Starting phenix.real_space_refine
on Wed Jun  4 14:02:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qd0_18339/06_2025/8qd0_18339.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qd0_18339/06_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_18339/06_2025/8qd0_18339.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qd0_18339/06_2025/8qd0_18339.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qd0_18339/06_2025/8qd0_18339.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qd0_18339/06_2025/8qd0_18339.cif"
  }
  resolution = 2.8
  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=  -0.000 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 2.62, per 1000 atoms: 0.80
  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: 1.05
  Conformation dependent library (CDL) restraints added in 553.3 milliseconds
  

  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: 0.28
  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: 0.89

  Time building geometry restraints manager: 1.07 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:             0.140
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.660
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.250
-------------------------------------------------------------------------------
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 (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:  1.25 (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
 TRP   0.027   0.002   TRP A 143 
 HIS   0.002   0.001   HIS A 338 
 PHE   0.009   0.001   PHE A 310 
 TYR   0.015   0.001   TYR A  94 
 ARG   0.004   0.000   ARG A 333 

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

*********************** 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  : 0.359 
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: 0.7396
  time to fit residues: 54.9040
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  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 21 optimal weight:    5.9990
   chunk 32 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 20 optimal weight:   20.0000
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   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 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 = 0.3922 r_free = 0.3922 target = 0.160992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.132423 restraints weight = 4297.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 2.42
r_work: 0.3498 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7269
moved from start:          0.2202

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= 0.161
  Angle     :  0.639   6.852   4590  Z= 0.332
  Chirality :  0.042   0.242    543
  Planarity :  0.005   0.062    555
  Dihedral  :  4.976  55.638    454
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 15.30 %
    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 (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:  1.68 (0.40), residues: 418
  helix:  1.57 (0.27), residues: 352
  sheet:  None (None), residues: 0
  loop : -1.22 (0.67), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 143 
 HIS   0.002   0.001   HIS A 338 
 PHE   0.014   0.002   PHE A 472 
 TYR   0.022   0.001   TYR A  94 
 ARG   0.003   0.001   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05182 (  271)
  hydrogen bonds       : angle       5.01375 (  810)
  covalent geometry    : bond        0.00341 ( 3371)
  covalent geometry    : angle       0.63913 ( 4590)

*********************** 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
  76 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.391 
Fit side-chains
REVERT: A  305 PHE cc_start: 0.6839 (m-80) cc_final: 0.5999 (m-80)
REVERT: A  370 ARG cc_start: 0.7543 (tpt90) cc_final: 0.7188 (mmt180)
  outliers start: 15
  outliers final: 1
  residues processed: 69
  average time/residue: 0.7685
  time to fit residues: 55.5293
Evaluate side-chains
  54 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
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 20 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 13 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 0 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3871 r_free = 0.3871 target = 0.157975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.131176 restraints weight = 4221.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 2.25
r_work: 0.3475 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.2800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3371  Z= 0.152
  Angle     :  0.604   7.656   4590  Z= 0.314
  Chirality :  0.040   0.233    543
  Planarity :  0.005   0.044    555
  Dihedral  :  4.894  52.979    454
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.71 %
    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 (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:  1.89 (0.41), residues: 418
  helix:  1.68 (0.27), residues: 355
  sheet:  None (None), residues: 0
  loop : -1.12 (0.70), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 143 
 HIS   0.002   0.001   HIS A 338 
 PHE   0.017   0.002   PHE A  91 
 TYR   0.021   0.001   TYR A  94 
 ARG   0.002   0.000   ARG A 370 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04727 (  271)
  hydrogen bonds       : angle       4.64943 (  810)
  covalent geometry    : bond        0.00328 ( 3371)
  covalent geometry    : angle       0.60356 ( 4590)

*********************** 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: 11
    poor density    : 59
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A  297 TYR cc_start: 0.6702 (m-80) cc_final: 0.6074 (t80)
REVERT: A  305 PHE cc_start: 0.6953 (m-80) cc_final: 0.6363 (m-80)
REVERT: A  370 ARG cc_start: 0.7299 (tpt90) cc_final: 0.7086 (mpt180)
REVERT: A  429 LEU cc_start: 0.6344 (mt) cc_final: 0.6129 (mt)
REVERT: A  441 LEU cc_start: 0.7611 (mt) cc_final: 0.7396 (mt)
  outliers start: 11
  outliers final: 4
  residues processed: 65
  average time/residue: 0.7716
  time to fit residues: 52.4775
Evaluate side-chains
  53 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 49
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  402 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 35 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 34 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 13 optimal weight:    7.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A  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 = 0.3866 r_free = 0.3866 target = 0.157512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.130770 restraints weight = 4320.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 2.28
r_work: 0.3473 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.3081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3371  Z= 0.160
  Angle     :  0.603   7.029   4590  Z= 0.311
  Chirality :  0.042   0.234    543
  Planarity :  0.005   0.049    555
  Dihedral  :  4.864  52.459    454
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 17.56 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.94 (0.41), residues: 418
  helix:  1.70 (0.27), residues: 355
  sheet:  None (None), residues: 0
  loop : -0.99 (0.72), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 102 
 HIS   0.003   0.001   HIS A 338 
 PHE   0.020   0.002   PHE A 100 
 TYR   0.023   0.001   TYR A  94 
 ARG   0.002   0.000   ARG A 493 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04544 (  271)
  hydrogen bonds       : angle       4.51179 (  810)
  covalent geometry    : bond        0.00357 ( 3371)
  covalent geometry    : angle       0.60283 ( 4590)

*********************** 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
  77 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A  242 ASP cc_start: 0.7875 (t0) cc_final: 0.7639 (t0)
REVERT: A  297 TYR cc_start: 0.6744 (m-80) cc_final: 0.6129 (t80)
REVERT: A  305 PHE cc_start: 0.7123 (m-80) cc_final: 0.6599 (m-80)
REVERT: A  376 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6520 (mp0)
REVERT: A  441 LEU cc_start: 0.7681 (mt) cc_final: 0.7435 (mt)
REVERT: A  486 PHE cc_start: 0.8390 (m-80) cc_final: 0.8133 (m-80)
  outliers start: 11
  outliers final: 4
  residues processed: 73
  average time/residue: 0.9456
  time to fit residues: 71.5275
Evaluate side-chains
  57 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  402 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 21 optimal weight:    9.9990
   chunk 39 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0570
   chunk 13 optimal weight:    0.0770
   chunk 31 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.8260

-------------------------------------------------------------------------------
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 = 0.3882 r_free = 0.3882 target = 0.158908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.132523 restraints weight = 4264.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 2.27
r_work: 0.3480 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
moved from start:          0.3177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3371  Z= 0.147
  Angle     :  0.593   7.776   4590  Z= 0.308
  Chirality :  0.041   0.229    543
  Planarity :  0.005   0.038    555
  Dihedral  :  4.871  53.303    454
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 19.83 %
    Favored  : 77.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  2.11 (0.41), residues: 418
  helix:  1.77 (0.27), residues: 353
  sheet:  None (None), residues: 0
  loop : -0.57 (0.75), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 102 
 HIS   0.003   0.001   HIS A 338 
 PHE   0.022   0.002   PHE A 100 
 TYR   0.022   0.001   TYR A  94 
 ARG   0.001   0.000   ARG A 492 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04401 (  271)
  hydrogen bonds       : angle       4.38756 (  810)
  covalent geometry    : bond        0.00322 ( 3371)
  covalent geometry    : angle       0.59301 ( 4590)

*********************** 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
  72 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A  127 SER cc_start: 0.8676 (OUTLIER) cc_final: 0.8313 (m)
REVERT: A  242 ASP cc_start: 0.7836 (t0) cc_final: 0.7499 (t0)
REVERT: A  245 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7181 (mp0)
REVERT: A  297 TYR cc_start: 0.6742 (m-80) cc_final: 0.6133 (t80)
REVERT: A  305 PHE cc_start: 0.7069 (m-80) cc_final: 0.6603 (m-80)
REVERT: A  369 ASP cc_start: 0.8493 (t70) cc_final: 0.8276 (t0)
REVERT: A  376 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6520 (mp0)
REVERT: A  441 LEU cc_start: 0.7654 (mt) cc_final: 0.7388 (mt)
REVERT: A  486 PHE cc_start: 0.8415 (m-80) cc_final: 0.8187 (m-80)
  outliers start: 9
  outliers final: 4
  residues processed: 69
  average time/residue: 0.8301
  time to fit residues: 59.7661
Evaluate side-chains
  58 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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 25 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 40 optimal weight:    0.1980
   chunk 9 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.9784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.158853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.130681 restraints weight = 4373.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 2.44
r_work: 0.3493 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
moved from start:          0.3357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3371  Z= 0.153
  Angle     :  0.591   7.066   4590  Z= 0.309
  Chirality :  0.041   0.221    543
  Planarity :  0.005   0.048    555
  Dihedral  :  4.934  52.834    454
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 20.96 %
    Favored  : 75.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  2.12 (0.41), residues: 418
  helix:  1.78 (0.27), residues: 353
  sheet:  None (None), residues: 0
  loop : -0.54 (0.75), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 102 
 HIS   0.002   0.001   HIS A 338 
 PHE   0.015   0.002   PHE A 472 
 TYR   0.022   0.001   TYR A  94 
 ARG   0.001   0.000   ARG A 492 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04401 (  271)
  hydrogen bonds       : angle       4.38227 (  810)
  covalent geometry    : bond        0.00339 ( 3371)
  covalent geometry    : angle       0.59123 ( 4590)

*********************** 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
  68 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.382 
Fit side-chains
REVERT: A   82 ARG cc_start: 0.6970 (OUTLIER) cc_final: 0.6494 (tpp80)
REVERT: A  242 ASP cc_start: 0.7991 (t0) cc_final: 0.7690 (t0)
REVERT: A  245 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7320 (mp0)
REVERT: A  297 TYR cc_start: 0.6770 (m-80) cc_final: 0.6103 (t80)
REVERT: A  369 ASP cc_start: 0.8489 (t70) cc_final: 0.8248 (t0)
REVERT: A  376 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6508 (mp0)
REVERT: A  441 LEU cc_start: 0.7603 (mt) cc_final: 0.7348 (mt)
REVERT: A  486 PHE cc_start: 0.8395 (m-80) cc_final: 0.8081 (m-80)
  outliers start: 12
  outliers final: 4
  residues processed: 65
  average time/residue: 0.8573
  time to fit residues: 58.0389
Evaluate side-chains
  61 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 5 optimal weight:    0.3980
   chunk 14 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 40 optimal weight:    3.9990
   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  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 = 0.3925 r_free = 0.3925 target = 0.161524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.134167 restraints weight = 4234.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 2.42
r_work: 0.3515 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start:          0.3488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3371  Z= 0.133
  Angle     :  0.581   7.495   4590  Z= 0.299
  Chirality :  0.040   0.224    543
  Planarity :  0.005   0.039    555
  Dihedral  :  4.957  56.462    454
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 23.51 %
    Favored  : 74.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  2.22 (0.41), residues: 418
  helix:  1.87 (0.27), residues: 354
  sheet:  None (None), residues: 0
  loop : -0.69 (0.73), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 102 
 HIS   0.003   0.001   HIS A 338 
 PHE   0.013   0.001   PHE A 472 
 TYR   0.021   0.001   TYR A 392 
 ARG   0.001   0.000   ARG A 493 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04154 (  271)
  hydrogen bonds       : angle       4.26406 (  810)
  covalent geometry    : bond        0.00282 ( 3371)
  covalent geometry    : angle       0.58056 ( 4590)

*********************** 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
  66 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A   82 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.6264 (tpp80)
REVERT: A  242 ASP cc_start: 0.7932 (t0) cc_final: 0.7611 (t0)
REVERT: A  245 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7199 (mp0)
REVERT: A  297 TYR cc_start: 0.6792 (m-80) cc_final: 0.6091 (t80)
REVERT: A  369 ASP cc_start: 0.8472 (t70) cc_final: 0.8226 (t0)
REVERT: A  376 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6518 (mp0)
REVERT: A  402 TRP cc_start: 0.5464 (OUTLIER) cc_final: 0.5028 (p-90)
REVERT: A  441 LEU cc_start: 0.7605 (mt) cc_final: 0.7362 (mt)
REVERT: A  486 PHE cc_start: 0.8399 (m-80) cc_final: 0.8089 (m-80)
  outliers start: 7
  outliers final: 2
  residues processed: 64
  average time/residue: 0.8207
  time to fit residues: 54.7920
Evaluate side-chains
  55 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
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  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 13 optimal weight:    0.0980
   chunk 2 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0470
   chunk 19 optimal weight:    3.9990
   chunk 40 optimal weight:    0.4980
   chunk 3 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 20 optimal weight:    9.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.4478

-------------------------------------------------------------------------------
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 = 0.3948 r_free = 0.3948 target = 0.163765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.136800 restraints weight = 4227.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3655 rms_B_bonded: 2.43
r_work: 0.3546 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7246
moved from start:          0.3695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3371  Z= 0.128
  Angle     :  0.585   7.662   4590  Z= 0.302
  Chirality :  0.040   0.229    543
  Planarity :  0.005   0.045    555
  Dihedral  :  4.994  56.577    454
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 23.51 %
    Favored  : 74.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  2.36 (0.41), residues: 418
  helix:  1.93 (0.27), residues: 355
  sheet:  None (None), residues: 0
  loop : -0.45 (0.76), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 102 
 HIS   0.003   0.001   HIS A 338 
 PHE   0.013   0.001   PHE A 472 
 TYR   0.021   0.001   TYR A  94 
 ARG   0.001   0.000   ARG A 493 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04045 (  271)
  hydrogen bonds       : angle       4.21054 (  810)
  covalent geometry    : bond        0.00263 ( 3371)
  covalent geometry    : angle       0.58473 ( 4590)

*********************** 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: 8
    poor density    : 58
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A   82 ARG cc_start: 0.6630 (OUTLIER) cc_final: 0.6215 (tpp80)
REVERT: A   95 SER cc_start: 0.8244 (t) cc_final: 0.8017 (m)
REVERT: A  242 ASP cc_start: 0.7914 (t0) cc_final: 0.7558 (t0)
REVERT: A  245 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7182 (mp0)
REVERT: A  297 TYR cc_start: 0.6807 (m-80) cc_final: 0.6089 (t80)
REVERT: A  369 ASP cc_start: 0.8445 (t70) cc_final: 0.8205 (t0)
REVERT: A  376 GLU cc_start: 0.7304 (mm-30) cc_final: 0.6557 (mp0)
REVERT: A  402 TRP cc_start: 0.5470 (OUTLIER) cc_final: 0.5087 (p-90)
REVERT: A  441 LEU cc_start: 0.7650 (mt) cc_final: 0.7391 (mt)
REVERT: A  486 PHE cc_start: 0.8415 (m-80) cc_final: 0.8153 (m-80)
  outliers start: 8
  outliers final: 3
  residues processed: 65
  average time/residue: 0.7091
  time to fit residues: 48.3421
Evaluate side-chains
  58 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
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  402 TRP
Chi-restraints excluded: chain A residue  444 ILE
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 29 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3915 r_free = 0.3915 target = 0.161009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.133479 restraints weight = 4302.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 2.40
r_work: 0.3495 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7240
moved from start:          0.3680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3371  Z= 0.141
  Angle     :  0.592   7.563   4590  Z= 0.307
  Chirality :  0.041   0.233    543
  Planarity :  0.005   0.036    555
  Dihedral  :  4.910  52.933    454
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 23.80 %
    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 (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:  2.30 (0.41), residues: 418
  helix:  1.91 (0.27), residues: 354
  sheet:  None (None), residues: 0
  loop : -0.58 (0.74), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 102 
 HIS   0.006   0.001   HIS A 338 
 PHE   0.015   0.001   PHE A 472 
 TYR   0.023   0.001   TYR A  94 
 ARG   0.001   0.000   ARG A 493 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04151 (  271)
  hydrogen bonds       : angle       4.26211 (  810)
  covalent geometry    : bond        0.00305 ( 3371)
  covalent geometry    : angle       0.59193 ( 4590)

*********************** 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: 9
    poor density    : 56
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A   82 ARG cc_start: 0.6613 (OUTLIER) cc_final: 0.6213 (tpp80)
REVERT: A  242 ASP cc_start: 0.7919 (t0) cc_final: 0.7612 (t0)
REVERT: A  245 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7330 (mp0)
REVERT: A  297 TYR cc_start: 0.6739 (m-80) cc_final: 0.5999 (t80)
REVERT: A  376 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6539 (mp0)
REVERT: A  389 MET cc_start: 0.7561 (tpt) cc_final: 0.7197 (tpt)
REVERT: A  402 TRP cc_start: 0.5473 (OUTLIER) cc_final: 0.5029 (p-90)
REVERT: A  441 LEU cc_start: 0.7585 (mt) cc_final: 0.7335 (mt)
REVERT: A  486 PHE cc_start: 0.8414 (m-80) cc_final: 0.8109 (m-80)
  outliers start: 9
  outliers final: 2
  residues processed: 64
  average time/residue: 0.8187
  time to fit residues: 54.7470
Evaluate side-chains
  58 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 54
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
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  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 36 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0980
   chunk 20 optimal weight:   10.0000
   chunk 38 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 40 optimal weight:    6.9990
   chunk 14 optimal weight:    0.8980
   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  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 = 0.3941 r_free = 0.3941 target = 0.163266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.135972 restraints weight = 4190.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 2.40
r_work: 0.3535 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7251
moved from start:          0.3785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3371  Z= 0.142
  Angle     :  0.629   8.920   4590  Z= 0.326
  Chirality :  0.041   0.233    543
  Planarity :  0.005   0.048    555
  Dihedral  :  4.946  53.342    454
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.17
  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 (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:  2.41 (0.41), residues: 418
  helix:  2.04 (0.27), residues: 349
  sheet:  None (None), residues: 0
  loop : -0.68 (0.71), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 102 
 HIS   0.004   0.001   HIS A 338 
 PHE   0.014   0.001   PHE A 472 
 TYR   0.023   0.001   TYR A  94 
 ARG   0.001   0.000   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04121 (  271)
  hydrogen bonds       : angle       4.27587 (  810)
  covalent geometry    : bond        0.00311 ( 3371)
  covalent geometry    : angle       0.62875 ( 4590)

********************** 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
  64 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.356 
Fit side-chains
REVERT: A   82 ARG cc_start: 0.6627 (OUTLIER) cc_final: 0.6236 (tpp80)
REVERT: A  242 ASP cc_start: 0.7898 (t0) cc_final: 0.7581 (t0)
REVERT: A  245 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7291 (mp0)
REVERT: A  297 TYR cc_start: 0.6780 (m-80) cc_final: 0.6015 (t80)
REVERT: A  376 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6544 (mp0)
REVERT: A  389 MET cc_start: 0.7583 (tpt) cc_final: 0.7259 (tpt)
REVERT: A  402 TRP cc_start: 0.5406 (OUTLIER) cc_final: 0.4979 (p-90)
REVERT: A  411 MET cc_start: 0.7853 (ttm) cc_final: 0.7637 (ttm)
REVERT: A  441 LEU cc_start: 0.7563 (mt) cc_final: 0.7317 (mt)
REVERT: A  486 PHE cc_start: 0.8396 (m-80) cc_final: 0.8131 (m-80)
  outliers start: 7
  outliers final: 2
  residues processed: 63
  average time/residue: 0.8405
  time to fit residues: 55.1064
Evaluate side-chains
  59 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
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  402 TRP
Chi-restraints excluded: chain A residue  444 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3925 r_free = 0.3925 target = 0.161878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.133941 restraints weight = 4247.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 2.39
r_work: 0.3504 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.3772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3371  Z= 0.148
  Angle     :  0.632   8.733   4590  Z= 0.327
  Chirality :  0.041   0.231    543
  Planarity :  0.005   0.038    555
  Dihedral  :  4.907  51.896    454
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 23.80 %
    Favored  : 74.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  2.35 (0.41), residues: 418
  helix:  1.99 (0.27), residues: 351
  sheet:  None (None), residues: 0
  loop : -0.71 (0.74), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 102 
 HIS   0.004   0.001   HIS A 338 
 PHE   0.015   0.002   PHE A 472 
 TYR   0.023   0.001   TYR A  94 
 ARG   0.001   0.000   ARG A 370 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04176 (  271)
  hydrogen bonds       : angle       4.28771 (  810)
  covalent geometry    : bond        0.00330 ( 3371)
  covalent geometry    : angle       0.63173 ( 4590)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2601.15 seconds
wall clock time: 45 minutes 13.03 seconds (2713.03 seconds total)