Starting phenix.real_space_refine
on Wed Jun  4 23:04:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hfi_34721/06_2025/8hfi_34721.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hfi_34721/06_2025/8hfi_34721.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hfi_34721/06_2025/8hfi_34721.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hfi_34721/06_2025/8hfi_34721.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hfi_34721/06_2025/8hfi_34721.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hfi_34721/06_2025/8hfi_34721.cif"
  }
  resolution = 2.5
  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=   0.144
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: 5
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     Cl      1      4.86       5
     C    2963      2.51       5
     N     681      2.21       5
     O     778      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 4443
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4383
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 548, 4383
          Classifications: {'peptide': 548}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 528}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 60
          Unusual residues: {' CL': 1, 'DSM': 1}
          Classifications: {'undetermined': 2, 'water': 39}
          Link IDs: {None: 40}
  Time building chain proxies: 3.91, per 1000 atoms: 0.88
  Number of scatterers: 4443
  At special positions: 0
  Unit cell: (69.28, 68.1975, 97.425, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      20     16.00
     O     778      8.00
     N     681      7.00
     C    2963      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 176 " - pdb=" SG  CYS A 185 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.18
  Conformation dependent library (CDL) restraints added in 505.4 milliseconds
  

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1008

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 1 sheets defined
      83.0% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 60 through 74
      removed outlier: 3.552A  pdb=" N   PHE A  65 " --> pdb=" O   LYS A  61 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   VAL A  74 " --> pdb=" O   VAL A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 89
      removed outlier: 3.518A  pdb=" N   VAL A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   PHE A  82 " --> pdb=" O   ASN A  78 " (cutoff:3.500A)
      Proline residue:  A  83  - end of helix
    Processing helix  chain 'A' and resid 91 through 93
      No H-bonds generated for 'chain 'A' and resid 91 through 93'
    Processing helix  chain 'A' and resid 94 through 105
    Processing helix  chain 'A' and resid 105 through 121
    Processing helix  chain 'A' and resid 125 through 130
      removed outlier: 3.623A  pdb=" N   TRP A 128 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ILE A 130 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 133
      No H-bonds generated for 'chain 'A' and resid 131 through 133'
    Processing helix  chain 'A' and resid 134 through 166
      removed outlier: 3.520A  pdb=" N   GLY A 149 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   PHE A 150 " --> pdb=" O   LEU A 146 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   TYR A 151 " --> pdb=" O   TYR A 147 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   VAL A 154 " --> pdb=" O   PHE A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 217
    Processing helix  chain 'A' and resid 220 through 224
    Processing helix  chain 'A' and resid 234 through 253
    Processing helix  chain 'A' and resid 262 through 283
      removed outlier: 3.854A  pdb=" N   THR A 266 " --> pdb=" O   VAL A 262 " (cutoff:3.500A)
      Proline residue:  A 270  - end of helix
      removed outlier: 3.826A  pdb=" N   THR A 283 " --> pdb=" O   VAL A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 296
    Processing helix  chain 'A' and resid 298 through 304
      removed outlier: 3.767A  pdb=" N   GLU A 304 " --> pdb=" O   ARG A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 320
    Processing helix  chain 'A' and resid 324 through 331
    Processing helix  chain 'A' and resid 338 through 373
    Processing helix  chain 'A' and resid 375 through 379
      removed outlier: 3.798A  pdb=" N   VAL A 379 " --> pdb=" O   ILE A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 397
      Proline residue:  A 392  - end of helix
      removed outlier: 3.705A  pdb=" N   THR A 397 " --> pdb=" O   GLU A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 435
      removed outlier: 3.659A  pdb=" N   GLY A 422 " --> pdb=" O   ASP A 418 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   VAL A 427 " --> pdb=" O   GLY A 423 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ASP A 434 " --> pdb=" O   GLY A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 441
    Processing helix  chain 'A' and resid 441 through 459
    Processing helix  chain 'A' and resid 464 through 476
      removed outlier: 3.613A  pdb=" N   VAL A 468 " --> pdb=" O   GLY A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 496
    Processing helix  chain 'A' and resid 497 through 510
    Processing helix  chain 'A' and resid 514 through 523
    Processing helix  chain 'A' and resid 523 through 539
    Processing helix  chain 'A' and resid 551 through 567
      removed outlier: 3.594A  pdb=" N   ASN A 555 " --> pdb=" O   PRO A 551 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   SER A 565 " --> pdb=" O   ILE A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 580
    Processing helix  chain 'A' and resid 583 through 592
    Processing helix  chain 'A' and resid 594 through 604
      removed outlier: 3.790A  pdb=" N   HIS A 598 " --> pdb=" O   GLU A 595 " (cutoff:3.500A)
      removed outlier: 5.507A  pdb=" N   HIS A 599 " --> pdb=" O   ASN A 596 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ALA A 602 " --> pdb=" O   HIS A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 609
    Processing helix  chain 'A' and resid 610 through 616
      removed outlier: 3.813A  pdb=" N   TRP A 614 " --> pdb=" O   GLN A 610 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545

    299 hydrogen bonds defined for protein.
    855 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: 1.24

  Time building geometry restraints manager: 1.38 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 647
        1.30 -     1.43: 1376
        1.43 -     1.55: 2493
        1.55 -     1.68: 0
        1.68 -     1.81: 31
  Bond restraints: 4547
  Sorted by residual:
  bond pdb=" C   SER A 318 "
       pdb=" O   SER A 318 "
    ideal  model  delta    sigma   weight residual
    1.236  1.167  0.070 1.15e-02 7.56e+03 3.70e+01
  bond pdb=" CA  SER A 318 "
       pdb=" CB  SER A 318 "
    ideal  model  delta    sigma   weight residual
    1.529  1.457  0.072 1.55e-02 4.16e+03 2.13e+01
  bond pdb=" N   GLY A  60 "
       pdb=" CA  GLY A  60 "
    ideal  model  delta    sigma   weight residual
    1.451  1.491 -0.040 1.60e-02 3.91e+03 6.30e+00
  bond pdb=" C5  DSM A 701 "
       pdb=" C6  DSM A 701 "
    ideal  model  delta    sigma   weight residual
    1.524  1.549 -0.025 2.00e-02 2.50e+03 1.52e+00
  bond pdb=" CG1 ILE A 481 "
       pdb=" CD1 ILE A 481 "
    ideal  model  delta    sigma   weight residual
    1.513  1.467  0.046 3.90e-02 6.57e+02 1.38e+00
  ... (remaining 4542 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 6113
        2.08 -     4.17: 71
        4.17 -     6.25: 10
        6.25 -     8.33: 5
        8.33 -    10.41: 3
  Bond angle restraints: 6202
  Sorted by residual:
  angle pdb=" C   PHE A 317 "
        pdb=" N   SER A 318 "
        pdb=" CA  SER A 318 "
      ideal   model   delta    sigma   weight residual
     120.44  127.79   -7.35 1.30e+00 5.92e-01 3.20e+01
  angle pdb=" CA  SER A 318 "
        pdb=" C   SER A 318 "
        pdb=" O   SER A 318 "
      ideal   model   delta    sigma   weight residual
     120.82  116.52    4.30 1.05e+00 9.07e-01 1.67e+01
  angle pdb=" C   GLY A 106 "
        pdb=" N   MET A 107 "
        pdb=" CA  MET A 107 "
      ideal   model   delta    sigma   weight residual
     119.78  114.75    5.03 1.24e+00 6.50e-01 1.64e+01
  angle pdb=" N   TYR A 205 "
        pdb=" CA  TYR A 205 "
        pdb=" C   TYR A 205 "
      ideal   model   delta    sigma   weight residual
     110.80  118.44   -7.64 2.13e+00 2.20e-01 1.29e+01
  angle pdb=" C4  DSM A 701 "
        pdb=" C13 DSM A 701 "
        pdb=" C5  DSM A 701 "
      ideal   model   delta    sigma   weight residual
     115.54  125.95  -10.41 3.00e+00 1.11e-01 1.20e+01
  ... (remaining 6197 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 2242
       17.44 -    34.87: 216
       34.87 -    52.31: 65
       52.31 -    69.74: 14
       69.74 -    87.18: 2
  Dihedral angle restraints: 2539
    sinusoidal: 955
      harmonic: 1584
  Sorted by residual:
  dihedral pdb=" CA  ILE A 103 "
           pdb=" C   ILE A 103 "
           pdb=" N   ILE A 104 "
           pdb=" CA  ILE A 104 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.31  -23.69     0      5.00e+00 4.00e-02 2.24e+01
  dihedral pdb=" C   TYR A 205 "
           pdb=" N   TYR A 205 "
           pdb=" CA  TYR A 205 "
           pdb=" CB  TYR A 205 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.79   10.19     0      2.50e+00 1.60e-01 1.66e+01
  dihedral pdb=" N   TYR A 205 "
           pdb=" C   TYR A 205 "
           pdb=" CA  TYR A 205 "
           pdb=" CB  TYR A 205 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  132.66   -9.86     0      2.50e+00 1.60e-01 1.55e+01
  ... (remaining 2536 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.091: 670
       0.091 -    0.181: 19
       0.181 -    0.271: 0
       0.271 -    0.362: 0
       0.362 -    0.452: 1
  Chirality restraints: 690
  Sorted by residual:
  chirality pdb=" CA  TYR A 205 "
            pdb=" N   TYR A 205 "
            pdb=" C   TYR A 205 "
            pdb=" CB  TYR A 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.11e+00
  chirality pdb=" CA  ILE A 103 "
            pdb=" N   ILE A 103 "
            pdb=" C   ILE A 103 "
            pdb=" CB  ILE A 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.15e-01
  chirality pdb=" CA  ILE A 606 "
            pdb=" N   ILE A 606 "
            pdb=" C   ILE A 606 "
            pdb=" CB  ILE A 606 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  ... (remaining 687 not shown)

  Planarity restraints: 752
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 103 "    0.020 2.00e-02 2.50e+03   4.06e-02 1.65e+01
        pdb=" C   ILE A 103 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   ILE A 103 "    0.027 2.00e-02 2.50e+03
        pdb=" N   ILE A 104 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 318 "    0.016 2.00e-02 2.50e+03   3.34e-02 1.11e+01
        pdb=" C   SER A 318 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   SER A 318 "    0.022 2.00e-02 2.50e+03
        pdb=" N   LEU A 319 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1  DSM A 701 "   -0.013 2.00e-02 2.50e+03   2.22e-02 9.86e+00
        pdb=" C13 DSM A 701 "    0.010 2.00e-02 2.50e+03
        pdb=" C14 DSM A 701 "   -0.041 2.00e-02 2.50e+03
        pdb=" C2  DSM A 701 "   -0.000 2.00e-02 2.50e+03
        pdb=" C3  DSM A 701 "    0.017 2.00e-02 2.50e+03
        pdb=" C4  DSM A 701 "    0.005 2.00e-02 2.50e+03
        pdb=" C5  DSM A 701 "   -0.014 2.00e-02 2.50e+03
        pdb=" N1  DSM A 701 "    0.038 2.00e-02 2.50e+03
  ... (remaining 749 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 33
        2.59 -     3.16: 3814
        3.16 -     3.74: 7288
        3.74 -     4.32: 10368
        4.32 -     4.90: 17016
  Nonbonded interactions: 38519
  Sorted by model distance:
  nonbonded pdb=" O   HOH A 808 "
            pdb=" O   HOH A 838 "
     model   vdw
     2.008 3.040
  nonbonded pdb=" O   HOH A 812 "
            pdb=" O   HOH A 821 "
     model   vdw
     2.045 3.040
  nonbonded pdb=" O   PHE A 475 "
            pdb=" O   HOH A 801 "
     model   vdw
     2.089 3.040
  nonbonded pdb=" O   ALA A 589 "
            pdb=" OG1 THR A 593 "
     model   vdw
     2.166 3.040
  nonbonded pdb=" OG1 THR A 474 "
            pdb=" O   HOH A 802 "
     model   vdw
     2.180 3.040
  ... (remaining 38514 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:             0.340
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.750
  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:10.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
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   0.072   4548  Z= 0.185
  Angle     :  0.628  10.413   6204  Z= 0.331
  Chirality :  0.041   0.452    690
  Planarity :  0.004   0.041    752
  Dihedral  : 15.560  87.178   1528
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 16.23 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.38), residues: 544
  helix:  1.42 (0.28), residues: 375
  sheet:  None (None), residues: 0
  loop :  0.22 (0.53), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  80 
 HIS   0.001   0.000   HIS A 220 
 PHE   0.011   0.001   PHE A 409 
 TYR   0.013   0.001   TYR A  84 
 ARG   0.001   0.000   ARG A 512 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13786 (  299)
  hydrogen bonds       : angle       5.50049 (  855)
  SS BOND              : bond        0.00338 (    1)
  SS BOND              : angle       0.69318 (    2)
  covalent geometry    : bond        0.00340 ( 4547)
  covalent geometry    : angle       0.62831 ( 6202)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.477 
Fit side-chains
REVERT: A  488 GLU cc_start: 0.8457 (tt0) cc_final: 0.8223 (tt0)
  outliers start: 5
  outliers final: 5
  residues processed: 60
  average time/residue: 0.8649
  time to fit residues: 54.8651
Evaluate side-chains
  56 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  318 SER
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain A residue  396 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 40 optimal weight:    0.7980
   chunk 22 optimal weight:    4.9990
   chunk 13 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9980
   chunk 21 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 280 HIS
A 375 ASN
A 507 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.132196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.108452 restraints weight = 5140.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 1.50
r_work: 0.2929 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2812 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.0890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   4548  Z= 0.170
  Angle     :  0.623   8.572   6204  Z= 0.312
  Chirality :  0.043   0.143    690
  Planarity :  0.005   0.042    752
  Dihedral  :  7.519  61.121    605
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 14.29 %
    Favored  : 83.77 %
  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:  1.49 (0.37), residues: 544
  helix:  1.28 (0.27), residues: 387
  sheet:  None (None), residues: 0
  loop :  0.49 (0.55), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  80 
 HIS   0.002   0.001   HIS A 220 
 PHE   0.013   0.002   PHE A 409 
 TYR   0.015   0.001   TYR A  84 
 ARG   0.002   0.000   ARG A 442 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06084 (  299)
  hydrogen bonds       : angle       4.83990 (  855)
  SS BOND              : bond        0.00470 (    1)
  SS BOND              : angle       0.98930 (    2)
  covalent geometry    : bond        0.00404 ( 4547)
  covalent geometry    : angle       0.62328 ( 6202)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.476 
Fit side-chains
REVERT: A  242 MET cc_start: 0.8674 (mtp) cc_final: 0.8361 (mtp)
REVERT: A  368 MET cc_start: 0.8662 (mtp) cc_final: 0.8430 (mtp)
  outliers start: 9
  outliers final: 7
  residues processed: 58
  average time/residue: 0.6895
  time to fit residues: 42.9051
Evaluate side-chains
  57 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  450 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 27 optimal weight:    0.7980
   chunk 7 optimal weight:    5.9990
   chunk 29 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 375 ASN
A 507 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.134507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.111211 restraints weight = 5159.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 1.49
r_work: 0.2925 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2808 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.1085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4548  Z= 0.129
  Angle     :  0.557   8.234   6204  Z= 0.277
  Chirality :  0.040   0.132    690
  Planarity :  0.004   0.038    752
  Dihedral  :  7.340  63.486    602
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.15 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.37), residues: 544
  helix:  1.58 (0.27), residues: 382
  sheet:  None (None), residues: 0
  loop :  0.43 (0.54), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 553 
 HIS   0.002   0.001   HIS A 599 
 PHE   0.012   0.001   PHE A 409 
 TYR   0.016   0.001   TYR A  84 
 ARG   0.001   0.000   ARG A 442 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05110 (  299)
  hydrogen bonds       : angle       4.58495 (  855)
  SS BOND              : bond        0.00336 (    1)
  SS BOND              : angle       0.83080 (    2)
  covalent geometry    : bond        0.00285 ( 4547)
  covalent geometry    : angle       0.55689 ( 6202)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.549 
Fit side-chains
REVERT: A  368 MET cc_start: 0.8559 (mtp) cc_final: 0.8302 (mtp)
REVERT: A  488 GLU cc_start: 0.8670 (tt0) cc_final: 0.8332 (tt0)
REVERT: A  515 LEU cc_start: 0.8949 (tp) cc_final: 0.8746 (tp)
  outliers start: 8
  outliers final: 4
  residues processed: 61
  average time/residue: 1.2704
  time to fit residues: 81.7091
Evaluate side-chains
  57 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  444 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 38 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 11 optimal weight:    6.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 370 HIS
A 375 ASN
A 507 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.134540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.111108 restraints weight = 5163.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 1.51
r_work: 0.2968 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2852 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.1276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4548  Z= 0.128
  Angle     :  0.551   8.320   6204  Z= 0.273
  Chirality :  0.040   0.131    690
  Planarity :  0.004   0.037    752
  Dihedral  :  7.041  63.897    600
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 15.37 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.37), residues: 544
  helix:  1.58 (0.26), residues: 386
  sheet:  None (None), residues: 0
  loop :  0.44 (0.54), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 553 
 HIS   0.002   0.001   HIS A 599 
 PHE   0.012   0.001   PHE A 409 
 TYR   0.016   0.001   TYR A  84 
 ARG   0.001   0.000   ARG A 341 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05085 (  299)
  hydrogen bonds       : angle       4.53283 (  855)
  SS BOND              : bond        0.00347 (    1)
  SS BOND              : angle       0.83616 (    2)
  covalent geometry    : bond        0.00282 ( 4547)
  covalent geometry    : angle       0.55076 ( 6202)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.891 
Fit side-chains
REVERT: A  242 MET cc_start: 0.8686 (mtp) cc_final: 0.8430 (mtp)
REVERT: A  368 MET cc_start: 0.8591 (mtp) cc_final: 0.8209 (mtp)
REVERT: A  488 GLU cc_start: 0.8643 (tt0) cc_final: 0.8410 (tt0)
REVERT: A  515 LEU cc_start: 0.8933 (tp) cc_final: 0.8717 (tp)
  outliers start: 9
  outliers final: 5
  residues processed: 64
  average time/residue: 1.3948
  time to fit residues: 94.0724
Evaluate side-chains
  57 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  444 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0670
   chunk 36 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 28 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.7720

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

Flipped N/Q/H residues before XYZ refinement:
A 507 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.135068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.111765 restraints weight = 5250.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 1.52
r_work: 0.2953 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2837 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.1368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4548  Z= 0.124
  Angle     :  0.542   8.440   6204  Z= 0.268
  Chirality :  0.040   0.130    690
  Planarity :  0.004   0.036    752
  Dihedral  :  7.009  64.474    600
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 16.23 %
    Favored  : 81.60 %
  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:  1.94 (0.37), residues: 544
  helix:  1.71 (0.27), residues: 381
  sheet:  None (None), residues: 0
  loop :  0.43 (0.55), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 553 
 HIS   0.002   0.001   HIS A 599 
 PHE   0.012   0.001   PHE A 409 
 TYR   0.016   0.001   TYR A  84 
 ARG   0.001   0.000   ARG A 512 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04919 (  299)
  hydrogen bonds       : angle       4.47329 (  855)
  SS BOND              : bond        0.00332 (    1)
  SS BOND              : angle       0.80545 (    2)
  covalent geometry    : bond        0.00272 ( 4547)
  covalent geometry    : angle       0.54170 ( 6202)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.570 
Fit side-chains
REVERT: A  242 MET cc_start: 0.8637 (mtp) cc_final: 0.8378 (mtp)
REVERT: A  336 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8362 (p0)
REVERT: A  368 MET cc_start: 0.8602 (mtp) cc_final: 0.8211 (mtp)
REVERT: A  488 GLU cc_start: 0.8658 (tt0) cc_final: 0.8340 (tt0)
REVERT: A  515 LEU cc_start: 0.8918 (tp) cc_final: 0.8661 (tp)
  outliers start: 10
  outliers final: 6
  residues processed: 61
  average time/residue: 1.0448
  time to fit residues: 67.5696
Evaluate side-chains
  58 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain A residue  444 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0170
   chunk 39 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    1.0024

-------------------------------------------------------------------------------
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 = 0.3575 r_free = 0.3575 target = 0.133504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.110035 restraints weight = 5160.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 1.51
r_work: 0.2908 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2792 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4548  Z= 0.138
  Angle     :  0.561   8.244   6204  Z= 0.279
  Chirality :  0.041   0.135    690
  Planarity :  0.004   0.037    752
  Dihedral  :  7.053  63.518    600
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 16.45 %
    Favored  : 81.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.37), residues: 544
  helix:  1.57 (0.26), residues: 386
  sheet:  None (None), residues: 0
  loop :  0.42 (0.55), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 553 
 HIS   0.003   0.001   HIS A 599 
 PHE   0.013   0.001   PHE A 409 
 TYR   0.016   0.001   TYR A  84 
 ARG   0.001   0.000   ARG A 512 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05368 (  299)
  hydrogen bonds       : angle       4.55535 (  855)
  SS BOND              : bond        0.00395 (    1)
  SS BOND              : angle       0.82460 (    2)
  covalent geometry    : bond        0.00313 ( 4547)
  covalent geometry    : angle       0.56130 ( 6202)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.555 
Fit side-chains
REVERT: A  242 MET cc_start: 0.8700 (mtp) cc_final: 0.8439 (mtp)
REVERT: A  336 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8379 (p0)
REVERT: A  368 MET cc_start: 0.8649 (mtp) cc_final: 0.8341 (mtp)
REVERT: A  459 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7784 (t80)
REVERT: A  488 GLU cc_start: 0.8685 (tt0) cc_final: 0.8444 (tt0)
REVERT: A  515 LEU cc_start: 0.8930 (tp) cc_final: 0.8689 (tp)
  outliers start: 9
  outliers final: 6
  residues processed: 59
  average time/residue: 1.7286
  time to fit residues: 107.2423
Evaluate side-chains
  60 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  459 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 34 optimal weight:    0.5980
   chunk 37 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 29 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3594 r_free = 0.3594 target = 0.134977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.111779 restraints weight = 5177.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 1.50
r_work: 0.3009 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2894 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.1450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4548  Z= 0.123
  Angle     :  0.540   8.403   6204  Z= 0.267
  Chirality :  0.040   0.130    690
  Planarity :  0.004   0.035    752
  Dihedral  :  6.994  64.275    600
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 16.88 %
    Favored  : 81.39 %
  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:  1.82 (0.37), residues: 544
  helix:  1.62 (0.26), residues: 387
  sheet:  None (None), residues: 0
  loop :  0.36 (0.55), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 553 
 HIS   0.002   0.001   HIS A 599 
 PHE   0.012   0.001   PHE A 409 
 TYR   0.017   0.001   TYR A  84 
 ARG   0.001   0.000   ARG A 341 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04911 (  299)
  hydrogen bonds       : angle       4.46511 (  855)
  SS BOND              : bond        0.00333 (    1)
  SS BOND              : angle       0.76574 (    2)
  covalent geometry    : bond        0.00269 ( 4547)
  covalent geometry    : angle       0.54019 ( 6202)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.774 
Fit side-chains
REVERT: A  242 MET cc_start: 0.8683 (mtp) cc_final: 0.8410 (mtp)
REVERT: A  336 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8367 (p0)
REVERT: A  368 MET cc_start: 0.8611 (mtp) cc_final: 0.8263 (mtp)
REVERT: A  459 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7751 (t80)
REVERT: A  488 GLU cc_start: 0.8675 (tt0) cc_final: 0.8447 (tt0)
REVERT: A  515 LEU cc_start: 0.8919 (tp) cc_final: 0.8668 (tp)
  outliers start: 8
  outliers final: 6
  residues processed: 58
  average time/residue: 1.2262
  time to fit residues: 75.7014
Evaluate side-chains
  58 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  459 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 16 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0060
   chunk 21 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.6798

-------------------------------------------------------------------------------
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 = 0.3602 r_free = 0.3602 target = 0.135644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.112495 restraints weight = 5126.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 1.49
r_work: 0.3137 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3033 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.1582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4548  Z= 0.117
  Angle     :  0.531   8.457   6204  Z= 0.262
  Chirality :  0.039   0.128    690
  Planarity :  0.004   0.035    752
  Dihedral  :  6.930  64.613    600
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.10 %
    Favored  : 80.74 %
  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:  1.97 (0.37), residues: 544
  helix:  1.77 (0.27), residues: 382
  sheet:  None (None), residues: 0
  loop :  0.33 (0.55), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 553 
 HIS   0.002   0.001   HIS A 599 
 PHE   0.011   0.001   PHE A 409 
 TYR   0.016   0.001   TYR A  84 
 ARG   0.001   0.000   ARG A 512 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04729 (  299)
  hydrogen bonds       : angle       4.41468 (  855)
  SS BOND              : bond        0.00306 (    1)
  SS BOND              : angle       0.76225 (    2)
  covalent geometry    : bond        0.00251 ( 4547)
  covalent geometry    : angle       0.53123 ( 6202)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.493 
Fit side-chains
REVERT: A  242 MET cc_start: 0.8724 (mtp) cc_final: 0.8448 (mtp)
REVERT: A  336 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8371 (p0)
REVERT: A  368 MET cc_start: 0.8597 (mtp) cc_final: 0.8173 (mtp)
REVERT: A  459 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7780 (t80)
REVERT: A  488 GLU cc_start: 0.8656 (tt0) cc_final: 0.8367 (tt0)
REVERT: A  515 LEU cc_start: 0.8925 (tp) cc_final: 0.8664 (tp)
  outliers start: 10
  outliers final: 6
  residues processed: 61
  average time/residue: 0.6917
  time to fit residues: 45.1758
Evaluate side-chains
  59 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  459 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 40 optimal weight:    0.2980
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 50 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3604 r_free = 0.3604 target = 0.135833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.112710 restraints weight = 5175.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 1.49
r_work: 0.3140 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4548  Z= 0.116
  Angle     :  0.533   8.146   6204  Z= 0.262
  Chirality :  0.039   0.129    690
  Planarity :  0.004   0.035    752
  Dihedral  :  6.865  62.693    600
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 17.53 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.37), residues: 544
  helix:  1.70 (0.27), residues: 387
  sheet:  None (None), residues: 0
  loop :  0.37 (0.55), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 553 
 HIS   0.001   0.001   HIS A 599 
 PHE   0.011   0.001   PHE A 409 
 TYR   0.017   0.001   TYR A  84 
 ARG   0.001   0.000   ARG A  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04711 (  299)
  hydrogen bonds       : angle       4.40097 (  855)
  SS BOND              : bond        0.00298 (    1)
  SS BOND              : angle       0.75223 (    2)
  covalent geometry    : bond        0.00248 ( 4547)
  covalent geometry    : angle       0.53252 ( 6202)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.445 
Fit side-chains
REVERT: A  242 MET cc_start: 0.8721 (mtp) cc_final: 0.8444 (mtp)
REVERT: A  336 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8361 (p0)
REVERT: A  368 MET cc_start: 0.8589 (mtp) cc_final: 0.8182 (mtp)
REVERT: A  459 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7771 (t80)
REVERT: A  488 GLU cc_start: 0.8659 (tt0) cc_final: 0.8449 (tt0)
REVERT: A  515 LEU cc_start: 0.8927 (tp) cc_final: 0.8662 (tp)
  outliers start: 8
  outliers final: 6
  residues processed: 58
  average time/residue: 0.7086
  time to fit residues: 44.0168
Evaluate side-chains
  59 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  459 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 3 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3596 r_free = 0.3596 target = 0.135138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.111834 restraints weight = 5093.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 1.50
r_work: 0.3098 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4548  Z= 0.122
  Angle     :  0.541   8.143   6204  Z= 0.267
  Chirality :  0.040   0.131    690
  Planarity :  0.004   0.035    752
  Dihedral  :  6.886  62.546    600
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.53 %
    Favored  : 80.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.37), residues: 544
  helix:  1.67 (0.26), residues: 387
  sheet:  None (None), residues: 0
  loop :  0.33 (0.55), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 553 
 HIS   0.002   0.001   HIS A 599 
 PHE   0.012   0.001   PHE A 409 
 TYR   0.016   0.001   TYR A  84 
 ARG   0.001   0.000   ARG A 442 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04934 (  299)
  hydrogen bonds       : angle       4.43796 (  855)
  SS BOND              : bond        0.00330 (    1)
  SS BOND              : angle       0.77435 (    2)
  covalent geometry    : bond        0.00266 ( 4547)
  covalent geometry    : angle       0.54082 ( 6202)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.460 
Fit side-chains
REVERT: A  242 MET cc_start: 0.8725 (mtp) cc_final: 0.8443 (mtp)
REVERT: A  336 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8374 (p0)
REVERT: A  368 MET cc_start: 0.8613 (mtp) cc_final: 0.8267 (mtp)
REVERT: A  459 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7783 (t80)
REVERT: A  488 GLU cc_start: 0.8649 (tt0) cc_final: 0.8428 (tt0)
REVERT: A  515 LEU cc_start: 0.8923 (tp) cc_final: 0.8663 (tp)
  outliers start: 9
  outliers final: 6
  residues processed: 58
  average time/residue: 0.7134
  time to fit residues: 44.3456
Evaluate side-chains
  59 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  459 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 12 optimal weight:    0.2980
   chunk 47 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3602 r_free = 0.3602 target = 0.135615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.112372 restraints weight = 5157.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 1.50
r_work: 0.3106 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3001 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.1591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4548  Z= 0.119
  Angle     :  0.536   8.097   6204  Z= 0.265
  Chirality :  0.040   0.130    690
  Planarity :  0.004   0.034    752
  Dihedral  :  6.856  62.271    600
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 17.53 %
    Favored  : 80.74 %
  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:  1.89 (0.37), residues: 544
  helix:  1.68 (0.27), residues: 387
  sheet:  None (None), residues: 0
  loop :  0.33 (0.55), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 553 
 HIS   0.002   0.001   HIS A 599 
 PHE   0.011   0.001   PHE A 409 
 TYR   0.016   0.001   TYR A  84 
 ARG   0.001   0.000   ARG A  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04800 (  299)
  hydrogen bonds       : angle       4.41660 (  855)
  SS BOND              : bond        0.00322 (    1)
  SS BOND              : angle       0.77221 (    2)
  covalent geometry    : bond        0.00258 ( 4547)
  covalent geometry    : angle       0.53623 ( 6202)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3580.15 seconds
wall clock time: 64 minutes 12.20 seconds (3852.20 seconds total)