Starting phenix.real_space_refine
on Wed Jul 23 23:16:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9n95_49160/07_2025/9n95_49160.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9n95_49160/07_2025/9n95_49160.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9n95_49160/07_2025/9n95_49160.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9n95_49160/07_2025/9n95_49160.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9n95_49160/07_2025/9n95_49160.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9n95_49160/07_2025/9n95_49160.cif"
  }
  resolution = 3.65
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      26      5.16       5
     C    3038      2.51       5
     N     715      2.21       5
     O     780      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 4559
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4559
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 4559
          Classifications: {'peptide': 570}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 22, 'TRANS': 547}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 134
          Unresolved non-hydrogen angles: 156
          Unresolved non-hydrogen dihedrals: 117
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 73
  Time building chain proxies: 3.82, per 1000 atoms: 0.84
  Number of scatterers: 4559
  At special positions: 0
  Unit cell: (86.87, 86.14, 81.76, 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      26     16.00
     O     780      8.00
     N     715      7.00
     C    3038      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: 1.01
  Conformation dependent library (CDL) restraints added in 474.3 milliseconds
  

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1096

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 1 sheets defined
      71.4% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 48
      No H-bonds generated for 'chain 'A' and resid 46 through 48'
    Processing helix  chain 'A' and resid 49 through 72
    Processing helix  chain 'A' and resid 116 through 123
    Processing helix  chain 'A' and resid 126 through 131
    Processing helix  chain 'A' and resid 133 through 159
      removed outlier: 3.707A  pdb=" N   ILE A 137 " --> pdb=" O   GLY A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 167
    Processing helix  chain 'A' and resid 192 through 218
    Processing helix  chain 'A' and resid 241 through 249
    Processing helix  chain 'A' and resid 272 through 274
      No H-bonds generated for 'chain 'A' and resid 272 through 274'
    Processing helix  chain 'A' and resid 275 through 283
    Processing helix  chain 'A' and resid 325 through 342
      removed outlier: 3.643A  pdb=" N   THR A 336 " --> pdb=" O   LEU A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 368
      removed outlier: 3.872A  pdb=" N   ALA A 360 " --> pdb=" O   GLU A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 391
    Processing helix  chain 'A' and resid 392 through 395
      removed outlier: 3.758A  pdb=" N   TRP A 395 " --> pdb=" O   THR A 392 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 392 through 395'
    Processing helix  chain 'A' and resid 409 through 414
      removed outlier: 3.985A  pdb=" N   SER A 412 " --> pdb=" O   LYS A 409 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   GLN A 414 " --> pdb=" O   LEU A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 446
      removed outlier: 3.600A  pdb=" N   TRP A 419 " --> pdb=" O   GLY A 415 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   THR A 438 " --> pdb=" O   PHE A 434 " (cutoff:3.500A)
      Proline residue:  A 439  - end of helix
    Processing helix  chain 'A' and resid 447 through 450
      removed outlier: 3.793A  pdb=" N   ASN A 450 " --> pdb=" O   ASP A 447 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 447 through 450'
    Processing helix  chain 'A' and resid 465 through 491
      Proline residue:  A 480  - end of helix
    Processing helix  chain 'A' and resid 495 through 498
    Processing helix  chain 'A' and resid 499 through 515
    Processing helix  chain 'A' and resid 515 through 532
      removed outlier: 3.599A  pdb=" N   SER A 519 " --> pdb=" O   LEU A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 547
    Processing helix  chain 'A' and resid 553 through 565
    Processing helix  chain 'A' and resid 565 through 574
    Processing helix  chain 'A' and resid 574 through 587
    Processing helix  chain 'A' and resid 606 through 624
      removed outlier: 3.703A  pdb=" N   TYR A 624 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 653
      removed outlier: 4.114A  pdb=" N   PHE A 634 " --> pdb=" O   ILE A 630 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   TYR A 651 " --> pdb=" O   ARG A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 672
      removed outlier: 4.200A  pdb=" N   HIS A 664 " --> pdb=" O   GLU A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 690
      removed outlier: 3.858A  pdb=" N   ILE A 676 " --> pdb=" O   LEU A 672 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 694 through 710
      removed outlier: 4.110A  pdb=" N   LEU A 702 " --> pdb=" O   LEU A 698 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 231 through 232

    274 hydrogen bonds defined for protein.
    807 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: 1.22

  Time building geometry restraints manager: 1.22 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1364
        1.34 -     1.46: 1181
        1.46 -     1.58: 2101
        1.58 -     1.70: 0
        1.70 -     1.81: 41
  Bond restraints: 4687
  Sorted by residual:
  bond pdb=" N   VAL A 257 "
       pdb=" CA  VAL A 257 "
    ideal  model  delta    sigma   weight residual
    1.452  1.495 -0.043 1.18e-02 7.18e+03 1.32e+01
  bond pdb=" N   VAL A 258 "
       pdb=" CA  VAL A 258 "
    ideal  model  delta    sigma   weight residual
    1.459  1.501 -0.042 1.25e-02 6.40e+03 1.15e+01
  bond pdb=" N   ILE A 321 "
       pdb=" CA  ILE A 321 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.25e-02 6.40e+03 9.65e+00
  bond pdb=" N   ASP A 259 "
       pdb=" CA  ASP A 259 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.034 1.16e-02 7.43e+03 8.42e+00
  bond pdb=" N   VAL A 260 "
       pdb=" CA  VAL A 260 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.25e-02 6.40e+03 8.25e+00
  ... (remaining 4682 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 6171
        1.85 -     3.69: 174
        3.69 -     5.54: 36
        5.54 -     7.39: 7
        7.39 -     9.23: 3
  Bond angle restraints: 6391
  Sorted by residual:
  angle pdb=" C   THR A 229 "
        pdb=" CA  THR A 229 "
        pdb=" CB  THR A 229 "
      ideal   model   delta    sigma   weight residual
     115.79  109.08    6.71 1.19e+00 7.06e-01 3.18e+01
  angle pdb=" C   TYR A 324 "
        pdb=" CA  TYR A 324 "
        pdb=" CB  TYR A 324 "
      ideal   model   delta    sigma   weight residual
     115.89  109.21    6.68 1.32e+00 5.74e-01 2.56e+01
  angle pdb=" C   GLN A 552 "
        pdb=" CA  GLN A 552 "
        pdb=" CB  GLN A 552 "
      ideal   model   delta    sigma   weight residual
     115.79  110.29    5.50 1.19e+00 7.06e-01 2.13e+01
  angle pdb=" C   TYR A 252 "
        pdb=" CA  TYR A 252 "
        pdb=" CB  TYR A 252 "
      ideal   model   delta    sigma   weight residual
     110.17  101.49    8.68 1.97e+00 2.58e-01 1.94e+01
  angle pdb=" N   VAL A 257 "
        pdb=" CA  VAL A 257 "
        pdb=" C   VAL A 257 "
      ideal   model   delta    sigma   weight residual
     112.96  109.08    3.88 1.00e+00 1.00e+00 1.51e+01
  ... (remaining 6386 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.21: 2303
       17.21 -    34.42: 294
       34.42 -    51.63: 78
       51.63 -    68.84: 21
       68.84 -    86.05: 2
  Dihedral angle restraints: 2698
    sinusoidal: 1015
      harmonic: 1683
  Sorted by residual:
  dihedral pdb=" C   TYR A 252 "
           pdb=" N   TYR A 252 "
           pdb=" CA  TYR A 252 "
           pdb=" CB  TYR A 252 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -114.10   -8.50     0      2.50e+00 1.60e-01 1.16e+01
  dihedral pdb=" CA  ASP A 447 "
           pdb=" CB  ASP A 447 "
           pdb=" CG  ASP A 447 "
           pdb=" OD1 ASP A 447 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.66   55.66     1      2.00e+01 2.50e-03 1.05e+01
  dihedral pdb=" CA  GLU A 223 "
           pdb=" C   GLU A 223 "
           pdb=" N   ASN A 224 "
           pdb=" CA  ASN A 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.02   15.98     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 2695 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 554
       0.043 -    0.087: 156
       0.087 -    0.130: 30
       0.130 -    0.173: 5
       0.173 -    0.216: 2
  Chirality restraints: 747
  Sorted by residual:
  chirality pdb=" CA  VAL A 257 "
            pdb=" N   VAL A 257 "
            pdb=" C   VAL A 257 "
            pdb=" CB  VAL A 257 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CA  TYR A 252 "
            pdb=" N   TYR A 252 "
            pdb=" C   TYR A 252 "
            pdb=" CB  TYR A 252 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.01e-01
  chirality pdb=" CA  ILE A 321 "
            pdb=" N   ILE A 321 "
            pdb=" C   ILE A 321 "
            pdb=" CB  ILE A 321 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.98e-01
  ... (remaining 744 not shown)

  Planarity restraints: 778
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 241 "    0.019 2.00e-02 2.50e+03   3.70e-02 1.37e+01
        pdb=" C   LYS A 241 "   -0.064 2.00e-02 2.50e+03
        pdb=" O   LYS A 241 "    0.024 2.00e-02 2.50e+03
        pdb=" N   GLU A 242 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 325 "   -0.013 2.00e-02 2.50e+03   2.69e-02 7.24e+00
        pdb=" C   THR A 325 "    0.047 2.00e-02 2.50e+03
        pdb=" O   THR A 325 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ARG A 326 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 255 "    0.009 2.00e-02 2.50e+03   1.76e-02 3.09e+00
        pdb=" C   CYS A 255 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   CYS A 255 "    0.012 2.00e-02 2.50e+03
        pdb=" N   GLU A 256 "    0.010 2.00e-02 2.50e+03
  ... (remaining 775 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 442
        2.74 -     3.28: 4946
        3.28 -     3.82: 7814
        3.82 -     4.36: 8954
        4.36 -     4.90: 14785
  Nonbonded interactions: 36941
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 139 "
            pdb=" OD2 ASP A 646 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   PHE A 434 "
            pdb=" OG1 THR A 438 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   PRO A 253 "
            pdb=" OG1 THR A 254 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" OD2 ASP A 172 "
            pdb=" OG  SER A 177 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" OD2 ASP A 135 "
            pdb=" N   LEU A 659 "
     model   vdw
     2.347 3.120
  ... (remaining 36936 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.060
  Process input model:                     15.670
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  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:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7186
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      :  0.004   0.043   4687  Z= 0.235
  Angle     :  0.774   9.234   6391  Z= 0.457
  Chirality :  0.043   0.216    747
  Planarity :  0.004   0.037    778
  Dihedral  : 16.875  86.054   1602
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 15.12
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  7.89 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  : 23.30 %
    Favored  : 76.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.38), residues: 558
  helix:  0.95 (0.27), residues: 377
  sheet:  None (None), residues: 0
  loop : -2.06 (0.50), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 681 
 HIS   0.007   0.001   HIS A 247 
 PHE   0.016   0.001   PHE A 665 
 TYR   0.011   0.001   TYR A 264 
 ARG   0.005   0.001   ARG A 647 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11784 (  274)
  hydrogen bonds       : angle       5.48031 (  807)
  covalent geometry    : bond        0.00408 ( 4687)
  covalent geometry    : angle       0.77412 ( 6391)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 49
  time to evaluate  : 0.497 
Fit side-chains
REVERT: A  125 ASP cc_start: 0.6767 (t0) cc_final: 0.6282 (t0)
REVERT: A  264 TYR cc_start: 0.4170 (OUTLIER) cc_final: 0.2941 (p90)
REVERT: A  502 MET cc_start: 0.8049 (tpp) cc_final: 0.7256 (tmm)
  outliers start: 2
  outliers final: 0
  residues processed: 51
  average time/residue: 0.1414
  time to fit residues: 9.8758
Evaluate side-chains
  47 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 46
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 23 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0870
   chunk 29 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 643 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.180124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.154849 restraints weight = 5050.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.155759 restraints weight = 4076.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.155759 restraints weight = 3581.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.1065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4687  Z= 0.151
  Angle     :  0.623   6.942   6391  Z= 0.323
  Chirality :  0.041   0.152    747
  Planarity :  0.004   0.041    778
  Dihedral  :  5.013  43.204    608
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  7.71 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 22.06 %
    Favored  : 74.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.37), residues: 558
  helix:  1.09 (0.27), residues: 379
  sheet:  None (None), residues: 0
  loop : -2.16 (0.50), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 681 
 HIS   0.004   0.001   HIS A 138 
 PHE   0.011   0.001   PHE A 665 
 TYR   0.011   0.001   TYR A 638 
 ARG   0.006   0.001   ARG A 647 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03768 (  274)
  hydrogen bonds       : angle       4.55213 (  807)
  covalent geometry    : bond        0.00345 ( 4687)
  covalent geometry    : angle       0.62333 ( 6391)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 48
  time to evaluate  : 0.490 
Fit side-chains
REVERT: A  125 ASP cc_start: 0.6643 (t0) cc_final: 0.6137 (t0)
REVERT: A  169 ASP cc_start: 0.7093 (m-30) cc_final: 0.6877 (t70)
REVERT: A  235 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7383 (tt)
REVERT: A  264 TYR cc_start: 0.4475 (OUTLIER) cc_final: 0.3382 (p90)
REVERT: A  502 MET cc_start: 0.8076 (tpp) cc_final: 0.7201 (tmm)
REVERT: A  652 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7949 (t80)
  outliers start: 17
  outliers final: 7
  residues processed: 62
  average time/residue: 0.1304
  time to fit residues: 11.4128
Evaluate side-chains
  53 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  327 MET
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  504 THR
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  652 PHE
Chi-restraints excluded: chain A residue  703 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   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 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.174396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.149752 restraints weight = 5100.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.150535 restraints weight = 4243.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.150744 restraints weight = 3726.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.1687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4687  Z= 0.169
  Angle     :  0.627   6.459   6391  Z= 0.324
  Chirality :  0.042   0.140    747
  Planarity :  0.004   0.034    778
  Dihedral  :  5.129  47.356    608
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  8.60 %
    Favored  : 91.04 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 22.47 %
    Favored  : 73.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.07 (0.37), residues: 558
  helix:  1.07 (0.27), residues: 378
  sheet:  None (None), residues: 0
  loop : -2.22 (0.48), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 681 
 HIS   0.004   0.001   HIS A 145 
 PHE   0.013   0.001   PHE A 556 
 TYR   0.012   0.001   TYR A 139 
 ARG   0.004   0.001   ARG A 647 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03836 (  274)
  hydrogen bonds       : angle       4.47061 (  807)
  covalent geometry    : bond        0.00390 ( 4687)
  covalent geometry    : angle       0.62655 ( 6391)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 0.439 
Fit side-chains
REVERT: A   65 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7241 (mm)
REVERT: A  125 ASP cc_start: 0.6472 (t0) cc_final: 0.6011 (t0)
REVERT: A  192 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8410 (mt)
REVERT: A  235 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7450 (tt)
REVERT: A  264 TYR cc_start: 0.5079 (OUTLIER) cc_final: 0.3814 (p90)
REVERT: A  420 LEU cc_start: 0.8142 (tp) cc_final: 0.7869 (mt)
REVERT: A  502 MET cc_start: 0.8104 (tpp) cc_final: 0.7882 (tpp)
  outliers start: 18
  outliers final: 11
  residues processed: 77
  average time/residue: 0.1010
  time to fit residues: 11.4671
Evaluate side-chains
  74 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  504 THR
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  652 PHE
Chi-restraints excluded: chain A residue  672 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 31 optimal weight:    0.3980
   chunk 36 optimal weight:    0.4980
   chunk 47 optimal weight:    0.5980
   chunk 41 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.179705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.150551 restraints weight = 5088.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.153259 restraints weight = 3312.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.154935 restraints weight = 2530.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
moved from start:          0.2066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4687  Z= 0.142
  Angle     :  0.618   9.860   6391  Z= 0.308
  Chirality :  0.040   0.145    747
  Planarity :  0.004   0.031    778
  Dihedral  :  4.979  46.241    608
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  8.42 %
    Favored  : 91.22 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 23.92 %
    Favored  : 71.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.37), residues: 558
  helix:  1.28 (0.27), residues: 378
  sheet:  None (None), residues: 0
  loop : -2.15 (0.49), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 681 
 HIS   0.003   0.001   HIS A 145 
 PHE   0.010   0.001   PHE A 684 
 TYR   0.011   0.001   TYR A 252 
 ARG   0.004   0.001   ARG A 647 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03512 (  274)
  hydrogen bonds       : angle       4.31210 (  807)
  covalent geometry    : bond        0.00326 ( 4687)
  covalent geometry    : angle       0.61780 ( 6391)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 59
  time to evaluate  : 0.488 
Fit side-chains
REVERT: A   65 ILE cc_start: 0.7000 (OUTLIER) cc_final: 0.6685 (mm)
REVERT: A  125 ASP cc_start: 0.6635 (t0) cc_final: 0.6123 (t0)
REVERT: A  192 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8184 (mt)
REVERT: A  264 TYR cc_start: 0.4456 (OUTLIER) cc_final: 0.3452 (p90)
REVERT: A  408 TRP cc_start: 0.9239 (m-90) cc_final: 0.8809 (m-90)
REVERT: A  502 MET cc_start: 0.7976 (tpp) cc_final: 0.7709 (tpp)
REVERT: A  652 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.8037 (t80)
  outliers start: 23
  outliers final: 14
  residues processed: 76
  average time/residue: 0.1116
  time to fit residues: 12.4187
Evaluate side-chains
  72 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 54
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  327 MET
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  359 MET
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  511 ILE
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  627 THR
Chi-restraints excluded: chain A residue  652 PHE
Chi-restraints excluded: chain A residue  670 GLN
Chi-restraints excluded: chain A residue  672 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0170
   chunk 56 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0670
   chunk 7 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.5356

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.179422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.149716 restraints weight = 5162.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.152463 restraints weight = 3284.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.154355 restraints weight = 2471.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7115
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4687  Z= 0.140
  Angle     :  0.620   8.066   6391  Z= 0.308
  Chirality :  0.040   0.133    747
  Planarity :  0.004   0.030    778
  Dihedral  :  4.982  49.105    608
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  8.60 %
    Favored  : 91.04 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 24.33 %
    Favored  : 70.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.37), residues: 558
  helix:  1.27 (0.27), residues: 382
  sheet:  None (None), residues: 0
  loop : -1.98 (0.51), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 681 
 HIS   0.003   0.001   HIS A 145 
 PHE   0.010   0.001   PHE A 665 
 TYR   0.012   0.001   TYR A 252 
 ARG   0.004   0.001   ARG A 647 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03480 (  274)
  hydrogen bonds       : angle       4.25944 (  807)
  covalent geometry    : bond        0.00320 ( 4687)
  covalent geometry    : angle       0.61990 ( 6391)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 52
  time to evaluate  : 0.480 
Fit side-chains
REVERT: A  125 ASP cc_start: 0.6627 (t0) cc_final: 0.6112 (t0)
REVERT: A  192 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8174 (mt)
REVERT: A  264 TYR cc_start: 0.4844 (OUTLIER) cc_final: 0.3740 (p90)
REVERT: A  408 TRP cc_start: 0.9247 (m-90) cc_final: 0.8821 (m-90)
REVERT: A  502 MET cc_start: 0.7833 (tpp) cc_final: 0.7571 (tpp)
REVERT: A  652 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8064 (t80)
  outliers start: 27
  outliers final: 16
  residues processed: 73
  average time/residue: 0.1041
  time to fit residues: 11.1522
Evaluate side-chains
  71 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 52
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  327 MET
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  359 MET
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  511 ILE
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  627 THR
Chi-restraints excluded: chain A residue  652 PHE
Chi-restraints excluded: chain A residue  672 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 16 optimal weight:    0.3980
   chunk 48 optimal weight:    0.5980
   chunk 9 optimal weight:    0.0770
   chunk 14 optimal weight:    0.0470
   chunk 28 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0050
   chunk 41 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.2250

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.190672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.160267 restraints weight = 4953.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.163381 restraints weight = 3039.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.165416 restraints weight = 2245.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7037
moved from start:          0.2514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   4687  Z= 0.112
  Angle     :  0.585   7.932   6391  Z= 0.290
  Chirality :  0.038   0.126    747
  Planarity :  0.004   0.031    778
  Dihedral  :  4.824  49.437    608
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  8.60 %
    Favored  : 91.04 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 25.57 %
    Favored  : 70.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.38), residues: 558
  helix:  1.53 (0.27), residues: 382
  sheet:  None (None), residues: 0
  loop : -1.96 (0.52), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 395 
 HIS   0.003   0.001   HIS A 386 
 PHE   0.009   0.001   PHE A 684 
 TYR   0.010   0.001   TYR A 638 
 ARG   0.003   0.000   ARG A 228 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03102 (  274)
  hydrogen bonds       : angle       4.12636 (  807)
  covalent geometry    : bond        0.00238 ( 4687)
  covalent geometry    : angle       0.58502 ( 6391)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 47
  time to evaluate  : 0.480 
Fit side-chains
REVERT: A  125 ASP cc_start: 0.6589 (OUTLIER) cc_final: 0.6098 (t0)
REVERT: A  192 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8121 (mt)
REVERT: A  264 TYR cc_start: 0.4328 (OUTLIER) cc_final: 0.3465 (p90)
REVERT: A  408 TRP cc_start: 0.9174 (m-90) cc_final: 0.8765 (m-90)
REVERT: A  502 MET cc_start: 0.7789 (tpp) cc_final: 0.7547 (tpp)
REVERT: A  652 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.8135 (t80)
  outliers start: 18
  outliers final: 9
  residues processed: 61
  average time/residue: 0.1096
  time to fit residues: 9.8126
Evaluate side-chains
  59 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  125 ASP
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  359 MET
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  652 PHE
Chi-restraints excluded: chain A residue  672 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 10 optimal weight:    0.3980
   chunk 21 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0770
   chunk 52 optimal weight:    0.9990
   chunk 48 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.181286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.151823 restraints weight = 5008.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.154413 restraints weight = 3297.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.156278 restraints weight = 2512.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7129
moved from start:          0.2637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4687  Z= 0.129
  Angle     :  0.596   8.593   6391  Z= 0.296
  Chirality :  0.040   0.140    747
  Planarity :  0.004   0.030    778
  Dihedral  :  4.867  51.674    608
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  8.42 %
    Favored  : 91.22 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 24.95 %
    Favored  : 70.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.37), residues: 558
  helix:  1.49 (0.27), residues: 382
  sheet:  None (None), residues: 0
  loop : -1.96 (0.51), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 395 
 HIS   0.005   0.001   HIS A 247 
 PHE   0.009   0.001   PHE A 684 
 TYR   0.010   0.001   TYR A 139 
 ARG   0.003   0.000   ARG A 647 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03232 (  274)
  hydrogen bonds       : angle       4.11976 (  807)
  covalent geometry    : bond        0.00294 ( 4687)
  covalent geometry    : angle       0.59597 ( 6391)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 46
  time to evaluate  : 0.485 
Fit side-chains
REVERT: A  125 ASP cc_start: 0.6599 (t0) cc_final: 0.6096 (t0)
REVERT: A  192 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8197 (mt)
REVERT: A  264 TYR cc_start: 0.4671 (OUTLIER) cc_final: 0.3731 (p90)
REVERT: A  408 TRP cc_start: 0.9239 (m-90) cc_final: 0.8842 (m-90)
REVERT: A  502 MET cc_start: 0.7849 (tpp) cc_final: 0.7575 (tpp)
REVERT: A  652 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.8094 (t80)
  outliers start: 20
  outliers final: 15
  residues processed: 62
  average time/residue: 0.1022
  time to fit residues: 9.4356
Evaluate side-chains
  64 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 46
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  327 MET
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  359 MET
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  504 THR
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  627 THR
Chi-restraints excluded: chain A residue  652 PHE
Chi-restraints excluded: chain A residue  672 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 41 optimal weight:    0.2980
   chunk 6 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 32 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 2 optimal weight:    0.4980
   chunk 56 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0270
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.4038

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.179205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.152828 restraints weight = 5057.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.154266 restraints weight = 3896.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.155466 restraints weight = 3282.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.2833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4687  Z= 0.121
  Angle     :  0.585   8.198   6391  Z= 0.289
  Chirality :  0.039   0.141    747
  Planarity :  0.004   0.031    778
  Dihedral  :  4.817  53.259    608
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  9.32 %
    Favored  : 90.32 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 26.19 %
    Favored  : 70.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.38), residues: 558
  helix:  1.58 (0.27), residues: 382
  sheet:  None (None), residues: 0
  loop : -1.96 (0.51), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 395 
 HIS   0.003   0.001   HIS A 247 
 PHE   0.010   0.001   PHE A 684 
 TYR   0.010   0.001   TYR A 139 
 ARG   0.004   0.000   ARG A 647 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03124 (  274)
  hydrogen bonds       : angle       4.07209 (  807)
  covalent geometry    : bond        0.00271 ( 4687)
  covalent geometry    : angle       0.58470 ( 6391)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 46
  time to evaluate  : 0.444 
Fit side-chains
REVERT: A  192 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8300 (mt)
REVERT: A  264 TYR cc_start: 0.4711 (OUTLIER) cc_final: 0.3695 (p90)
REVERT: A  408 TRP cc_start: 0.9258 (m-90) cc_final: 0.8999 (m-90)
REVERT: A  502 MET cc_start: 0.7934 (tpp) cc_final: 0.7693 (tpp)
REVERT: A  652 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.8042 (t80)
  outliers start: 18
  outliers final: 14
  residues processed: 60
  average time/residue: 0.1039
  time to fit residues: 9.2328
Evaluate side-chains
  61 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 44
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  359 MET
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  504 THR
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  652 PHE
Chi-restraints excluded: chain A residue  672 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 34 optimal weight:    0.5980
   chunk 41 optimal weight:    0.3980
   chunk 39 optimal weight:    0.9990
   chunk 8 optimal weight:    0.4980
   chunk 38 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0370
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 46 optimal weight:    0.0470
   chunk 29 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.3156

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.180732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.156243 restraints weight = 5000.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.156610 restraints weight = 3584.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.157088 restraints weight = 3080.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
moved from start:          0.2932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4687  Z= 0.116
  Angle     :  0.584   8.931   6391  Z= 0.289
  Chirality :  0.039   0.133    747
  Planarity :  0.004   0.031    778
  Dihedral  :  4.833  55.845    608
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  8.24 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 25.57 %
    Favored  : 70.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.37), residues: 558
  helix:  1.70 (0.27), residues: 376
  sheet:  None (None), residues: 0
  loop : -1.89 (0.49), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 395 
 HIS   0.003   0.001   HIS A 386 
 PHE   0.010   0.001   PHE A 684 
 TYR   0.010   0.001   TYR A 139 
 ARG   0.003   0.000   ARG A 647 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03070 (  274)
  hydrogen bonds       : angle       4.03953 (  807)
  covalent geometry    : bond        0.00255 ( 4687)
  covalent geometry    : angle       0.58403 ( 6391)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 45
  time to evaluate  : 0.486 
Fit side-chains
REVERT: A  192 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8300 (mt)
REVERT: A  222 GLU cc_start: 0.7774 (mp0) cc_final: 0.7558 (mp0)
REVERT: A  264 TYR cc_start: 0.4615 (OUTLIER) cc_final: 0.3490 (p90)
REVERT: A  408 TRP cc_start: 0.9246 (m-90) cc_final: 0.8963 (m-90)
REVERT: A  502 MET cc_start: 0.7932 (tpp) cc_final: 0.7700 (tpp)
REVERT: A  585 MET cc_start: 0.3788 (tmm) cc_final: 0.2384 (mtp)
REVERT: A  615 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7882 (mm)
REVERT: A  652 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.8069 (t80)
  outliers start: 20
  outliers final: 16
  residues processed: 60
  average time/residue: 0.1085
  time to fit residues: 9.6020
Evaluate side-chains
  65 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 45
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  327 MET
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  359 MET
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  652 PHE
Chi-restraints excluded: chain A residue  672 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 20 optimal weight:    0.0050
   chunk 2 optimal weight:    0.5980
   chunk 44 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 32 optimal weight:    0.4980
   chunk 7 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0030
   chunk 33 optimal weight:    0.2980
   chunk 9 optimal weight:    0.3980
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.2404

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.182653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.156803 restraints weight = 4986.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.158295 restraints weight = 3888.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.158440 restraints weight = 3211.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7227
moved from start:          0.3074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   4687  Z= 0.109
  Angle     :  0.570   8.107   6391  Z= 0.281
  Chirality :  0.038   0.126    747
  Planarity :  0.004   0.031    778
  Dihedral  :  4.757  56.698    608
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.32 %
    Favored  : 90.50 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 25.57 %
    Favored  : 70.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.38), residues: 558
  helix:  1.81 (0.27), residues: 376
  sheet:  None (None), residues: 0
  loop : -1.90 (0.49), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 395 
 HIS   0.003   0.001   HIS A 386 
 PHE   0.010   0.001   PHE A 684 
 TYR   0.010   0.001   TYR A 139 
 ARG   0.003   0.000   ARG A 647 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02938 (  274)
  hydrogen bonds       : angle       3.97447 (  807)
  covalent geometry    : bond        0.00233 ( 4687)
  covalent geometry    : angle       0.56958 ( 6391)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 48
  time to evaluate  : 0.460 
Fit side-chains
REVERT: A  192 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8284 (mt)
REVERT: A  349 MET cc_start: 0.5526 (mmt) cc_final: 0.5317 (mmt)
REVERT: A  408 TRP cc_start: 0.9222 (m-90) cc_final: 0.8912 (m-90)
REVERT: A  502 MET cc_start: 0.7904 (tpp) cc_final: 0.7659 (tpp)
REVERT: A  585 MET cc_start: 0.3759 (tmm) cc_final: 0.2325 (mtp)
REVERT: A  615 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7814 (mm)
REVERT: A  631 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8344 (tt)
REVERT: A  652 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.8041 (t80)
  outliers start: 21
  outliers final: 16
  residues processed: 65
  average time/residue: 0.1338
  time to fit residues: 12.1190
Evaluate side-chains
  65 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 45
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  359 MET
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  631 ILE
Chi-restraints excluded: chain A residue  652 PHE
Chi-restraints excluded: chain A residue  672 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 52 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0870
   chunk 4 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 50 optimal weight:    0.6980
   chunk 48 optimal weight:    0.5980
   chunk 47 optimal weight:    0.5980
   chunk 20 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 HIS
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.180612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.154081 restraints weight = 4973.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.155528 restraints weight = 3906.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.156312 restraints weight = 3289.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4687  Z= 0.131
  Angle     :  0.600   8.312   6391  Z= 0.298
  Chirality :  0.040   0.128    747
  Planarity :  0.004   0.030    778
  Dihedral  :  4.879  57.956    608
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.96 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 25.36 %
    Favored  : 69.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.37), residues: 558
  helix:  1.72 (0.27), residues: 376
  sheet:  None (None), residues: 0
  loop : -1.88 (0.49), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 395 
 HIS   0.003   0.001   HIS A 145 
 PHE   0.009   0.001   PHE A 684 
 TYR   0.011   0.001   TYR A 139 
 ARG   0.004   0.001   ARG A 647 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03107 (  274)
  hydrogen bonds       : angle       4.03054 (  807)
  covalent geometry    : bond        0.00302 ( 4687)
  covalent geometry    : angle       0.59984 ( 6391)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1903.17 seconds
wall clock time: 33 minutes 40.69 seconds (2020.69 seconds total)