Starting phenix.real_space_refine
on Fri Aug 22 15:15:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hru_34980/08_2025/8hru_34980.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hru_34980/08_2025/8hru_34980.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hru_34980/08_2025/8hru_34980.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hru_34980/08_2025/8hru_34980.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hru_34980/08_2025/8hru_34980.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hru_34980/08_2025/8hru_34980.cif"
  }
  resolution = 3.9
  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=   0.007 sd=   0.066
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      29      5.16       5
     C    3115      2.51       5
     N     806      2.21       5
     O     920      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4870
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4870
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569}
  Time building chain proxies: 1.46, per 1000 atoms: 0.30
  Number of scatterers: 4870
  At special positions: 0
  Unit cell: (85.324, 85.324, 71.96, 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      29     16.00
     O     920      8.00
     N     806      7.00
     C    3115      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.04

  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: 0.40
  Conformation dependent library (CDL) restraints added in 136.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1130

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 3 sheets defined
      64.5% alpha, 2.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 5.108A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LEU A  39 " --> pdb=" O   GLU A  35 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ALA A  46 " --> pdb=" O   GLN A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 80
      removed outlier: 3.730A  pdb=" N   GLN A  60 " --> pdb=" O   GLU A  56 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ASN A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ASN A  63 " --> pdb=" O   VAL A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 101
      removed outlier: 3.891A  pdb=" N   ALA A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.848A  pdb=" N   VAL A 107 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LEU A 108 " --> pdb=" O   SER A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 129
      removed outlier: 3.578A  pdb=" N   THR A 125 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 152
      removed outlier: 3.567A  pdb=" N   ILE A 151 " --> pdb=" O   GLY A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 167
      removed outlier: 3.585A  pdb=" N   ARG A 161 " --> pdb=" O   ASP A 157 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ALA A 164 " --> pdb=" O   GLU A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 172
      removed outlier: 3.752A  pdb=" N   GLU A 171 " --> pdb=" O   SER A 167 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   VAL A 172 " --> pdb=" O   TRP A 168 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 167 through 172'
    Processing helix  chain 'A' and resid 176 through 193
      removed outlier: 3.563A  pdb=" N   GLU A 189 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 204
    Processing helix  chain 'A' and resid 220 through 249
      removed outlier: 3.952A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   HIS A 228 " --> pdb=" O   GLU A 224 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLU A 231 " --> pdb=" O   GLU A 227 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   GLU A 232 " --> pdb=" O   HIS A 228 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
      removed outlier: 3.863A  pdb=" N   MET A 249 " --> pdb=" O   ARG A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 275 through 279
      removed outlier: 3.606A  pdb=" N   LEU A 278 " --> pdb=" O   TRP A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 301
      removed outlier: 4.057A  pdb=" N   VAL A 298 " --> pdb=" O   THR A 294 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   ASP A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.569A  pdb=" N   PHE A 314 " --> pdb=" O   GLU A 310 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   PHE A 315 " --> pdb=" O   ALA A 311 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.895A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLU A 329 " --> pdb=" O   GLN A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.607A  pdb=" N   HIS A 378 " --> pdb=" O   HIS A 374 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 401
      removed outlier: 3.838A  pdb=" N   HIS A 401 " --> pdb=" O   GLU A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 413
    Processing helix  chain 'A' and resid 414 through 421
      removed outlier: 3.709A  pdb=" N   ILE A 421 " --> pdb=" O   HIS A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 447
      removed outlier: 3.643A  pdb=" N   ASN A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 465
    Processing helix  chain 'A' and resid 474 through 482
      removed outlier: 4.260A  pdb=" N   MET A 480 " --> pdb=" O   LYS A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 4.955A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LEU A 520 " --> pdb=" O   TYR A 516 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   GLN A 524 " --> pdb=" O   LEU A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
      removed outlier: 3.679A  pdb=" N   LYS A 541 " --> pdb=" O   PRO A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.750A  pdb=" N   GLY A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LYS A 553 " --> pdb=" O   GLU A 549 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 564
      removed outlier: 4.154A  pdb=" N   GLU A 564 " --> pdb=" O   GLY A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 574
      removed outlier: 3.793A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 599
      removed outlier: 3.631A  pdb=" N   ASP A 597 " --> pdb=" O   THR A 593 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133
      removed outlier: 4.361A  pdb=" N   VAL A 132 " --> pdb=" O   LEU A 142 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LEU A 142 " --> pdb=" O   VAL A 132 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 5.845A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352
      removed outlier: 5.838A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)

    220 hydrogen bonds defined for protein.
    639 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: 0.54

  Time building geometry restraints manager: 0.54 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1578
        1.35 -     1.47: 1270
        1.47 -     1.59: 2107
        1.59 -     1.71: 2
        1.71 -     1.83: 50
  Bond restraints: 5007
  Sorted by residual:
  bond pdb=" CG  PRO A 289 "
       pdb=" CD  PRO A 289 "
    ideal  model  delta    sigma   weight residual
    1.503  1.272  0.231 3.40e-02 8.65e+02 4.61e+01
  bond pdb=" N   PRO A 289 "
       pdb=" CD  PRO A 289 "
    ideal  model  delta    sigma   weight residual
    1.473  1.535 -0.062 1.40e-02 5.10e+03 1.93e+01
  bond pdb=" CB  PRO A 289 "
       pdb=" CG  PRO A 289 "
    ideal  model  delta    sigma   weight residual
    1.492  1.686 -0.194 5.00e-02 4.00e+02 1.51e+01
  bond pdb=" CB  PRO A 258 "
       pdb=" CG  PRO A 258 "
    ideal  model  delta    sigma   weight residual
    1.492  1.611 -0.119 5.00e-02 4.00e+02 5.69e+00
  bond pdb=" N   PRO A 289 "
       pdb=" CA  PRO A 289 "
    ideal  model  delta    sigma   weight residual
    1.469  1.444  0.024 1.28e-02 6.10e+03 3.62e+00
  ... (remaining 5002 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.54: 6730
        3.54 -     7.07: 57
        7.07 -    10.61: 11
       10.61 -    14.15: 3
       14.15 -    17.69: 2
  Bond angle restraints: 6803
  Sorted by residual:
  angle pdb=" CA  PRO A 289 "
        pdb=" N   PRO A 289 "
        pdb=" CD  PRO A 289 "
      ideal   model   delta    sigma   weight residual
     112.00   94.31   17.69 1.40e+00 5.10e-01 1.60e+02
  angle pdb=" N   PRO A 289 "
        pdb=" CD  PRO A 289 "
        pdb=" CG  PRO A 289 "
      ideal   model   delta    sigma   weight residual
     103.20   88.77   14.43 1.50e+00 4.44e-01 9.25e+01
  angle pdb=" CA  PRO A 289 "
        pdb=" CB  PRO A 289 "
        pdb=" CG  PRO A 289 "
      ideal   model   delta    sigma   weight residual
     104.50   92.34   12.16 1.90e+00 2.77e-01 4.09e+01
  angle pdb=" CA  PRO A 258 "
        pdb=" N   PRO A 258 "
        pdb=" CD  PRO A 258 "
      ideal   model   delta    sigma   weight residual
     112.00  105.47    6.53 1.40e+00 5.10e-01 2.18e+01
  angle pdb=" CA  LYS A 353 "
        pdb=" CB  LYS A 353 "
        pdb=" CG  LYS A 353 "
      ideal   model   delta    sigma   weight residual
     114.10  121.64   -7.54 2.00e+00 2.50e-01 1.42e+01
  ... (remaining 6798 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.24: 2461
       16.24 -    32.48: 363
       32.48 -    48.71: 101
       48.71 -    64.95: 18
       64.95 -    81.19: 16
  Dihedral angle restraints: 2959
    sinusoidal: 1205
      harmonic: 1754
  Sorted by residual:
  dihedral pdb=" CB  CYS A 133 "
           pdb=" SG  CYS A 133 "
           pdb=" SG  CYS A 141 "
           pdb=" CB  CYS A 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  133.57  -40.57     1      1.00e+01 1.00e-02 2.31e+01
  dihedral pdb=" CA  CYS A 530 "
           pdb=" C   CYS A 530 "
           pdb=" N   GLN A 531 "
           pdb=" CA  GLN A 531 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.21   21.79     0      5.00e+00 4.00e-02 1.90e+01
  dihedral pdb=" CA  MET A 579 "
           pdb=" C   MET A 579 "
           pdb=" N   ASN A 580 "
           pdb=" CA  ASN A 580 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.91  -17.09     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 2956 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 538
       0.053 -    0.106: 144
       0.106 -    0.159: 23
       0.159 -    0.212: 3
       0.212 -    0.265: 2
  Chirality restraints: 710
  Sorted by residual:
  chirality pdb=" CB  ILE A 151 "
            pdb=" CA  ILE A 151 "
            pdb=" CG1 ILE A 151 "
            pdb=" CG2 ILE A 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" CB  THR A 118 "
            pdb=" CA  THR A 118 "
            pdb=" OG1 THR A 118 "
            pdb=" CG2 THR A 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CG  LEU A 391 "
            pdb=" CB  LEU A 391 "
            pdb=" CD1 LEU A 391 "
            pdb=" CD2 LEU A 391 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.35e-01
  ... (remaining 707 not shown)

  Planarity restraints: 881
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 288 "   -0.079 5.00e-02 4.00e+02   1.06e-01 1.79e+01
        pdb=" N   PRO A 289 "    0.182 5.00e-02 4.00e+02
        pdb=" CA  PRO A 289 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 289 "   -0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 499 "    0.055 5.00e-02 4.00e+02   8.22e-02 1.08e+01
        pdb=" N   PRO A 500 "   -0.142 5.00e-02 4.00e+02
        pdb=" CA  PRO A 500 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 500 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 257 "   -0.042 5.00e-02 4.00e+02   6.07e-02 5.89e+00
        pdb=" N   PRO A 258 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 258 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 258 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 878 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 62
        2.58 -     3.16: 4222
        3.16 -     3.74: 8348
        3.74 -     4.32: 10856
        4.32 -     4.90: 17365
  Nonbonded interactions: 40853
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 482 "
            pdb=" NH1 ARG A 482 "
     model   vdw
     2.000 3.120
  nonbonded pdb=" O   THR A  92 "
            pdb=" NE2 GLN A  96 "
     model   vdw
     2.165 3.120
  nonbonded pdb=" O   ALA A 403 "
            pdb=" NE2 GLN A 522 "
     model   vdw
     2.196 3.120
  nonbonded pdb=" O   THR A 118 "
            pdb=" OG1 THR A 122 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" NH2 ARG A 245 "
            pdb=" O   PHE A 603 "
     model   vdw
     2.226 3.120
  ... (remaining 40848 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.120
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.300
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7050
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   0.231   5010  Z= 0.228
  Angle     :  0.980  17.687   6809  Z= 0.547
  Chirality :  0.050   0.265    710
  Planarity :  0.007   0.106    881
  Dihedral  : 17.398  81.191   1820
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 21.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  : 26.57 %
    Favored  : 73.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -1.28 (0.35), residues: 595
  helix: -0.65 (0.28), residues: 334
  sheet: -2.31 (1.19), residues: 10
  loop : -0.87 (0.42), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 482 
 TYR   0.034   0.002   TYR A 521 
 PHE   0.024   0.002   PHE A 588 
 TRP   0.038   0.003   TRP A 302 
 HIS   0.006   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00601 ( 5007)
  covalent geometry    : angle       0.98005 ( 6803)
  SS BOND              : bond        0.00386 (    3)
  SS BOND              : angle       0.79530 (    6)
  hydrogen bonds       : bond        0.16411 (  220)
  hydrogen bonds       : angle       6.57013 (  639)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 96
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7125 (mmp) cc_final: 0.6647 (mmp)
REVERT: A  350 ASP cc_start: 0.8261 (t0) cc_final: 0.6556 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 97
  average time/residue: 0.0563
  time to fit residues: 7.2422
Evaluate side-chains
  87 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:   10.0000
   chunk 56 optimal weight:    9.9990
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 58 optimal weight:   20.0000
   overall best weight:    3.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN
** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 572 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.130408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.112217 restraints weight = 15846.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.115302 restraints weight = 10028.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.117504 restraints weight = 7103.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.118913 restraints weight = 5459.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.120080 restraints weight = 4522.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.4200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   5010  Z= 0.179
  Angle     :  0.723  10.747   6809  Z= 0.361
  Chirality :  0.045   0.155    710
  Planarity :  0.005   0.064    881
  Dihedral  :  4.956  20.130    642
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 18.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 21.44 %
    Favored  : 74.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.93 (0.35), residues: 595
  helix: -0.38 (0.28), residues: 345
  sheet: -2.39 (1.37), residues: 10
  loop : -0.68 (0.44), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 482 
 TYR   0.020   0.002   TYR A 521 
 PHE   0.019   0.002   PHE A 525 
 TRP   0.021   0.002   TRP A 477 
 HIS   0.005   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 5007)
  covalent geometry    : angle       0.72237 ( 6803)
  SS BOND              : bond        0.00464 (    3)
  SS BOND              : angle       1.01621 (    6)
  hydrogen bonds       : bond        0.04190 (  220)
  hydrogen bonds       : angle       5.08355 (  639)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 TYR cc_start: 0.8095 (m-80) cc_final: 0.7787 (m-80)
REVERT: A  481 LYS cc_start: 0.6157 (mttt) cc_final: 0.5480 (mttt)
  outliers start: 19
  outliers final: 10
  residues processed: 110
  average time/residue: 0.0557
  time to fit residues: 8.2126
Evaluate side-chains
  96 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   38 ASP
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  382 ASP
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  584 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 33 optimal weight:   10.0000
   chunk 2 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0970
   chunk 5 optimal weight:    5.9990
   chunk 50 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    2.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN
** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 572 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.131287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.112473 restraints weight = 15682.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.115837 restraints weight = 9650.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.118225 restraints weight = 6664.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.119761 restraints weight = 5017.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.120979 restraints weight = 4082.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.4181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7079
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5010  Z= 0.133
  Angle     :  0.675  13.023   6809  Z= 0.331
  Chirality :  0.044   0.169    710
  Planarity :  0.004   0.049    881
  Dihedral  :  4.708  20.086    642
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 15.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 22.20 %
    Favored  : 74.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.63 (0.36), residues: 595
  helix: -0.14 (0.29), residues: 342
  sheet: -1.95 (1.62), residues: 10
  loop : -0.54 (0.45), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 482 
 TYR   0.038   0.002   TYR A 521 
 PHE   0.013   0.001   PHE A 525 
 TRP   0.027   0.002   TRP A 594 
 HIS   0.003   0.001   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 5007)
  covalent geometry    : angle       0.67447 ( 6803)
  SS BOND              : bond        0.00360 (    3)
  SS BOND              : angle       0.91053 (    6)
  hydrogen bonds       : bond        0.03884 (  220)
  hydrogen bonds       : angle       4.85009 (  639)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 TRP cc_start: 0.7698 (t-100) cc_final: 0.6215 (t-100)
REVERT: A  237 TYR cc_start: 0.6883 (t80) cc_final: 0.6117 (t80)
REVERT: A  255 TYR cc_start: 0.8149 (m-80) cc_final: 0.7873 (m-80)
REVERT: A  297 MET cc_start: 0.8605 (mpp) cc_final: 0.8375 (mpp)
REVERT: A  446 ILE cc_start: 0.7022 (tp) cc_final: 0.6713 (tp)
REVERT: A  481 LYS cc_start: 0.5988 (mttt) cc_final: 0.5657 (mttt)
  outliers start: 19
  outliers final: 11
  residues processed: 113
  average time/residue: 0.0498
  time to fit residues: 7.7002
Evaluate side-chains
  98 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ASP
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  382 ASP
Chi-restraints excluded: chain A residue  472 GLN
Chi-restraints excluded: chain A residue  509 ASP
Chi-restraints excluded: chain A residue  584 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 50 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 47 optimal weight:   10.0000
   chunk 45 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 40 optimal weight:    7.9990
   chunk 33 optimal weight:   20.0000
   chunk 22 optimal weight:    5.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 572 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.130457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.111820 restraints weight = 15194.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.115075 restraints weight = 9231.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.117584 restraints weight = 6358.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.119135 restraints weight = 4749.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.120348 restraints weight = 3818.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.4174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7085
moved from start:          0.2543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5010  Z= 0.133
  Angle     :  0.678  12.775   6809  Z= 0.331
  Chirality :  0.044   0.171    710
  Planarity :  0.004   0.047    881
  Dihedral  :  4.697  19.637    642
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 16.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 22.58 %
    Favored  : 74.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.42 (0.36), residues: 595
  helix: -0.06 (0.28), residues: 347
  sheet: -1.81 (1.70), residues: 10
  loop : -0.33 (0.45), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 482 
 TYR   0.027   0.002   TYR A 521 
 PHE   0.011   0.002   PHE A 525 
 TRP   0.040   0.002   TRP A 594 
 HIS   0.005   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 5007)
  covalent geometry    : angle       0.67714 ( 6803)
  SS BOND              : bond        0.00390 (    3)
  SS BOND              : angle       1.45461 (    6)
  hydrogen bonds       : bond        0.03768 (  220)
  hydrogen bonds       : angle       4.74278 (  639)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 ASP cc_start: 0.8683 (m-30) cc_final: 0.8111 (p0)
REVERT: A  168 TRP cc_start: 0.7930 (t-100) cc_final: 0.6603 (t-100)
REVERT: A  237 TYR cc_start: 0.6926 (t80) cc_final: 0.6291 (t80)
REVERT: A  255 TYR cc_start: 0.8138 (m-80) cc_final: 0.7884 (m-80)
REVERT: A  579 MET cc_start: 0.7034 (ppp) cc_final: 0.6819 (ppp)
REVERT: A  601 ASN cc_start: 0.9030 (p0) cc_final: 0.8411 (p0)
  outliers start: 18
  outliers final: 14
  residues processed: 109
  average time/residue: 0.0596
  time to fit residues: 8.8242
Evaluate side-chains
  108 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   38 ASP
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  382 ASP
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain A residue  472 GLN
Chi-restraints excluded: chain A residue  509 ASP
Chi-restraints excluded: chain A residue  584 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 53 optimal weight:    8.9990
   chunk 48 optimal weight:   10.0000
   chunk 6 optimal weight:   20.0000
   chunk 17 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0030
   chunk 41 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   chunk 15 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    1.3994

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

Flipped N/Q/H residues before XYZ refinement:
** A 522 GLN ** 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 = 0.4362 r_free = 0.4362 target = 0.132996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.113996 restraints weight = 15473.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.117387 restraints weight = 9497.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.119863 restraints weight = 6573.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.121486 restraints weight = 4953.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.122724 restraints weight = 4003.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.4205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
moved from start:          0.2911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5010  Z= 0.115
  Angle     :  0.675  11.676   6809  Z= 0.325
  Chirality :  0.044   0.173    710
  Planarity :  0.004   0.045    881
  Dihedral  :  4.504  19.051    642
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 23.72 %
    Favored  : 72.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.23 (0.36), residues: 595
  helix:  0.13 (0.29), residues: 343
  sheet: -2.04 (1.58), residues: 10
  loop : -0.27 (0.45), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 482 
 TYR   0.036   0.001   TYR A 521 
 PHE   0.010   0.001   PHE A  28 
 TRP   0.043   0.002   TRP A 271 
 HIS   0.006   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 5007)
  covalent geometry    : angle       0.67515 ( 6803)
  SS BOND              : bond        0.00245 (    3)
  SS BOND              : angle       0.96990 (    6)
  hydrogen bonds       : bond        0.03710 (  220)
  hydrogen bonds       : angle       4.65218 (  639)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 ASP cc_start: 0.8671 (m-30) cc_final: 0.8106 (p0)
REVERT: A  168 TRP cc_start: 0.7884 (t-100) cc_final: 0.7470 (t-100)
REVERT: A  237 TYR cc_start: 0.6995 (t80) cc_final: 0.6502 (t80)
REVERT: A  255 TYR cc_start: 0.8106 (m-80) cc_final: 0.7861 (m-80)
REVERT: A  481 LYS cc_start: 0.6891 (mttt) cc_final: 0.6348 (ptpt)
REVERT: A  525 PHE cc_start: 0.7819 (m-10) cc_final: 0.7004 (m-80)
REVERT: A  541 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7828 (ptpt)
REVERT: A  579 MET cc_start: 0.7168 (ppp) cc_final: 0.6878 (ppp)
REVERT: A  601 ASN cc_start: 0.8970 (p0) cc_final: 0.8361 (p0)
  outliers start: 22
  outliers final: 15
  residues processed: 118
  average time/residue: 0.0591
  time to fit residues: 9.4219
Evaluate side-chains
  108 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  382 ASP
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain A residue  472 GLN
Chi-restraints excluded: chain A residue  509 ASP
Chi-restraints excluded: chain A residue  541 LYS
Chi-restraints excluded: chain A residue  584 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 57 optimal weight:   10.0000
   chunk 35 optimal weight:    4.9990
   chunk 11 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   chunk 55 optimal weight:    2.9990
   chunk 47 optimal weight:   30.0000
   chunk 20 optimal weight:    1.9990
   chunk 34 optimal weight:   30.0000
   chunk 21 optimal weight:    3.9990
   chunk 24 optimal weight:   10.0000
   chunk 26 optimal weight:    4.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 522 GLN ** 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 = 0.4300 r_free = 0.4300 target = 0.128000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.108815 restraints weight = 15953.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.112178 restraints weight = 9714.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.114531 restraints weight = 6722.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.116278 restraints weight = 5085.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.117464 restraints weight = 4084.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.4136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7154
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5010  Z= 0.173
  Angle     :  0.750  10.288   6809  Z= 0.370
  Chirality :  0.047   0.188    710
  Planarity :  0.004   0.043    881
  Dihedral  :  4.726  17.511    642
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 19.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 23.53 %
    Favored  : 72.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.27 (0.36), residues: 595
  helix:  0.09 (0.29), residues: 343
  sheet: -2.18 (1.54), residues: 10
  loop : -0.27 (0.45), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 482 
 TYR   0.028   0.002   TYR A 521 
 PHE   0.029   0.002   PHE A 588 
 TRP   0.054   0.003   TRP A 271 
 HIS   0.005   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 5007)
  covalent geometry    : angle       0.74899 ( 6803)
  SS BOND              : bond        0.00413 (    3)
  SS BOND              : angle       1.19721 (    6)
  hydrogen bonds       : bond        0.03911 (  220)
  hydrogen bonds       : angle       4.94461 (  639)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 ASP cc_start: 0.8716 (m-30) cc_final: 0.8128 (p0)
REVERT: A  123 MET cc_start: 0.8369 (mmp) cc_final: 0.8119 (mmt)
REVERT: A  237 TYR cc_start: 0.7238 (t80) cc_final: 0.6705 (t80)
REVERT: A  255 TYR cc_start: 0.8182 (m-80) cc_final: 0.7966 (m-80)
REVERT: A  271 TRP cc_start: 0.6341 (m100) cc_final: 0.6000 (m-90)
REVERT: A  297 MET cc_start: 0.8535 (mpp) cc_final: 0.8319 (mpp)
REVERT: A  481 LYS cc_start: 0.6923 (mttt) cc_final: 0.6248 (ptpt)
REVERT: A  525 PHE cc_start: 0.7752 (m-10) cc_final: 0.7134 (m-80)
  outliers start: 21
  outliers final: 13
  residues processed: 104
  average time/residue: 0.0639
  time to fit residues: 8.8954
Evaluate side-chains
  99 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ASP
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  382 ASP
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain A residue  584 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 50 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   chunk 31 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 51 optimal weight:    9.9990
   chunk 12 optimal weight:    6.9990
   chunk 23 optimal weight:    9.9990
   chunk 7 optimal weight:   10.0000
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 522 GLN ** 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 = 0.4278 r_free = 0.4278 target = 0.126321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.107763 restraints weight = 15958.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.111087 restraints weight = 9731.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.113380 restraints weight = 6730.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.114880 restraints weight = 5078.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.116018 restraints weight = 4123.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.4117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7182
moved from start:          0.3590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5010  Z= 0.178
  Angle     :  0.790  13.048   6809  Z= 0.382
  Chirality :  0.047   0.191    710
  Planarity :  0.004   0.042    881
  Dihedral  :  4.916  19.762    642
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 19.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 25.43 %
    Favored  : 70.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.20 (0.37), residues: 595
  helix:  0.17 (0.29), residues: 336
  sheet: -2.40 (1.50), residues: 10
  loop : -0.26 (0.45), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 482 
 TYR   0.027   0.002   TYR A 521 
 PHE   0.021   0.002   PHE A 588 
 TRP   0.036   0.003   TRP A 168 
 HIS   0.005   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 5007)
  covalent geometry    : angle       0.78899 ( 6803)
  SS BOND              : bond        0.00430 (    3)
  SS BOND              : angle       1.24950 (    6)
  hydrogen bonds       : bond        0.03892 (  220)
  hydrogen bonds       : angle       4.92877 (  639)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 ASP cc_start: 0.8662 (m-30) cc_final: 0.8093 (p0)
REVERT: A  237 TYR cc_start: 0.7380 (t80) cc_final: 0.6725 (t80)
REVERT: A  255 TYR cc_start: 0.8063 (m-80) cc_final: 0.7856 (m-80)
REVERT: A  390 PHE cc_start: 0.7351 (t80) cc_final: 0.6457 (t80)
REVERT: A  525 PHE cc_start: 0.7761 (m-10) cc_final: 0.7209 (m-80)
  outliers start: 20
  outliers final: 17
  residues processed: 103
  average time/residue: 0.0521
  time to fit residues: 7.3694
Evaluate side-chains
  102 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ASP
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  381 TYR
Chi-restraints excluded: chain A residue  382 ASP
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain A residue  502 SER
Chi-restraints excluded: chain A residue  509 ASP
Chi-restraints excluded: chain A residue  584 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 21 optimal weight:    7.9990
   chunk 41 optimal weight:    5.9990
   chunk 56 optimal weight:   10.0000
   chunk 19 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 2 optimal weight:    9.9990
   chunk 23 optimal weight:    8.9990
   chunk 38 optimal weight:   10.0000
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 277 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 = 0.4286 r_free = 0.4286 target = 0.126879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.108018 restraints weight = 15863.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.111411 restraints weight = 9595.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.113844 restraints weight = 6599.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.115567 restraints weight = 4938.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.116623 restraints weight = 3941.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.4125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.3858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5010  Z= 0.160
  Angle     :  0.779  11.806   6809  Z= 0.375
  Chirality :  0.047   0.202    710
  Planarity :  0.004   0.043    881
  Dihedral  :  4.839  18.945    642
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 18.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 25.43 %
    Favored  : 70.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.24 (0.37), residues: 595
  helix:  0.18 (0.29), residues: 337
  sheet: -2.46 (1.43), residues: 10
  loop : -0.34 (0.45), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 482 
 TYR   0.033   0.002   TYR A 521 
 PHE   0.017   0.002   PHE A 588 
 TRP   0.048   0.003   TRP A 594 
 HIS   0.004   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 5007)
  covalent geometry    : angle       0.77856 ( 6803)
  SS BOND              : bond        0.00397 (    3)
  SS BOND              : angle       1.12660 (    6)
  hydrogen bonds       : bond        0.03811 (  220)
  hydrogen bonds       : angle       4.93176 (  639)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 ASP cc_start: 0.8724 (m-30) cc_final: 0.8158 (p0)
REVERT: A  190 MET cc_start: 0.6958 (tpt) cc_final: 0.6738 (tpt)
REVERT: A  255 TYR cc_start: 0.8086 (m-80) cc_final: 0.7877 (m-80)
REVERT: A  481 LYS cc_start: 0.7105 (mttt) cc_final: 0.6494 (ptpt)
REVERT: A  525 PHE cc_start: 0.7817 (m-10) cc_final: 0.7234 (m-80)
  outliers start: 22
  outliers final: 16
  residues processed: 101
  average time/residue: 0.0520
  time to fit residues: 7.0225
Evaluate side-chains
  102 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ASP
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  381 TYR
Chi-restraints excluded: chain A residue  382 ASP
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain A residue  509 ASP
Chi-restraints excluded: chain A residue  584 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 22 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 21 optimal weight:    9.9990
   chunk 54 optimal weight:    0.0030
   chunk 57 optimal weight:    4.9990
   chunk 39 optimal weight:    8.9990
   chunk 9 optimal weight:   10.0000
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.9998

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

Flipped N/Q/H residues before XYZ refinement:
A  53 ASN
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.129761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.110735 restraints weight = 15668.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.114150 restraints weight = 9599.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.116635 restraints weight = 6625.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.118209 restraints weight = 4989.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.119510 restraints weight = 4033.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.4168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7131
moved from start:          0.4039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5010  Z= 0.136
  Angle     :  0.761  12.669   6809  Z= 0.368
  Chirality :  0.046   0.186    710
  Planarity :  0.004   0.056    881
  Dihedral  :  4.747  18.515    642
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 17.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 27.51 %
    Favored  : 69.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.19 (0.37), residues: 595
  helix:  0.22 (0.29), residues: 335
  sheet: -2.23 (1.40), residues: 10
  loop : -0.35 (0.45), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 482 
 TYR   0.033   0.002   TYR A 521 
 PHE   0.015   0.002   PHE A 588 
 TRP   0.046   0.002   TRP A 168 
 HIS   0.003   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 5007)
  covalent geometry    : angle       0.76131 ( 6803)
  SS BOND              : bond        0.00271 (    3)
  SS BOND              : angle       0.89025 (    6)
  hydrogen bonds       : bond        0.03778 (  220)
  hydrogen bonds       : angle       4.81869 (  639)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 LYS cc_start: 0.9217 (mttt) cc_final: 0.8906 (mmtt)
REVERT: A   67 ASP cc_start: 0.8723 (m-30) cc_final: 0.8166 (p0)
REVERT: A  228 HIS cc_start: 0.8826 (t70) cc_final: 0.7990 (t70)
REVERT: A  237 TYR cc_start: 0.7430 (t80) cc_final: 0.6676 (t80)
REVERT: A  243 TYR cc_start: 0.8272 (t80) cc_final: 0.7915 (t80)
REVERT: A  255 TYR cc_start: 0.8093 (m-80) cc_final: 0.7888 (m-80)
REVERT: A  390 PHE cc_start: 0.7526 (t80) cc_final: 0.6431 (t80)
REVERT: A  481 LYS cc_start: 0.6848 (mttt) cc_final: 0.6647 (pttt)
REVERT: A  525 PHE cc_start: 0.7787 (m-10) cc_final: 0.7210 (m-80)
REVERT: A  595 LEU cc_start: 0.8500 (mm) cc_final: 0.8068 (mm)
  outliers start: 17
  outliers final: 14
  residues processed: 98
  average time/residue: 0.0510
  time to fit residues: 6.8012
Evaluate side-chains
  99 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ASP
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  382 ASP
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain A residue  584 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 19 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   chunk 1 optimal weight:    7.9990
   chunk 45 optimal weight:    7.9990
   chunk 44 optimal weight:    0.0980
   chunk 54 optimal weight:    0.0570
   chunk 17 optimal weight:    6.9990
   chunk 39 optimal weight:    7.9990
   chunk 36 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    2.5902

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

Flipped N/Q/H residues before XYZ refinement:
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 277 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 = 0.4297 r_free = 0.4297 target = 0.128231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.108986 restraints weight = 16251.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.112276 restraints weight = 10056.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.114662 restraints weight = 7016.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.115996 restraints weight = 5324.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.117432 restraints weight = 4429.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.4141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.4241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5010  Z= 0.149
  Angle     :  0.789  13.619   6809  Z= 0.381
  Chirality :  0.047   0.185    710
  Planarity :  0.004   0.043    881
  Dihedral  :  4.755  17.831    642
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 17.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 28.27 %
    Favored  : 69.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.21 (0.36), residues: 595
  helix:  0.18 (0.29), residues: 335
  sheet: -2.17 (1.34), residues: 10
  loop : -0.32 (0.45), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 460 
 TYR   0.032   0.002   TYR A 521 
 PHE   0.012   0.001   PHE A 327 
 TRP   0.049   0.002   TRP A 168 
 HIS   0.004   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 5007)
  covalent geometry    : angle       0.78927 ( 6803)
  SS BOND              : bond        0.00336 (    3)
  SS BOND              : angle       0.96610 (    6)
  hydrogen bonds       : bond        0.03834 (  220)
  hydrogen bonds       : angle       4.93382 (  639)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 LYS cc_start: 0.9225 (mttt) cc_final: 0.8925 (mmtt)
REVERT: A   62 MET cc_start: 0.8763 (ptm) cc_final: 0.8409 (ptt)
REVERT: A   67 ASP cc_start: 0.8685 (m-30) cc_final: 0.8135 (p0)
REVERT: A  228 HIS cc_start: 0.8820 (t70) cc_final: 0.7938 (t70)
REVERT: A  243 TYR cc_start: 0.8309 (t80) cc_final: 0.7950 (t80)
REVERT: A  255 TYR cc_start: 0.8100 (m-80) cc_final: 0.7875 (m-80)
REVERT: A  481 LYS cc_start: 0.6943 (mttt) cc_final: 0.6710 (pttt)
REVERT: A  525 PHE cc_start: 0.7745 (m-10) cc_final: 0.7203 (m-80)
REVERT: A  595 LEU cc_start: 0.8509 (mm) cc_final: 0.8085 (mm)
  outliers start: 14
  outliers final: 13
  residues processed: 100
  average time/residue: 0.0567
  time to fit residues: 7.5347
Evaluate side-chains
  100 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ASP
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  382 ASP
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain A residue  584 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 52 optimal weight:    0.3980
   chunk 22 optimal weight:    4.9990
   chunk 51 optimal weight:    7.9990
   chunk 31 optimal weight:    9.9990
   chunk 44 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 20 optimal weight:    4.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 277 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 = 0.4363 r_free = 0.4363 target = 0.133102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.113823 restraints weight = 15820.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.117362 restraints weight = 9739.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.119797 restraints weight = 6747.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.121233 restraints weight = 5096.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.122697 restraints weight = 4189.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.4206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7092
moved from start:          0.4438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5010  Z= 0.130
  Angle     :  0.784  13.703   6809  Z= 0.380
  Chirality :  0.046   0.181    710
  Planarity :  0.004   0.043    881
  Dihedral  :  4.709  18.151    642
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 15.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 27.89 %
    Favored  : 69.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.31 (0.36), residues: 595
  helix:  0.11 (0.29), residues: 338
  sheet: -1.89 (1.37), residues: 10
  loop : -0.39 (0.44), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 482 
 TYR   0.033   0.002   TYR A 521 
 PHE   0.043   0.002   PHE A 588 
 TRP   0.045   0.003   TRP A 168 
 HIS   0.003   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 5007)
  covalent geometry    : angle       0.78354 ( 6803)
  SS BOND              : bond        0.00229 (    3)
  SS BOND              : angle       0.91830 (    6)
  hydrogen bonds       : bond        0.03873 (  220)
  hydrogen bonds       : angle       4.95023 (  639)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 805.34 seconds
wall clock time: 14 minutes 37.65 seconds (877.65 seconds total)