Starting phenix.real_space_refine
on Wed Jul 23 10:59:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ju0_36658/07_2025/8ju0_36658.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ju0_36658/07_2025/8ju0_36658.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ju0_36658/07_2025/8ju0_36658.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ju0_36658/07_2025/8ju0_36658.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ju0_36658/07_2025/8ju0_36658.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ju0_36658/07_2025/8ju0_36658.cif"
  }
  resolution = 2.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.003 sd=   0.171
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    2117      2.51       5
     N     519      2.21       5
     O     532      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 3199
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3170
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 431, 3170
          Classifications: {'peptide': 431}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'PTRANS': 20, 'TRANS': 410}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 162
          Unresolved non-hydrogen angles: 209
          Unresolved non-hydrogen dihedrals: 124
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 109
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'SNL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.62, per 1000 atoms: 0.82
  Number of scatterers: 3199
  At special positions: 0
  Unit cell: (58.455, 90.93, 68.1975, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      31     16.00
     O     532      8.00
     N     519      7.00
     C    2117      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.86
  Conformation dependent library (CDL) restraints added in 399.8 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 0 sheets defined
      82.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 37
      removed outlier: 3.573A  pdb=" N   LEU A  27 " --> pdb=" O   LEU A  23 " (cutoff:3.500A)
      Proline residue:  A  34  - end of helix
    Processing helix  chain 'A' and resid 38 through 43
    Processing helix  chain 'A' and resid 54 through 62
    Processing helix  chain 'A' and resid 65 through 73
    Processing helix  chain 'A' and resid 83 through 88
    Processing helix  chain 'A' and resid 104 through 110
      removed outlier: 3.683A  pdb=" N   SER A 108 " --> pdb=" O   ASP A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 116
    Processing helix  chain 'A' and resid 133 through 139
    Processing helix  chain 'A' and resid 141 through 143
      No H-bonds generated for 'chain 'A' and resid 141 through 143'
    Processing helix  chain 'A' and resid 144 through 194
      removed outlier: 4.073A  pdb=" N   LEU A 148 " --> pdb=" O   ASP A 144 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ASP A 149 " --> pdb=" O   SER A 145 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   GLN A 152 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LEU A 155 " --> pdb=" O   PHE A 151 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   GLY A 167 " --> pdb=" O   SER A 163 " (cutoff:3.500A)
      removed outlier: 4.909A  pdb=" N   ASP A 171 " --> pdb=" O   GLY A 167 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   ARG A 172 " --> pdb=" O   TYR A 168 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   PHE A 173 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   ARG A 175 " --> pdb=" O   ASP A 171 " (cutoff:3.500A)
      removed outlier: 9.416A  pdb=" N   LYS A 176 " --> pdb=" O   ARG A 172 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LEU A 177 " --> pdb=" O   PHE A 173 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   CYS A 178 " --> pdb=" O   GLY A 174 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   LEU A 179 " --> pdb=" O   ARG A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 227
      removed outlier: 3.942A  pdb=" N   LYS A 214 " --> pdb=" O   GLY A 210 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   GLY A 215 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 258
    Processing helix  chain 'A' and resid 260 through 275
      Proline residue:  A 271  - end of helix
    Processing helix  chain 'A' and resid 334 through 338
      removed outlier: 3.835A  pdb=" N   LEU A 337 " --> pdb=" O   PHE A 334 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   PHE A 338 " --> pdb=" O   ALA A 335 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 334 through 338'
    Processing helix  chain 'A' and resid 340 through 372
    Processing helix  chain 'A' and resid 374 through 400
      Proline residue:  A 388  - end of helix
      removed outlier: 4.174A  pdb=" N   PHE A 391 " --> pdb=" O   ILE A 387 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASP A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ARG A 399 " --> pdb=" O   ILE A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 423
      removed outlier: 3.674A  pdb=" N   ILE A 421 " --> pdb=" O   CYS A 417 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   PHE A 422 " --> pdb=" O   LEU A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 456
      removed outlier: 3.623A  pdb=" N   LEU A 451 " --> pdb=" O   GLN A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 488
      Proline residue:  A 481  - end of helix
      removed outlier: 4.396A  pdb=" N   ARG A 486 " --> pdb=" O   PHE A 482 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ARG A 488 " --> pdb=" O   VAL A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 510
    Processing helix  chain 'A' and resid 511 through 513
      No H-bonds generated for 'chain 'A' and resid 511 through 513'

    235 hydrogen bonds defined for protein.
    699 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.86

  Time building geometry restraints manager: 0.99 seconds

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

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

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

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

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

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

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

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.760
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6925
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.213   3286  Z= 0.312
  Angle     :  0.811  17.392   4500  Z= 0.350
  Chirality :  0.063   0.904    536
  Planarity :  0.004   0.050    551
  Dihedral  : 13.409  71.290   1153
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.42), residues: 425
  helix:  1.50 (0.30), residues: 313
  sheet:  None (None), residues: 0
  loop : -0.12 (0.62), residues: 112

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

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

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

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.296 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.5568
  time to fit residues: 25.5168
Evaluate side-chains
  33 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 20 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.7580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.201537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.158895 restraints weight = 2969.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3740 rms_B_bonded: 1.72
r_work: 0.3513 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3360 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6950
moved from start:          0.1060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3286  Z= 0.169
  Angle     :  0.562   5.427   4500  Z= 0.283
  Chirality :  0.038   0.130    536
  Planarity :  0.004   0.047    551
  Dihedral  :  5.238  25.094    529
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 10.58 %
    Favored  : 87.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.42), residues: 425
  helix:  1.69 (0.30), residues: 313
  sheet:  None (None), residues: 0
  loop : -0.12 (0.64), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  64 
 HIS   0.003   0.001   HIS A 260 
 PHE   0.010   0.001   PHE A  44 
 TYR   0.015   0.001   TYR A 240 
 ARG   0.003   0.000   ARG A 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04847 (  235)
  hydrogen bonds       : angle       4.64854 (  699)
  SS BOND              : bond        0.00485 (    3)
  SS BOND              : angle       0.90830 (    6)
  covalent geometry    : bond        0.00396 ( 3283)
  covalent geometry    : angle       0.56118 ( 4494)

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

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A  447 GLN cc_start: 0.7435 (mm110) cc_final: 0.6986 (mm110)
REVERT: A  448 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8200 (mpp)
  outliers start: 7
  outliers final: 3
  residues processed: 36
  average time/residue: 0.7478
  time to fit residues: 28.3635
Evaluate side-chains
  35 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain A residue  472 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 38 optimal weight:    4.9990
   chunk 13 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.6980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.200561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.159749 restraints weight = 2951.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3746 rms_B_bonded: 1.64
r_work: 0.3520 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3370 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7001
moved from start:          0.1220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3286  Z= 0.156
  Angle     :  0.538   6.051   4500  Z= 0.272
  Chirality :  0.038   0.198    536
  Planarity :  0.004   0.045    551
  Dihedral  :  5.015  27.070    529
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.82 %
    Favored  : 85.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.42), residues: 425
  helix:  1.61 (0.30), residues: 319
  sheet:  None (None), residues: 0
  loop :  0.00 (0.67), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  64 
 HIS   0.002   0.001   HIS A  49 
 PHE   0.011   0.001   PHE A  44 
 TYR   0.013   0.001   TYR A 240 
 ARG   0.003   0.000   ARG A 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04591 (  235)
  hydrogen bonds       : angle       4.55652 (  699)
  SS BOND              : bond        0.00482 (    3)
  SS BOND              : angle       0.91478 (    6)
  covalent geometry    : bond        0.00365 ( 3283)
  covalent geometry    : angle       0.53707 ( 4494)

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

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.280 
Fit side-chains
REVERT: A  144 ASP cc_start: 0.7788 (m-30) cc_final: 0.7430 (m-30)
REVERT: A  200 MET cc_start: 0.7589 (mmm) cc_final: 0.7245 (tpp)
REVERT: A  420 MET cc_start: 0.8002 (mtp) cc_final: 0.7285 (mtt)
REVERT: A  447 GLN cc_start: 0.7412 (mm110) cc_final: 0.7190 (mm110)
  outliers start: 5
  outliers final: 2
  residues processed: 35
  average time/residue: 0.8034
  time to fit residues: 29.5899
Evaluate side-chains
  34 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 32
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  472 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.6580

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.200430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.159335 restraints weight = 3014.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3745 rms_B_bonded: 1.67
r_work: 0.3517 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3367 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7008
moved from start:          0.1346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3286  Z= 0.149
  Angle     :  0.527   6.293   4500  Z= 0.267
  Chirality :  0.038   0.162    536
  Planarity :  0.004   0.044    551
  Dihedral  :  4.773  25.065    529
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.42 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.43), residues: 425
  helix:  1.66 (0.30), residues: 319
  sheet:  None (None), residues: 0
  loop :  0.04 (0.66), residues: 106

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04495 (  235)
  hydrogen bonds       : angle       4.49038 (  699)
  SS BOND              : bond        0.00472 (    3)
  SS BOND              : angle       0.89213 (    6)
  covalent geometry    : bond        0.00348 ( 3283)
  covalent geometry    : angle       0.52593 ( 4494)

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

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 34
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A  144 ASP cc_start: 0.7792 (m-30) cc_final: 0.7439 (m-30)
REVERT: A  200 MET cc_start: 0.7579 (mmm) cc_final: 0.7225 (tpp)
REVERT: A  448 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8107 (mpp)
  outliers start: 7
  outliers final: 4
  residues processed: 38
  average time/residue: 0.7160
  time to fit residues: 28.7694
Evaluate side-chains
  37 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.7380

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.198523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.157275 restraints weight = 2946.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 1.65
r_work: 0.3509 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3355 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6911
moved from start:          0.1449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3286  Z= 0.158
  Angle     :  0.536   5.799   4500  Z= 0.271
  Chirality :  0.038   0.140    536
  Planarity :  0.004   0.043    551
  Dihedral  :  4.805  24.066    529
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 14.74 %
    Favored  : 82.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.42), residues: 425
  helix:  1.61 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.12 (0.66), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  64 
 HIS   0.003   0.001   HIS A  49 
 PHE   0.011   0.001   PHE A  44 
 TYR   0.011   0.001   TYR A 352 
 ARG   0.002   0.000   ARG A 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04543 (  235)
  hydrogen bonds       : angle       4.52701 (  699)
  SS BOND              : bond        0.00496 (    3)
  SS BOND              : angle       0.91560 (    6)
  covalent geometry    : bond        0.00371 ( 3283)
  covalent geometry    : angle       0.53500 ( 4494)

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

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 35
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A  144 ASP cc_start: 0.7722 (m-30) cc_final: 0.7373 (m-30)
REVERT: A  420 MET cc_start: 0.7938 (mtp) cc_final: 0.7241 (mtt)
REVERT: A  447 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7215 (mm110)
  outliers start: 9
  outliers final: 5
  residues processed: 40
  average time/residue: 0.6973
  time to fit residues: 29.4167
Evaluate side-chains
  39 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 40 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0670
   chunk 33 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 0 optimal weight:    8.9990
   chunk 8 optimal weight:    0.2980
   chunk 39 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.4718

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.201851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.161378 restraints weight = 3070.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3763 rms_B_bonded: 1.67
r_work: 0.3537 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3385 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6980
moved from start:          0.1463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3286  Z= 0.130
  Angle     :  0.509   6.265   4500  Z= 0.258
  Chirality :  0.037   0.133    536
  Planarity :  0.004   0.042    551
  Dihedral  :  4.607  24.472    529
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 14.74 %
    Favored  : 82.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.42), residues: 425
  helix:  1.72 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.11 (0.65), residues: 104

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04253 (  235)
  hydrogen bonds       : angle       4.35625 (  699)
  SS BOND              : bond        0.00392 (    3)
  SS BOND              : angle       0.71516 (    6)
  covalent geometry    : bond        0.00290 ( 3283)
  covalent geometry    : angle       0.50841 ( 4494)

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

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 34
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A  144 ASP cc_start: 0.7754 (m-30) cc_final: 0.7416 (m-30)
REVERT: A  435 MET cc_start: 0.7548 (tpp) cc_final: 0.7298 (tpp)
REVERT: A  447 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7236 (mm110)
  outliers start: 9
  outliers final: 6
  residues processed: 39
  average time/residue: 0.6751
  time to fit residues: 27.8180
Evaluate side-chains
  40 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 34
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  443 THR
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 38 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 18 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0670
   overall best weight:    0.5718

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.201118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.160887 restraints weight = 2967.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 1.63
r_work: 0.3533 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3382 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6936
moved from start:          0.1530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3286  Z= 0.139
  Angle     :  0.516   6.719   4500  Z= 0.261
  Chirality :  0.038   0.125    536
  Planarity :  0.004   0.041    551
  Dihedral  :  4.593  25.138    529
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 14.42 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.42), residues: 425
  helix:  1.71 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.11 (0.66), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 354 
 HIS   0.003   0.001   HIS A  49 
 PHE   0.010   0.001   PHE A  44 
 TYR   0.011   0.001   TYR A 352 
 ARG   0.002   0.000   ARG A 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04346 (  235)
  hydrogen bonds       : angle       4.40582 (  699)
  SS BOND              : bond        0.00430 (    3)
  SS BOND              : angle       0.77465 (    6)
  covalent geometry    : bond        0.00317 ( 3283)
  covalent geometry    : angle       0.51569 ( 4494)

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

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 33
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A  144 ASP cc_start: 0.7731 (m-30) cc_final: 0.7379 (m-30)
REVERT: A  420 MET cc_start: 0.7952 (mtp) cc_final: 0.7271 (mtt)
REVERT: A  435 MET cc_start: 0.7459 (tpp) cc_final: 0.7197 (tpp)
REVERT: A  448 MET cc_start: 0.8126 (mpp) cc_final: 0.7901 (mpp)
  outliers start: 11
  outliers final: 8
  residues processed: 41
  average time/residue: 1.0779
  time to fit residues: 46.6386
Evaluate side-chains
  40 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 32
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  408 MET
Chi-restraints excluded: chain A residue  443 THR
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0010
   chunk 11 optimal weight:    0.5980
   chunk 34 optimal weight:    0.0020
   chunk 19 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.3594

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.204164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.163727 restraints weight = 2997.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3789 rms_B_bonded: 1.64
r_work: 0.3570 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3418 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6907
moved from start:          0.1534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3286  Z= 0.121
  Angle     :  0.507   6.951   4500  Z= 0.257
  Chirality :  0.037   0.132    536
  Planarity :  0.004   0.041    551
  Dihedral  :  4.459  25.137    529
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 14.74 %
    Favored  : 82.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.07 (0.43), residues: 425
  helix:  1.93 (0.30), residues: 315
  sheet:  None (None), residues: 0
  loop : -0.21 (0.64), residues: 110

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04105 (  235)
  hydrogen bonds       : angle       4.23284 (  699)
  SS BOND              : bond        0.00340 (    3)
  SS BOND              : angle       0.69842 (    6)
  covalent geometry    : bond        0.00263 ( 3283)
  covalent geometry    : angle       0.50661 ( 4494)

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

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 32
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A  420 MET cc_start: 0.7961 (mtp) cc_final: 0.7338 (mtt)
REVERT: A  435 MET cc_start: 0.7346 (tpp) cc_final: 0.7060 (tpp)
  outliers start: 9
  outliers final: 6
  residues processed: 38
  average time/residue: 0.6158
  time to fit residues: 24.8653
Evaluate side-chains
  37 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  443 THR
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0970
   chunk 40 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 11 optimal weight:    0.0030
   chunk 36 optimal weight:    0.5980
   chunk 32 optimal weight:    0.5980
   chunk 15 optimal weight:    6.9990
   chunk 17 optimal weight:    0.0570
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.2706

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.204177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.163271 restraints weight = 2978.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3808 rms_B_bonded: 1.64
r_work: 0.3590 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3438 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6879
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3286  Z= 0.114
  Angle     :  0.499   7.412   4500  Z= 0.252
  Chirality :  0.037   0.130    536
  Planarity :  0.004   0.041    551
  Dihedral  :  4.294  28.081    529
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.71 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.43), residues: 425
  helix:  1.87 (0.30), residues: 320
  sheet:  None (None), residues: 0
  loop : -0.05 (0.65), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  64 
 HIS   0.002   0.001   HIS A  49 
 PHE   0.008   0.001   PHE A  44 
 TYR   0.010   0.001   TYR A 352 
 ARG   0.002   0.000   ARG A 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03934 (  235)
  hydrogen bonds       : angle       4.11493 (  699)
  SS BOND              : bond        0.00338 (    3)
  SS BOND              : angle       0.60604 (    6)
  covalent geometry    : bond        0.00241 ( 3283)
  covalent geometry    : angle       0.49885 ( 4494)

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

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 35
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A  420 MET cc_start: 0.7991 (mtp) cc_final: 0.7321 (mtt)
  outliers start: 8
  outliers final: 6
  residues processed: 39
  average time/residue: 0.6377
  time to fit residues: 26.3815
Evaluate side-chains
  36 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  443 THR
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0010
   chunk 19 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 18 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 7 optimal weight:    7.9990
   overall best weight:    0.5986

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.200762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.160351 restraints weight = 2925.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3771 rms_B_bonded: 1.62
r_work: 0.3546 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3391 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6929
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3286  Z= 0.144
  Angle     :  0.558   9.075   4500  Z= 0.275
  Chirality :  0.038   0.137    536
  Planarity :  0.004   0.040    551
  Dihedral  :  4.471  27.323    529
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 15.06 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.95 (0.43), residues: 425
  helix:  1.77 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.08 (0.66), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A 367 
 PHE   0.010   0.001   PHE A  44 
 TYR   0.011   0.001   TYR A 352 
 ARG   0.002   0.000   ARG A 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04262 (  235)
  hydrogen bonds       : angle       4.31374 (  699)
  SS BOND              : bond        0.00450 (    3)
  SS BOND              : angle       1.06130 (    6)
  covalent geometry    : bond        0.00335 ( 3283)
  covalent geometry    : angle       0.55691 ( 4494)

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

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 34
  time to evaluate  : 0.333 
Fit side-chains
REVERT: A  200 MET cc_start: 0.7525 (mmm) cc_final: 0.7180 (tpp)
REVERT: A  420 MET cc_start: 0.7929 (mtp) cc_final: 0.7265 (mtt)
  outliers start: 10
  outliers final: 7
  residues processed: 39
  average time/residue: 0.8857
  time to fit residues: 36.2119
Evaluate side-chains
  38 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 31
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  443 THR
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 35 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 6 optimal weight:    0.3980
   chunk 37 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.6380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.200074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.159247 restraints weight = 2933.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3767 rms_B_bonded: 1.62
r_work: 0.3543 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3390 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6931
moved from start:          0.1675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3286  Z= 0.148
  Angle     :  0.566   8.916   4500  Z= 0.279
  Chirality :  0.038   0.140    536
  Planarity :  0.004   0.039    551
  Dihedral  :  4.519  25.692    529
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 16.35 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.43), residues: 425
  helix:  1.75 (0.30), residues: 319
  sheet:  None (None), residues: 0
  loop : -0.03 (0.65), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A 367 
 PHE   0.010   0.001   PHE A  44 
 TYR   0.012   0.001   TYR A 352 
 ARG   0.002   0.000   ARG A 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04330 (  235)
  hydrogen bonds       : angle       4.37169 (  699)
  SS BOND              : bond        0.00466 (    3)
  SS BOND              : angle       1.02541 (    6)
  covalent geometry    : bond        0.00345 ( 3283)
  covalent geometry    : angle       0.56493 ( 4494)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3572.78 seconds
wall clock time: 63 minutes 43.18 seconds (3823.18 seconds total)