ARG A 370 "
       pdb=" CA BARG A 370 "
    ideal  model  delta    sigma   weight residual
    1.457  1.551 -0.095 1.33e-02 5.65e+03 5.07e+01
  bond pdb=" C4A NAP A 500 "
       pdb=" N3A NAP A 500 "
    ideal  model  delta    sigma   weight residual
    1.332  1.440 -0.108 2.00e-02 2.50e+03 2.90e+01
  bond pdb=" C6A NAP A 500 "
       pdb=" N6A NAP A 500 "
    ideal  model  delta    sigma   weight residual
    1.335  1.435 -0.100 2.00e-02 2.50e+03 2.49e+01
  ... (remaining 3377 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 4514
        2.41 -     4.82: 61
        4.82 -     7.23: 13
        7.23 -     9.64: 7
        9.64 -    12.04: 2
  Bond angle restraints: 4597
  Sorted by residual:
  angle pdb=" N   THR A  88 "
        pdb=" CA  THR A  88 "
        pdb=" C   THR A  88 "
      ideal   model   delta    sigma   weight residual
     111.28  105.80    5.48 1.09e+00 8.42e-01 2.53e+01
  angle pdb=" N   MET A  90 "
        pdb=" CA  MET A  90 "
        pdb=" C   MET A  90 "
      ideal   model   delta    sigma   weight residual
     111.69  105.67    6.02 1.23e+00 6.61e-01 2.39e+01
  angle pdb=" C   ASP A   5 "
        pdb=" N   PRO A   6 "
        pdb=" CA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     118.85  124.04   -5.19 1.09e+00 8.42e-01 2.27e+01
  angle pdb=" N   GLU A 371 "
        pdb=" CA  GLU A 371 "
        pdb=" C   GLU A 371 "
      ideal   model   delta    sigma   weight residual
     112.90  106.91    5.99 1.31e+00 5.83e-01 2.09e+01
  angle pdb=" O1A NAP A 500 "
        pdb=" PA  NAP A 500 "
        pdb=" O2A NAP A 500 "
      ideal   model   delta    sigma   weight residual
     121.77  109.73   12.04 3.00e+00 1.11e-01 1.61e+01
  ... (remaining 4592 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.09: 1804
       17.09 -    34.19: 157
       34.19 -    51.28: 53
       51.28 -    68.38: 20
       68.38 -    85.47: 8
  Dihedral angle restraints: 2042
    sinusoidal: 848
      harmonic: 1194
  Sorted by residual:
  dihedral pdb=" CA  ASP A 340 "
           pdb=" CB  ASP A 340 "
           pdb=" CG  ASP A 340 "
           pdb=" OD1 ASP A 340 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.22   56.22     1      2.00e+01 2.50e-03 1.07e+01
  dihedral pdb=" N   ARG A 246 "
           pdb=" CA  ARG A 246 "
           pdb=" CB  ARG A 246 "
           pdb=" CG  ARG A 246 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.45  -59.55     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CB  LYS A 211 "
           pdb=" CG  LYS A 211 "
           pdb=" CD  LYS A 211 "
           pdb=" CE  LYS A 211 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  122.59   57.41     3      1.50e+01 4.44e-03 9.44e+00
  ... (remaining 2039 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 417
       0.060 -    0.119: 69
       0.119 -    0.179: 9
       0.179 -    0.238: 1
       0.238 -    0.298: 1
  Chirality restraints: 497
  Sorted by residual:
  chirality pdb=" C2B NAP A 500 "
            pdb=" C1B NAP A 500 "
            pdb=" C3B NAP A 500 "
            pdb=" O2B NAP A 500 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.46   -0.30 2.00e-01 2.50e+01 2.21e+00
  chirality pdb=" CA BARG A 370 "
            pdb=" N   ARG A 370 "
            pdb=" C   ARG A 370 "
            pdb=" CB BARG A 370 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" CA  GLU A 233 "
            pdb=" N   GLU A 233 "
            pdb=" C   GLU A 233 "
            pdb=" CB  GLU A 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.81e-01
  ... (remaining 494 not shown)

  Planarity restraints: 585
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD AARG A 370 "    0.244 9.50e-02 1.11e+02   1.09e-01 7.34e+00
        pdb=" NE AARG A 370 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ AARG A 370 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1AARG A 370 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2AARG A 370 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  58 "    0.198 9.50e-02 1.11e+02   8.86e-02 4.81e+00
        pdb=" NE  ARG A  58 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  58 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  58 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  58 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 149 "   -0.030 5.00e-02 4.00e+02   4.59e-02 3.37e+00
        pdb=" N   PRO A 150 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 150 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 150 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 582 not shown)

  Histogram of nonbonded interaction distances:
        2.44 -     2.93: 1364
        2.93 -     3.42: 3350
        3.42 -     3.92: 5796
        3.92 -     4.41: 6718
        4.41 -     4.90: 10885
  Nonbonded interactions: 28113
  Sorted by model distance:
  nonbonded pdb=" O   PRO A  34 "
            pdb=" O   HOH A 601 "
     model   vdw
     2.441 3.040
  nonbonded pdb=" O   ALA A 223 "
            pdb=" OG1 THR A 227 "
     model   vdw
     2.469 3.040
  nonbonded pdb=" O   LYS A 213 "
            pdb=" N   THR A 238 "
     model   vdw
     2.489 3.120
  nonbonded pdb=" N   ASP A 145 "
            pdb=" OG1 THR A 148 "
     model   vdw
     2.504 3.120
  nonbonded pdb=" OG1 THR A  68 "
            pdb=" OD1 ASP A 140 "
     model   vdw
     2.504 3.040
  ... (remaining 28108 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=0.50 max=1.00 mean=0.99
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:             1.550
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.590
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8563
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      :  0.007   0.167   3382  Z= 0.410
  Angle     :  0.800  12.044   4597  Z= 0.435
  Chirality :  0.048   0.298    497
  Planarity :  0.007   0.109    585
  Dihedral  : 16.462  85.471   1282
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  :  3.24 %
    Favored  : 93.81 %
  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:  1.22 (0.43), residues: 415
  helix:  1.73 (0.36), residues: 212
  sheet: -0.75 (0.66), residues: 70
  loop :  0.37 (0.57), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 414 
 TYR   0.007   0.001   TYR A 363 
 PHE   0.007   0.001   PHE A 341 
 TRP   0.009   0.001   TRP A 382 
 HIS   0.001   0.000   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00747 ( 3382)
  covalent geometry    : angle       0.80047 ( 4597)
  hydrogen bonds       : bond        0.13065 (  185)
  hydrogen bonds       : angle       5.89800 (  532)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 ASP cc_start: 0.6040 (OUTLIER) cc_final: 0.4802 (p0)
  outliers start: 10
  outliers final: 2
  residues processed: 72
  average time/residue: 0.6814
  time to fit residues: 50.1558
Evaluate side-chains
  56 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 53
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ASP
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  244 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 388 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.109823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.084856 restraints weight = 13793.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.2841 rms_B_bonded: 2.88
r_work: 0.2699 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2581 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2581
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2461
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2461 r_free = 0.2461    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2460 r_free = 0.2460    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2460
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8888
moved from start:          0.1271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3382  Z= 0.139
  Angle     :  0.493   5.401   4597  Z= 0.258
  Chirality :  0.043   0.127    497
  Planarity :  0.004   0.044    585
  Dihedral  : 10.334  56.573    501
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 10.62 %
    Favored  : 88.50 %
  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:  1.58 (0.44), residues: 415
  helix:  2.11 (0.35), residues: 211
  sheet: -0.52 (0.67), residues: 72
  loop :  0.36 (0.60), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 118 
 TYR   0.010   0.001   TYR A 363 
 PHE   0.009   0.001   PHE A 381 
 TRP   0.010   0.001   TRP A 382 
 HIS   0.002   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 3382)
  covalent geometry    : angle       0.49293 ( 4597)
  hydrogen bonds       : bond        0.04122 (  185)
  hydrogen bonds       : angle       4.42976 (  532)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 ASP cc_start: 0.7314 (p0) cc_final: 0.6493 (p0)
  outliers start: 3
  outliers final: 1
  residues processed: 56
  average time/residue: 0.6580
  time to fit residues: 37.7724
Evaluate side-chains
  55 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 15 optimal weight:    7.9990
   chunk 5 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 18 optimal weight:    0.2980
   chunk 24 optimal weight:    9.9990
   chunk 17 optimal weight:    0.0470
   overall best weight:    1.0482

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.112182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.087742 restraints weight = 12973.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.2860 rms_B_bonded: 2.77
r_work: 0.2719 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2601 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2601
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2509
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2509 r_free = 0.2509    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2509 r_free = 0.2509    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2509
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8918
moved from start:          0.1428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   3382  Z= 0.102
  Angle     :  0.443   4.401   4597  Z= 0.230
  Chirality :  0.042   0.138    497
  Planarity :  0.004   0.044    585
  Dihedral  :  8.053  54.721    493
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 11.80 %
    Favored  : 87.61 %
  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:  1.68 (0.43), residues: 415
  helix:  2.24 (0.34), residues: 213
  sheet: -0.50 (0.66), residues: 72
  loop :  0.29 (0.61), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 187 
 TYR   0.008   0.001   TYR A 363 
 PHE   0.009   0.001   PHE A 381 
 TRP   0.008   0.001   TRP A  63 
 HIS   0.004   0.001   HIS A 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 3382)
  covalent geometry    : angle       0.44312 ( 4597)
  hydrogen bonds       : bond        0.03528 (  185)
  hydrogen bonds       : angle       4.11294 (  532)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.134 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 56
  average time/residue: 0.6137
  time to fit residues: 35.2800
Evaluate side-chains
  57 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ASP
Chi-restraints excluded: chain A residue  149 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 12 optimal weight:    4.9990
   chunk 18 optimal weight:    0.3980
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** A 267 HIS ** 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 = 0.3213 r_free = 0.3213 target = 0.109915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.085236 restraints weight = 13018.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.2816 rms_B_bonded: 2.75
r_work: 0.2677 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2559 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2559
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2586
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2586 r_free = 0.2586    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2586 r_free = 0.2586    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2586
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8904
moved from start:          0.1537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3382  Z= 0.119
  Angle     :  0.455   4.012   4597  Z= 0.237
  Chirality :  0.042   0.132    497
  Planarity :  0.004   0.044    585
  Dihedral  :  7.689  59.045    493
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 12.39 %
    Favored  : 87.02 %
  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:  1.69 (0.43), residues: 415
  helix:  2.32 (0.34), residues: 213
  sheet: -0.48 (0.65), residues: 72
  loop :  0.17 (0.60), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 118 
 TYR   0.009   0.001   TYR A 363 
 PHE   0.009   0.001   PHE A 381 
 TRP   0.007   0.001   TRP A  63 
 HIS   0.007   0.001   HIS A 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 3382)
  covalent geometry    : angle       0.45538 ( 4597)
  hydrogen bonds       : bond        0.03661 (  185)
  hydrogen bonds       : angle       4.11480 (  532)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A  244 ASP cc_start: 0.7479 (p0) cc_final: 0.7140 (p0)
  outliers start: 2
  outliers final: 2
  residues processed: 56
  average time/residue: 0.6063
  time to fit residues: 34.8753
Evaluate side-chains
  56 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ASP
Chi-restraints excluded: chain A residue  149 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    9.9990
   chunk 37 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 21 optimal weight:   10.0000
   chunk 27 optimal weight:    6.9990
   chunk 34 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0060
   chunk 39 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.7400

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

Flipped N/Q/H residues before XYZ refinement:
** A 267 HIS ** 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 = 0.3254 r_free = 0.3254 target = 0.112589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.088153 restraints weight = 13035.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.2887 rms_B_bonded: 2.77
r_work: 0.2747 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2629 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2629
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2631
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2631 r_free = 0.2631    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2631 r_free = 0.2631    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2631
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8898
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   3382  Z= 0.091
  Angle     :  0.440   4.891   4597  Z= 0.228
  Chirality :  0.042   0.133    497
  Planarity :  0.004   0.045    585
  Dihedral  :  7.067  59.945    493
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 12.68 %
    Favored  : 86.73 %
  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:  1.82 (0.43), residues: 415
  helix:  2.44 (0.34), residues: 213
  sheet: -0.35 (0.66), residues: 72
  loop :  0.13 (0.60), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 118 
 TYR   0.007   0.001   TYR A 363 
 PHE   0.009   0.001   PHE A 381 
 TRP   0.008   0.001   TRP A  63 
 HIS   0.007   0.001   HIS A 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00194 ( 3382)
  covalent geometry    : angle       0.44014 ( 4597)
  hydrogen bonds       : bond        0.03205 (  185)
  hydrogen bonds       : angle       4.00253 (  532)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.102 
Fit side-chains
REVERT: A  149 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8116 (p0)
REVERT: A  244 ASP cc_start: 0.7409 (p0) cc_final: 0.7126 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 55
  average time/residue: 0.6125
  time to fit residues: 34.6622
Evaluate side-chains
  52 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 5 optimal weight:    0.1980
   chunk 17 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 1 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 25 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A 267 HIS ** 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 = 0.3243 r_free = 0.3243 target = 0.111545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.088018 restraints weight = 8802.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 2.27
r_work: 0.2742 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2629 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2629
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2647
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2647 r_free = 0.2647    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2647 r_free = 0.2647    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2647
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8873
moved from start:          0.1667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3382  Z= 0.101
  Angle     :  0.450   4.958   4597  Z= 0.233
  Chirality :  0.042   0.130    497
  Planarity :  0.004   0.045    585
  Dihedral  :  6.846  58.702    493
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 13.57 %
    Favored  : 85.55 %
  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:  1.81 (0.43), residues: 415
  helix:  2.44 (0.34), residues: 213
  sheet: -0.33 (0.66), residues: 72
  loop :  0.11 (0.60), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 118 
 TYR   0.008   0.001   TYR A 363 
 PHE   0.010   0.001   PHE A 381 
 TRP   0.007   0.001   TRP A  63 
 HIS   0.008   0.001   HIS A 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 3382)
  covalent geometry    : angle       0.45024 ( 4597)
  hydrogen bonds       : bond        0.03368 (  185)
  hydrogen bonds       : angle       4.02472 (  532)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 53
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A  149 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8152 (p0)
  outliers start: 3
  outliers final: 0
  residues processed: 55
  average time/residue: 0.6094
  time to fit residues: 34.3656
Evaluate side-chains
  52 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 9 optimal weight:    0.3980
   chunk 15 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 29 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 23 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 388 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.110947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.086563 restraints weight = 13007.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.2858 rms_B_bonded: 2.75
r_work: 0.2718 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2599 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2599
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2595
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2595 r_free = 0.2595    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2595 r_free = 0.2595    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2595
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8921
moved from start:          0.1713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3382  Z= 0.108
  Angle     :  0.458   5.070   4597  Z= 0.237
  Chirality :  0.042   0.126    497
  Planarity :  0.004   0.045    585
  Dihedral  :  6.774  58.086    493
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 14.16 %
    Favored  : 85.25 %
  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:  1.77 (0.43), residues: 415
  helix:  2.41 (0.34), residues: 213
  sheet: -0.33 (0.66), residues: 72
  loop :  0.06 (0.60), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 118 
 TYR   0.008   0.001   TYR A 363 
 PHE   0.011   0.001   PHE A 381 
 TRP   0.007   0.001   TRP A  63 
 HIS   0.010   0.002   HIS A 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 3382)
  covalent geometry    : angle       0.45767 ( 4597)
  hydrogen bonds       : bond        0.03475 (  185)
  hydrogen bonds       : angle       4.05006 (  532)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 53
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 54
  average time/residue: 0.6426
  time to fit residues: 35.5816
Evaluate side-chains
  54 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0670
   chunk 23 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 10 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.7720

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.112734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.088043 restraints weight = 16399.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.2881 rms_B_bonded: 3.04
r_work: 0.2733 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2733
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2733
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8820
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3382  Z= 0.092
  Angle     :  0.453   6.335   4597  Z= 0.232
  Chirality :  0.042   0.130    497
  Planarity :  0.004   0.045    585
  Dihedral  :  6.638  56.701    493
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 14.75 %
    Favored  : 84.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.43), residues: 415
  helix:  2.44 (0.34), residues: 213
  sheet: -0.21 (0.66), residues: 72
  loop :  0.09 (0.60), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 118 
 TYR   0.007   0.001   TYR A 363 
 PHE   0.009   0.001   PHE A 381 
 TRP   0.008   0.001   TRP A  63 
 HIS   0.010   0.002   HIS A 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00198 ( 3382)
  covalent geometry    : angle       0.45296 ( 4597)
  hydrogen bonds       : bond        0.03176 (  185)
  hydrogen bonds       : angle       3.97558 (  532)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.082 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8007 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 53
  average time/residue: 0.5661
  time to fit residues: 30.8902
Evaluate side-chains
  52 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 26 optimal weight:    7.9990
   chunk 17 optimal weight:    0.0670
   chunk 11 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 38 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0370
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.0200

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.111993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.088582 restraints weight = 8214.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 2.18
r_work: 0.2745 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2633 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2633
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2653
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2653 r_free = 0.2653    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2653 r_free = 0.2653    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2653
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8882
moved from start:          0.1766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3382  Z= 0.101
  Angle     :  0.461   6.065   4597  Z= 0.237
  Chirality :  0.042   0.130    497
  Planarity :  0.004   0.045    585
  Dihedral  :  6.669  57.108    493
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 14.45 %
    Favored  : 84.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.82 (0.43), residues: 415
  helix:  2.43 (0.35), residues: 213
  sheet: -0.21 (0.66), residues: 72
  loop :  0.08 (0.60), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 118 
 TYR   0.007   0.001   TYR A 363 
 PHE   0.010   0.001   PHE A 381 
 TRP   0.007   0.001   TRP A  63 
 HIS   0.010   0.002   HIS A 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 3382)
  covalent geometry    : angle       0.46132 ( 4597)
  hydrogen bonds       : bond        0.03342 (  185)
  hydrogen bonds       : angle       3.99510 (  532)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8134 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 55
  average time/residue: 0.6323
  time to fit residues: 35.7200
Evaluate side-chains
  52 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0040
   chunk 13 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    1.1998

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

Flipped N/Q/H residues before XYZ refinement:
A 337 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.111432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.087909 restraints weight = 8511.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.2866 rms_B_bonded: 2.22
r_work: 0.2743 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2635 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2635
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2644
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2644 r_free = 0.2644    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2644 r_free = 0.2644    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2644
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8888
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3382  Z= 0.109
  Angle     :  0.473   6.053   4597  Z= 0.243
  Chirality :  0.042   0.127    497
  Planarity :  0.004   0.045    585
  Dihedral  :  6.747  57.578    493
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 14.16 %
    Favored  : 85.25 %
  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:  1.79 (0.43), residues: 415
  helix:  2.39 (0.35), residues: 213
  sheet: -0.23 (0.66), residues: 72
  loop :  0.08 (0.60), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 118 
 TYR   0.008   0.001   TYR A 363 
 PHE   0.011   0.001   PHE A 381 
 TRP   0.007   0.001   TRP A  63 
 HIS   0.010   0.002   HIS A 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 3382)
  covalent geometry    : angle       0.47276 ( 4597)
  hydrogen bonds       : bond        0.03455 (  185)
  hydrogen bonds       : angle       4.02570 (  532)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 53
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 53
  average time/residue: 0.6295
  time to fit residues: 34.3316
Evaluate side-chains
  54 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0070
   chunk 8 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 2 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 36 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.6398

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.114458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.090665 restraints weight = 9732.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.2888 rms_B_bonded: 2.44
r_work: 0.2759 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2646 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2646
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2666
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2666 r_free = 0.2666    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2666 r_free = 0.2666    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2666
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8864
moved from start:          0.1808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3382  Z= 0.089
  Angle     :  0.459   6.037   4597  Z= 0.234
  Chirality :  0.042   0.130    497
  Planarity :  0.004   0.046    585
  Dihedral  :  6.651  56.674    493
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 14.45 %
    Favored  : 85.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.89 (0.43), residues: 415
  helix:  2.46 (0.35), residues: 213
  sheet: -0.16 (0.67), residues: 72
  loop :  0.15 (0.60), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 118 
 TYR   0.007   0.001   TYR A 363 
 PHE   0.008   0.001   PHE A 381 
 TRP   0.008   0.001   TRP A  63 
 HIS   0.009   0.001   HIS A 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00188 ( 3382)
  covalent geometry    : angle       0.45903 ( 4597)
  hydrogen bonds       : bond        0.03077 (  185)
  hydrogen bonds       : angle       3.93324 (  532)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1602.28 seconds
wall clock time: 28 minutes 18.69 seconds (1698.69 seconds total)