Starting phenix.real_space_refine
on Fri Aug 22 13:19:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qd0_18339/08_2025/8qd0_18339.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qd0_18339/08_2025/8qd0_18339.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qd0_18339/08_2025/8qd0_18339.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qd0_18339/08_2025/8qd0_18339.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qd0_18339/08_2025/8qd0_18339.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qd0_18339/08_2025/8qd0_18339.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.098
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      19      5.16       5
     C    2187      2.51       5
     N     522      2.21       5
     O     562      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 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: 3290
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3283
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 422, 3283
          Classifications: {'peptide': 422}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 406}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 7
          Unusual residues: {'CHT': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.80, per 1000 atoms: 0.24
  Number of scatterers: 3290
  At special positions: 0
  Unit cell: (83.658, 56.154, 65.322, 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      19     16.00
     O     562      8.00
     N     522      7.00
     C    2187      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.17
  Conformation dependent library (CDL) restraints added in 75.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  772

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 0 sheets defined
      91.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 82 through 107
      removed outlier: 4.255A  pdb=" N   ALA A  86 " --> pdb=" O   ARG A  82 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   TYR A 105 " --> pdb=" O   GLN A 101 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   GLY A 106 " --> pdb=" O   TRP A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 117
      removed outlier: 4.096A  pdb=" N   HIS A 114 " --> pdb=" O   ASN A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 168
      removed outlier: 3.922A  pdb=" N   ILE A 123 " --> pdb=" O   SER A 119 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   TRP A 125 " --> pdb=" O   PHE A 121 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LEU A 126 " --> pdb=" O   ALA A 122 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   SER A 127 " --> pdb=" O   ILE A 123 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   TYR A 130 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   MET A 131 " --> pdb=" O   SER A 127 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ILE A 135 " --> pdb=" O   MET A 131 " (cutoff:3.500A)
      Proline residue:  A 136  - end of helix
      removed outlier: 5.138A  pdb=" N   LEU A 139 " --> pdb=" O   ILE A 135 " (cutoff:3.500A)
      Proline residue:  A 140  - end of helix
      removed outlier: 7.574A  pdb=" N   LEU A 150 " --> pdb=" O   GLU A 146 " (cutoff:3.500A)
      removed outlier: 8.799A  pdb=" N   ARG A 151 " --> pdb=" O   LYS A 147 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   THR A 152 " --> pdb=" O   PHE A 148 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ILE A 153 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 172
    Processing helix  chain 'A' and resid 176 through 193
      removed outlier: 3.646A  pdb=" N   THR A 180 " --> pdb=" O   LEU A 176 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   VAL A 192 " --> pdb=" O   SER A 188 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   PHE A 193 " --> pdb=" O   VAL A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 206
      removed outlier: 3.557A  pdb=" N   ILE A 201 " --> pdb=" O   MET A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 237
      Proline residue:  A 233  - end of helix
    Processing helix  chain 'A' and resid 242 through 272
    Processing helix  chain 'A' and resid 281 through 291
    Processing helix  chain 'A' and resid 296 through 305
      removed outlier: 3.789A  pdb=" N   PHE A 305 " --> pdb=" O   ILE A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 330
      removed outlier: 3.552A  pdb=" N   ALA A 323 " --> pdb=" O   LEU A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 339
      removed outlier: 3.526A  pdb=" N   MET A 334 " --> pdb=" O   LEU A 330 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   TRP A 337 " --> pdb=" O   ARG A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 372
    Processing helix  chain 'A' and resid 373 through 396
    Processing helix  chain 'A' and resid 400 through 431
      removed outlier: 3.653A  pdb=" N   PHE A 414 " --> pdb=" O   THR A 410 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLY A 417 " --> pdb=" O   PHE A 413 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LEU A 419 " --> pdb=" O   MET A 415 " (cutoff:3.500A)
      Proline residue:  A 420  - end of helix
      removed outlier: 3.815A  pdb=" N   PHE A 423 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 465
      removed outlier: 3.609A  pdb=" N   SER A 438 " --> pdb=" O   SER A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 486
      removed outlier: 3.694A  pdb=" N   GLY A 469 " --> pdb=" O   GLY A 465 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   PHE A 486 " --> pdb=" O   ALA A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 502

    271 hydrogen bonds defined for protein.
    810 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: 0.35

  Time building geometry restraints manager: 0.23 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 608
        1.33 -     1.45: 840
        1.45 -     1.57: 1892
        1.57 -     1.69: 0
        1.69 -     1.81: 31
  Bond restraints: 3371
  Sorted by residual:
  bond pdb=" N   LEU A 441 "
       pdb=" CA  LEU A 441 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.23e-02 6.61e+03 1.01e+01
  bond pdb=" N   PRO A 276 "
       pdb=" CA  PRO A 276 "
    ideal  model  delta    sigma   weight residual
    1.467  1.434  0.033 1.24e-02 6.50e+03 7.16e+00
  bond pdb=" N   GLU A 435 "
       pdb=" CA  GLU A 435 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.028 1.25e-02 6.40e+03 4.92e+00
  bond pdb=" C   LEU A 441 "
       pdb=" O   LEU A 441 "
    ideal  model  delta    sigma   weight residual
    1.237  1.215  0.021 1.19e-02 7.06e+03 3.25e+00
  bond pdb=" C   PRO A 276 "
       pdb=" O   PRO A 276 "
    ideal  model  delta    sigma   weight residual
    1.233  1.211  0.022 1.24e-02 6.50e+03 3.08e+00
  ... (remaining 3366 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 4471
        1.74 -     3.48: 94
        3.48 -     5.22: 18
        5.22 -     6.96: 5
        6.96 -     8.71: 2
  Bond angle restraints: 4590
  Sorted by residual:
  angle pdb=" CA  PRO A 198 "
        pdb=" N   PRO A 198 "
        pdb=" CD  PRO A 198 "
      ideal   model   delta    sigma   weight residual
     112.00  106.44    5.56 1.40e+00 5.10e-01 1.58e+01
  angle pdb=" C   PRO A 276 "
        pdb=" CA  PRO A 276 "
        pdb=" CB  PRO A 276 "
      ideal   model   delta    sigma   weight residual
     111.40  106.40    5.00 1.54e+00 4.22e-01 1.05e+01
  angle pdb=" N   VAL A 237 "
        pdb=" CA  VAL A 237 "
        pdb=" C   VAL A 237 "
      ideal   model   delta    sigma   weight residual
     108.15  111.20   -3.05 9.90e-01 1.02e+00 9.47e+00
  angle pdb=" N   PRO A 198 "
        pdb=" CD  PRO A 198 "
        pdb=" CG  PRO A 198 "
      ideal   model   delta    sigma   weight residual
     103.20   98.66    4.54 1.50e+00 4.44e-01 9.16e+00
  angle pdb=" N   LEU A 441 "
        pdb=" CA  LEU A 441 "
        pdb=" C   LEU A 441 "
      ideal   model   delta    sigma   weight residual
     111.36  108.09    3.27 1.09e+00 8.42e-01 9.00e+00
  ... (remaining 4585 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.49: 1725
       17.49 -    34.99: 159
       34.99 -    52.48: 45
       52.48 -    69.97: 5
       69.97 -    87.47: 5
  Dihedral angle restraints: 1939
    sinusoidal: 728
      harmonic: 1211
  Sorted by residual:
  dihedral pdb=" CA  MET A 197 "
           pdb=" C   MET A 197 "
           pdb=" N   PRO A 198 "
           pdb=" CA  PRO A 198 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.03   20.97     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CD  ARG A 333 "
           pdb=" NE  ARG A 333 "
           pdb=" CZ  ARG A 333 "
           pdb=" NH1 ARG A 333 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -30.26   30.26     1      1.00e+01 1.00e-02 1.31e+01
  dihedral pdb=" CA  ASN A 320 "
           pdb=" CB  ASN A 320 "
           pdb=" CG  ASN A 320 "
           pdb=" OD1 ASN A 320 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -166.69  -73.31     2      2.00e+01 2.50e-03 1.10e+01
  ... (remaining 1936 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 427
       0.046 -    0.092: 101
       0.092 -    0.138: 14
       0.138 -    0.184: 0
       0.184 -    0.230: 1
  Chirality restraints: 543
  Sorted by residual:
  chirality pdb=" CB  ILE A 108 "
            pdb=" CA  ILE A 108 "
            pdb=" CG1 ILE A 108 "
            pdb=" CG2 ILE A 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CA  ARG A 333 "
            pdb=" N   ARG A 333 "
            pdb=" C   ARG A 333 "
            pdb=" CB  ARG A 333 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 4.69e-01
  chirality pdb=" CA  PRO A 432 "
            pdb=" N   PRO A 432 "
            pdb=" C   PRO A 432 "
            pdb=" CB  PRO A 432 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.11 2.00e-01 2.50e+01 3.25e-01
  ... (remaining 540 not shown)

  Planarity restraints: 555
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 333 "    0.563 9.50e-02 1.11e+02   2.52e-01 3.89e+01
        pdb=" NE  ARG A 333 "   -0.032 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 333 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 333 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 333 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 197 "    0.065 5.00e-02 4.00e+02   9.54e-02 1.46e+01
        pdb=" N   PRO A 198 "   -0.165 5.00e-02 4.00e+02
        pdb=" CA  PRO A 198 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 198 "    0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 143 "    0.009 2.00e-02 2.50e+03   1.02e-02 2.60e+00
        pdb=" CG  TRP A 143 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 143 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 143 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 143 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 143 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 143 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 143 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 143 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 143 "    0.000 2.00e-02 2.50e+03
  ... (remaining 552 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 1160
        2.85 -     3.36: 3528
        3.36 -     3.87: 5734
        3.87 -     4.39: 6688
        4.39 -     4.90: 11284
  Nonbonded interactions: 28394
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 101 "
            pdb=" NZ  LYS A 168 "
     model   vdw
     2.337 3.120
  nonbonded pdb=" OE1 GLU A 342 "
            pdb=" ND2 ASN A 345 "
     model   vdw
     2.371 3.120
  nonbonded pdb=" O   VAL A 391 "
            pdb=" OG1 THR A 395 "
     model   vdw
     2.444 3.040
  nonbonded pdb=" NH2 ARG A 151 "
            pdb=" O   ILE A 269 "
     model   vdw
     2.459 3.120
  nonbonded pdb=" O   ILE A 452 "
            pdb=" OG  SER A 456 "
     model   vdw
     2.483 3.040
  ... (remaining 28389 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:             0.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     3.930
  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:             0.000
  Load rotamer database and sin/cos tables:5.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
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      :  0.003   0.039   3371  Z= 0.165
  Angle     :  0.634   8.706   4590  Z= 0.358
  Chirality :  0.038   0.230    543
  Planarity :  0.012   0.252    555
  Dihedral  : 15.295  87.467   1167
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 18.41 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.25 (0.41), residues: 418
  helix:  1.22 (0.28), residues: 342
  sheet:  None (None), residues: 0
  loop : -0.70 (0.67), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 333 
 TYR   0.015   0.001   TYR A  94 
 PHE   0.009   0.001   PHE A 310 
 TRP   0.027   0.002   TRP A 143 
 HIS   0.002   0.001   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 3371)
  covalent geometry    : angle       0.63433 ( 4590)
  hydrogen bonds       : bond        0.22782 (  271)
  hydrogen bonds       : angle       7.75562 (  810)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.093 
Fit side-chains
REVERT: A  131 MET cc_start: 0.9037 (mtp) cc_final: 0.8684 (mtp)
REVERT: A  143 TRP cc_start: 0.7567 (t60) cc_final: 0.7112 (t60)
REVERT: A  297 TYR cc_start: 0.7128 (m-80) cc_final: 0.6641 (t80)
REVERT: A  305 PHE cc_start: 0.7155 (m-80) cc_final: 0.6620 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.3058
  time to fit residues: 22.6483
Evaluate side-chains
  62 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   chunk 22 optimal weight:    7.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 114 HIS
A 223 GLN
A 307 ASN
A 320 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.160327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.132429 restraints weight = 4307.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.3602 rms_B_bonded: 2.35
r_work: 0.3487 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3371  Z= 0.169
  Angle     :  0.642   7.019   4590  Z= 0.336
  Chirality :  0.042   0.239    543
  Planarity :  0.006   0.065    555
  Dihedral  :  4.947  53.780    454
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 16.15 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.67 (0.40), residues: 418
  helix:  1.56 (0.27), residues: 352
  sheet:  None (None), residues: 0
  loop : -1.23 (0.67), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 493 
 TYR   0.022   0.001   TYR A  94 
 PHE   0.015   0.002   PHE A 472 
 TRP   0.017   0.002   TRP A 143 
 HIS   0.002   0.001   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 3371)
  covalent geometry    : angle       0.64196 ( 4590)
  hydrogen bonds       : bond        0.05422 (  271)
  hydrogen bonds       : angle       5.06640 (  810)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A  305 PHE cc_start: 0.6866 (m-80) cc_final: 0.6280 (m-80)
REVERT: A  370 ARG cc_start: 0.7547 (tpt90) cc_final: 0.7180 (mmt180)
  outliers start: 12
  outliers final: 1
  residues processed: 63
  average time/residue: 0.3078
  time to fit residues: 20.2010
Evaluate side-chains
  51 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 21 optimal weight:    9.9990
   chunk 39 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   chunk 20 optimal weight:   20.0000
   chunk 15 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 35 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.159806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.132656 restraints weight = 4268.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3581 rms_B_bonded: 2.33
r_work: 0.3466 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7267
moved from start:          0.2814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3371  Z= 0.154
  Angle     :  0.609   7.667   4590  Z= 0.315
  Chirality :  0.041   0.236    543
  Planarity :  0.005   0.046    555
  Dihedral  :  4.910  52.638    454
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 16.15 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.40), residues: 418
  helix:  1.64 (0.27), residues: 354
  sheet:  None (None), residues: 0
  loop : -0.96 (0.71), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 492 
 TYR   0.021   0.001   TYR A  94 
 PHE   0.016   0.002   PHE A  91 
 TRP   0.015   0.002   TRP A 143 
 HIS   0.002   0.001   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 3371)
  covalent geometry    : angle       0.60933 ( 4590)
  hydrogen bonds       : bond        0.04740 (  271)
  hydrogen bonds       : angle       4.65060 (  810)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A  274 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6720 (tt0)
REVERT: A  297 TYR cc_start: 0.6675 (m-80) cc_final: 0.5924 (t80)
REVERT: A  305 PHE cc_start: 0.6936 (m-80) cc_final: 0.6412 (m-80)
REVERT: A  370 ARG cc_start: 0.7318 (tpt90) cc_final: 0.7097 (mpt180)
REVERT: A  437 ILE cc_start: 0.6998 (mm) cc_final: 0.6571 (mm)
REVERT: A  486 PHE cc_start: 0.8369 (m-80) cc_final: 0.8146 (m-80)
  outliers start: 13
  outliers final: 5
  residues processed: 64
  average time/residue: 0.2706
  time to fit residues: 18.0975
Evaluate side-chains
  54 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  402 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 104 GLN
A 109 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.156298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.130176 restraints weight = 4261.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 2.23
r_work: 0.3423 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.3048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3371  Z= 0.177
  Angle     :  0.615   7.238   4590  Z= 0.321
  Chirality :  0.042   0.237    543
  Planarity :  0.005   0.051    555
  Dihedral  :  4.875  50.387    454
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 16.71 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.74 (0.40), residues: 418
  helix:  1.55 (0.27), residues: 354
  sheet:  None (None), residues: 0
  loop : -0.86 (0.73), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 492 
 TYR   0.025   0.001   TYR A  94 
 PHE   0.021   0.002   PHE A 100 
 TRP   0.013   0.002   TRP A 102 
 HIS   0.003   0.001   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 3371)
  covalent geometry    : angle       0.61486 ( 4590)
  hydrogen bonds       : bond        0.04701 (  271)
  hydrogen bonds       : angle       4.58517 (  810)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 54
  time to evaluate  : 0.074 
Fit side-chains
REVERT: A  274 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6745 (tt0)
REVERT: A  297 TYR cc_start: 0.6773 (m-80) cc_final: 0.6045 (t80)
REVERT: A  437 ILE cc_start: 0.6876 (mm) cc_final: 0.6576 (mm)
REVERT: A  486 PHE cc_start: 0.8427 (m-80) cc_final: 0.8132 (m-80)
  outliers start: 15
  outliers final: 4
  residues processed: 64
  average time/residue: 0.2741
  time to fit residues: 18.3193
Evaluate side-chains
  54 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  402 TRP
Chi-restraints excluded: chain A residue  484 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 28 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 20 optimal weight:    9.9990
   chunk 24 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 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 = 0.3877 r_free = 0.3877 target = 0.157987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.131557 restraints weight = 4274.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 2.27
r_work: 0.3474 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.3079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3371  Z= 0.147
  Angle     :  0.583   7.350   4590  Z= 0.304
  Chirality :  0.041   0.227    543
  Planarity :  0.005   0.044    555
  Dihedral  :  4.894  52.596    454
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 17.85 %
    Favored  : 77.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.90 (0.41), residues: 418
  helix:  1.65 (0.27), residues: 354
  sheet:  None (None), residues: 0
  loop : -0.80 (0.73), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  82 
 TYR   0.021   0.001   TYR A  94 
 PHE   0.021   0.002   PHE A 100 
 TRP   0.014   0.001   TRP A 102 
 HIS   0.003   0.001   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 3371)
  covalent geometry    : angle       0.58273 ( 4590)
  hydrogen bonds       : bond        0.04460 (  271)
  hydrogen bonds       : angle       4.41510 (  810)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.085 
Fit side-chains
REVERT: A   82 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6406 (tpp80)
REVERT: A  127 SER cc_start: 0.8745 (OUTLIER) cc_final: 0.8363 (m)
REVERT: A  242 ASP cc_start: 0.7775 (t0) cc_final: 0.7352 (t0)
REVERT: A  245 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7268 (mp0)
REVERT: A  274 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6685 (tt0)
REVERT: A  297 TYR cc_start: 0.6779 (m-80) cc_final: 0.6094 (t80)
REVERT: A  369 ASP cc_start: 0.8572 (t70) cc_final: 0.8343 (t0)
REVERT: A  376 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6583 (mp0)
REVERT: A  437 ILE cc_start: 0.6912 (mm) cc_final: 0.6614 (mm)
REVERT: A  486 PHE cc_start: 0.8449 (m-80) cc_final: 0.8193 (m-80)
  outliers start: 15
  outliers final: 4
  residues processed: 75
  average time/residue: 0.3851
  time to fit residues: 29.8126
Evaluate side-chains
  60 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 ARG
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  402 TRP
Chi-restraints excluded: chain A residue  484 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 16 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9980
   chunk 35 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 109 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.160123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.132556 restraints weight = 4237.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 2.36
r_work: 0.3503 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.3331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3371  Z= 0.151
  Angle     :  0.596   7.206   4590  Z= 0.313
  Chirality :  0.041   0.228    543
  Planarity :  0.005   0.046    555
  Dihedral  :  4.899  53.117    454
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 19.55 %
    Favored  : 76.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  2.08 (0.41), residues: 418
  helix:  1.74 (0.27), residues: 353
  sheet:  None (None), residues: 0
  loop : -0.50 (0.76), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 493 
 TYR   0.022   0.001   TYR A  94 
 PHE   0.024   0.002   PHE A 100 
 TRP   0.016   0.001   TRP A 102 
 HIS   0.002   0.001   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 3371)
  covalent geometry    : angle       0.59646 ( 4590)
  hydrogen bonds       : bond        0.04361 (  271)
  hydrogen bonds       : angle       4.37983 (  810)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 0.100 
Fit side-chains
REVERT: A   82 ARG cc_start: 0.6972 (OUTLIER) cc_final: 0.6441 (tpp80)
REVERT: A  242 ASP cc_start: 0.7857 (t0) cc_final: 0.7576 (t0)
REVERT: A  245 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7217 (mp0)
REVERT: A  297 TYR cc_start: 0.6801 (m-80) cc_final: 0.6082 (t80)
REVERT: A  369 ASP cc_start: 0.8455 (t70) cc_final: 0.8226 (t0)
REVERT: A  370 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.5558 (mtt90)
REVERT: A  376 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6532 (mp0)
REVERT: A  437 ILE cc_start: 0.6839 (mm) cc_final: 0.6567 (mm)
REVERT: A  486 PHE cc_start: 0.8397 (m-80) cc_final: 0.8134 (m-80)
  outliers start: 15
  outliers final: 5
  residues processed: 67
  average time/residue: 0.3369
  time to fit residues: 23.3846
Evaluate side-chains
  59 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 ARG
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  370 ARG
Chi-restraints excluded: chain A residue  402 TRP
Chi-restraints excluded: chain A residue  428 GLU
Chi-restraints excluded: chain A residue  484 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 21 optimal weight:    9.9990
   chunk 40 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0980
   chunk 38 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   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  98 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 = 0.3920 r_free = 0.3920 target = 0.161146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.134059 restraints weight = 4295.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3622 rms_B_bonded: 2.37
r_work: 0.3511 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start:          0.3421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3371  Z= 0.139
  Angle     :  0.588   7.397   4590  Z= 0.305
  Chirality :  0.041   0.229    543
  Planarity :  0.005   0.042    555
  Dihedral  :  4.936  54.734    454
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 22.10 %
    Favored  : 74.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  2.17 (0.41), residues: 418
  helix:  1.81 (0.27), residues: 353
  sheet:  None (None), residues: 0
  loop : -0.51 (0.76), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 303 
 TYR   0.022   0.001   TYR A 392 
 PHE   0.016   0.002   PHE A 100 
 TRP   0.018   0.001   TRP A 102 
 HIS   0.003   0.001   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 3371)
  covalent geometry    : angle       0.58818 ( 4590)
  hydrogen bonds       : bond        0.04244 (  271)
  hydrogen bonds       : angle       4.31060 (  810)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A   82 ARG cc_start: 0.6638 (OUTLIER) cc_final: 0.6194 (tpp80)
REVERT: A  242 ASP cc_start: 0.7862 (t0) cc_final: 0.7317 (t0)
REVERT: A  245 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7353 (mp0)
REVERT: A  297 TYR cc_start: 0.6815 (m-80) cc_final: 0.6058 (t80)
REVERT: A  369 ASP cc_start: 0.8459 (t70) cc_final: 0.8217 (t0)
REVERT: A  376 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6484 (mp0)
REVERT: A  402 TRP cc_start: 0.5510 (OUTLIER) cc_final: 0.5057 (p-90)
REVERT: A  437 ILE cc_start: 0.6876 (mm) cc_final: 0.6623 (mm)
REVERT: A  486 PHE cc_start: 0.8382 (m-80) cc_final: 0.8119 (m-80)
  outliers start: 11
  outliers final: 3
  residues processed: 68
  average time/residue: 0.3407
  time to fit residues: 24.0737
Evaluate side-chains
  55 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 ARG
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  402 TRP
Chi-restraints excluded: chain A residue  484 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0970
   chunk 29 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.162041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.134749 restraints weight = 4337.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 2.36
r_work: 0.3527 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7267
moved from start:          0.3545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3371  Z= 0.135
  Angle     :  0.586   7.615   4590  Z= 0.305
  Chirality :  0.041   0.224    543
  Planarity :  0.005   0.045    555
  Dihedral  :  4.993  55.488    454
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 22.38 %
    Favored  : 75.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  2.27 (0.41), residues: 418
  helix:  1.89 (0.27), residues: 353
  sheet:  None (None), residues: 0
  loop : -0.52 (0.76), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 303 
 TYR   0.021   0.001   TYR A  94 
 PHE   0.014   0.001   PHE A 472 
 TRP   0.020   0.001   TRP A 102 
 HIS   0.003   0.001   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 3371)
  covalent geometry    : angle       0.58579 ( 4590)
  hydrogen bonds       : bond        0.04153 (  271)
  hydrogen bonds       : angle       4.26158 (  810)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.095 
Fit side-chains
REVERT: A   82 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.6217 (tpp80)
REVERT: A  242 ASP cc_start: 0.7706 (t0) cc_final: 0.7375 (t0)
REVERT: A  245 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7283 (mp0)
REVERT: A  297 TYR cc_start: 0.6785 (m-80) cc_final: 0.6024 (t80)
REVERT: A  369 ASP cc_start: 0.8477 (t70) cc_final: 0.8230 (t0)
REVERT: A  376 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6555 (mp0)
REVERT: A  402 TRP cc_start: 0.5459 (OUTLIER) cc_final: 0.5055 (p-90)
REVERT: A  437 ILE cc_start: 0.6929 (mm) cc_final: 0.6675 (mm)
REVERT: A  486 PHE cc_start: 0.8395 (m-80) cc_final: 0.8139 (m-80)
  outliers start: 9
  outliers final: 4
  residues processed: 63
  average time/residue: 0.2937
  time to fit residues: 19.3770
Evaluate side-chains
  56 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 ARG
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  402 TRP
Chi-restraints excluded: chain A residue  484 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 22 optimal weight:    0.3980
   chunk 4 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 5 optimal weight:    0.2980
   chunk 26 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 41 optimal weight:   10.0000
   chunk 29 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.161968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.134357 restraints weight = 4263.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 2.44
r_work: 0.3558 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start:          0.3644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3371  Z= 0.131
  Angle     :  0.589   7.814   4590  Z= 0.306
  Chirality :  0.040   0.228    543
  Planarity :  0.005   0.041    555
  Dihedral  :  4.957  54.852    454
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 23.80 %
    Favored  : 73.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  2.33 (0.41), residues: 418
  helix:  1.96 (0.27), residues: 351
  sheet:  None (None), residues: 0
  loop : -0.64 (0.73), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 303 
 TYR   0.024   0.001   TYR A 392 
 PHE   0.014   0.001   PHE A 100 
 TRP   0.022   0.001   TRP A 102 
 HIS   0.005   0.001   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 3371)
  covalent geometry    : angle       0.58855 ( 4590)
  hydrogen bonds       : bond        0.04094 (  271)
  hydrogen bonds       : angle       4.22482 (  810)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.091 
Fit side-chains
REVERT: A  242 ASP cc_start: 0.7706 (t0) cc_final: 0.7375 (t0)
REVERT: A  245 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7162 (mp0)
REVERT: A  297 TYR cc_start: 0.6894 (m-80) cc_final: 0.6163 (t80)
REVERT: A  305 PHE cc_start: 0.7140 (m-80) cc_final: 0.6696 (m-80)
REVERT: A  369 ASP cc_start: 0.8467 (t70) cc_final: 0.8235 (t0)
REVERT: A  376 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6603 (mp0)
REVERT: A  402 TRP cc_start: 0.5422 (OUTLIER) cc_final: 0.5019 (p-90)
REVERT: A  437 ILE cc_start: 0.6875 (mm) cc_final: 0.6640 (mm)
REVERT: A  486 PHE cc_start: 0.8405 (m-80) cc_final: 0.8118 (m-80)
  outliers start: 8
  outliers final: 4
  residues processed: 63
  average time/residue: 0.3054
  time to fit residues: 20.0727
Evaluate side-chains
  59 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  402 TRP
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain A residue  484 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.160553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.133194 restraints weight = 4250.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 2.33
r_work: 0.3516 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.3684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3371  Z= 0.163
  Angle     :  0.644   8.735   4590  Z= 0.335
  Chirality :  0.042   0.205    543
  Planarity :  0.005   0.045    555
  Dihedral  :  4.939  50.592    454
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 24.08 %
    Favored  : 73.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  2.19 (0.40), residues: 418
  helix:  1.83 (0.27), residues: 353
  sheet:  None (None), residues: 0
  loop : -0.52 (0.75), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 493 
 TYR   0.022   0.001   TYR A  94 
 PHE   0.016   0.002   PHE A 472 
 TRP   0.024   0.002   TRP A 102 
 HIS   0.004   0.001   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 3371)
  covalent geometry    : angle       0.64412 ( 4590)
  hydrogen bonds       : bond        0.04373 (  271)
  hydrogen bonds       : angle       4.35165 (  810)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A  242 ASP cc_start: 0.7743 (t0) cc_final: 0.7441 (t0)
REVERT: A  245 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7338 (mp0)
REVERT: A  297 TYR cc_start: 0.6916 (m-80) cc_final: 0.6264 (t80)
REVERT: A  376 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6631 (mp0)
REVERT: A  486 PHE cc_start: 0.8420 (m-80) cc_final: 0.8122 (m-80)
  outliers start: 8
  outliers final: 4
  residues processed: 65
  average time/residue: 0.3308
  time to fit residues: 22.3636
Evaluate side-chains
  56 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  402 TRP
Chi-restraints excluded: chain A residue  484 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 37 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 22 optimal weight:    0.4980
   chunk 27 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0970
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.163433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.136507 restraints weight = 4316.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 2.36
r_work: 0.3554 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.3791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3371  Z= 0.146
  Angle     :  0.655   8.713   4590  Z= 0.340
  Chirality :  0.041   0.209    543
  Planarity :  0.005   0.044    555
  Dihedral  :  4.972  54.085    454
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 24.65 %
    Favored  : 73.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  2.43 (0.40), residues: 418
  helix:  2.03 (0.27), residues: 347
  sheet:  None (None), residues: 0
  loop : -0.46 (0.73), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 493 
 TYR   0.022   0.001   TYR A 392 
 PHE   0.034   0.002   PHE A 100 
 TRP   0.028   0.001   TRP A 102 
 HIS   0.004   0.001   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 3371)
  covalent geometry    : angle       0.65548 ( 4590)
  hydrogen bonds       : bond        0.04225 (  271)
  hydrogen bonds       : angle       4.31883 (  810)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1005.62 seconds
wall clock time: 17 minutes 60.00 seconds (1080.00 seconds total)