Starting phenix.real_space_refine
on Thu Jun  5 19:40:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y6j_38988/06_2025/8y6j_38988_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y6j_38988/06_2025/8y6j_38988.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.46
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y6j_38988/06_2025/8y6j_38988.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y6j_38988/06_2025/8y6j_38988.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y6j_38988/06_2025/8y6j_38988_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y6j_38988/06_2025/8y6j_38988_neut.cif"
  }
  resolution = 3.46
  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=   0.002 sd=   0.038
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      42      5.16       5
     C    4368      2.51       5
     N    1062      2.21       5
     O    1178      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6650
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3325
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 425, 3325
          Classifications: {'peptide': 425}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 13, 'TRANS': 411}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "B"
      Number of atoms: 3325
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 425, 3325
          Classifications: {'peptide': 425}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 13, 'TRANS': 411}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 17
  Time building chain proxies: 4.36, per 1000 atoms: 0.66
  Number of scatterers: 6650
  At special positions: 0
  Unit cell: (73.84, 107.12, 81.12, 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      42     16.00
     O    1178      8.00
     N    1062      7.00
     C    4368      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 508 " - pdb=" SG  CYS A 518 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 508 " - pdb=" SG  CYS B 518 " 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: 1.70
  Conformation dependent library (CDL) restraints added in 954.1 milliseconds
  

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1604

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 0 sheets defined
      80.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 56 through 70
      removed outlier: 3.506A  pdb=" N   LYS A  60 " --> pdb=" O   ALA A  56 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LYS A  69 " --> pdb=" O   PHE A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 94
    Processing helix  chain 'A' and resid 103 through 116
    Processing helix  chain 'A' and resid 124 through 128
      removed outlier: 3.723A  pdb=" N   LEU A 128 " --> pdb=" O   MET A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 144
    Processing helix  chain 'A' and resid 144 through 159
    Processing helix  chain 'A' and resid 220 through 245
    Processing helix  chain 'A' and resid 245 through 256
      removed outlier: 4.133A  pdb=" N   ARG A 249 " --> pdb=" O   ASP A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 272
    Processing helix  chain 'A' and resid 283 through 287
    Processing helix  chain 'A' and resid 289 through 302
      Proline residue:  A 298  - end of helix
    Processing helix  chain 'A' and resid 306 through 323
      removed outlier: 3.512A  pdb=" N   LEU A 310 " --> pdb=" O   LEU A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 333
      removed outlier: 3.824A  pdb=" N   ALA A 328 " --> pdb=" O   LYS A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 371
      removed outlier: 3.856A  pdb=" N   TRP A 371 " --> pdb=" O   CYS A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 377
    Processing helix  chain 'A' and resid 380 through 396
      removed outlier: 4.125A  pdb=" N   ARG A 396 " --> pdb=" O   SER A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 408
    Processing helix  chain 'A' and resid 409 through 422
    Processing helix  chain 'A' and resid 424 through 430
    Processing helix  chain 'A' and resid 447 through 456
    Processing helix  chain 'A' and resid 459 through 473
    Processing helix  chain 'A' and resid 473 through 480
    Processing helix  chain 'A' and resid 485 through 499
    Processing helix  chain 'A' and resid 507 through 511
    Processing helix  chain 'A' and resid 524 through 529
    Processing helix  chain 'A' and resid 530 through 546
    Processing helix  chain 'B' and resid 57 through 70
      removed outlier: 3.629A  pdb=" N   LYS B  69 " --> pdb=" O   PHE B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 94
    Processing helix  chain 'B' and resid 103 through 116
    Processing helix  chain 'B' and resid 124 through 128
      removed outlier: 3.751A  pdb=" N   LEU B 128 " --> pdb=" O   MET B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 144
    Processing helix  chain 'B' and resid 144 through 159
    Processing helix  chain 'B' and resid 220 through 245
    Processing helix  chain 'B' and resid 245 through 256
      removed outlier: 4.106A  pdb=" N   ARG B 249 " --> pdb=" O   ASP B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 272
    Processing helix  chain 'B' and resid 283 through 287
    Processing helix  chain 'B' and resid 289 through 302
      Proline residue:  B 298  - end of helix
    Processing helix  chain 'B' and resid 306 through 323
      removed outlier: 3.560A  pdb=" N   LEU B 310 " --> pdb=" O   LEU B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 333
      removed outlier: 3.833A  pdb=" N   ALA B 328 " --> pdb=" O   LYS B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 344 through 371
      removed outlier: 3.870A  pdb=" N   TRP B 371 " --> pdb=" O   CYS B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 377
    Processing helix  chain 'B' and resid 380 through 398
      removed outlier: 4.116A  pdb=" N   ARG B 396 " --> pdb=" O   SER B 392 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   GLN B 397 " --> pdb=" O   VAL B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 408
    Processing helix  chain 'B' and resid 409 through 422
    Processing helix  chain 'B' and resid 424 through 430
    Processing helix  chain 'B' and resid 447 through 456
    Processing helix  chain 'B' and resid 459 through 473
    Processing helix  chain 'B' and resid 473 through 480
    Processing helix  chain 'B' and resid 485 through 499
    Processing helix  chain 'B' and resid 507 through 511
    Processing helix  chain 'B' and resid 524 through 529
    Processing helix  chain 'B' and resid 530 through 546

    467 hydrogen bonds defined for protein.
    1329 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: 1.97

  Time building geometry restraints manager: 2.00 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2020
        1.34 -     1.46: 1496
        1.46 -     1.58: 3210
        1.58 -     1.69: 0
        1.69 -     1.81: 66
  Bond restraints: 6792
  Sorted by residual:
  bond pdb=" CA  VAL A 456 "
       pdb=" CB  VAL A 456 "
    ideal  model  delta    sigma   weight residual
    1.528  1.545 -0.017 1.34e-02 5.57e+03 1.57e+00
  bond pdb=" CA  GLU B 548 "
       pdb=" CB  GLU B 548 "
    ideal  model  delta    sigma   weight residual
    1.530  1.551 -0.021 1.69e-02 3.50e+03 1.53e+00
  bond pdb=" CA  GLN B 332 "
       pdb=" CB  GLN B 332 "
    ideal  model  delta    sigma   weight residual
    1.532  1.551 -0.020 1.65e-02 3.67e+03 1.42e+00
  bond pdb=" CA  VAL B 456 "
       pdb=" CB  VAL B 456 "
    ideal  model  delta    sigma   weight residual
    1.528  1.544 -0.016 1.34e-02 5.57e+03 1.37e+00
  bond pdb=" CB  GLN A 332 "
       pdb=" CG  GLN A 332 "
    ideal  model  delta    sigma   weight residual
    1.520  1.555 -0.035 3.00e-02 1.11e+03 1.34e+00
  ... (remaining 6787 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 9093
        1.92 -     3.84: 104
        3.84 -     5.76: 14
        5.76 -     7.69: 5
        7.69 -     9.61: 2
  Bond angle restraints: 9218
  Sorted by residual:
  angle pdb=" CA  GLU B 548 "
        pdb=" CB  GLU B 548 "
        pdb=" CG  GLU B 548 "
      ideal   model   delta    sigma   weight residual
     114.10  123.71   -9.61 2.00e+00 2.50e-01 2.31e+01
  angle pdb=" CA  GLN B 332 "
        pdb=" CB  GLN B 332 "
        pdb=" CG  GLN B 332 "
      ideal   model   delta    sigma   weight residual
     114.10  123.08   -8.98 2.00e+00 2.50e-01 2.02e+01
  angle pdb=" N   GLU B 548 "
        pdb=" CA  GLU B 548 "
        pdb=" CB  GLU B 548 "
      ideal   model   delta    sigma   weight residual
     110.49  117.95   -7.46 1.69e+00 3.50e-01 1.95e+01
  angle pdb=" C   LYS B 547 "
        pdb=" N   GLU B 548 "
        pdb=" CA  GLU B 548 "
      ideal   model   delta    sigma   weight residual
     121.54  129.03   -7.49 1.91e+00 2.74e-01 1.54e+01
  angle pdb=" CA  GLN A 332 "
        pdb=" CB  GLN A 332 "
        pdb=" CG  GLN A 332 "
      ideal   model   delta    sigma   weight residual
     114.10  121.69   -7.59 2.00e+00 2.50e-01 1.44e+01
  ... (remaining 9213 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.59: 3342
       15.59 -    31.17: 497
       31.17 -    46.76: 138
       46.76 -    62.35: 32
       62.35 -    77.93: 5
  Dihedral angle restraints: 4014
    sinusoidal: 1540
      harmonic: 2474
  Sorted by residual:
  dihedral pdb=" CA  LYS B 547 "
           pdb=" C   LYS B 547 "
           pdb=" N   GLU B 548 "
           pdb=" CA  GLU B 548 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.47  -25.53     0      5.00e+00 4.00e-02 2.61e+01
  dihedral pdb=" CA  GLN B 397 "
           pdb=" C   GLN B 397 "
           pdb=" N   ALA B 398 "
           pdb=" CA  ALA B 398 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.79   19.21     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  GLN A 397 "
           pdb=" C   GLN A 397 "
           pdb=" N   ALA A 398 "
           pdb=" CA  ALA A 398 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.81   19.19     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 4011 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 835
       0.040 -    0.080: 233
       0.080 -    0.120: 35
       0.120 -    0.160: 2
       0.160 -    0.200: 1
  Chirality restraints: 1106
  Sorted by residual:
  chirality pdb=" CA  GLU B 548 "
            pdb=" N   GLU B 548 "
            pdb=" C   GLU B 548 "
            pdb=" CB  GLU B 548 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.99e-01
  chirality pdb=" CA  SER B 308 "
            pdb=" N   SER B 308 "
            pdb=" C   SER B 308 "
            pdb=" CB  SER B 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.75e-01
  chirality pdb=" CA  SER A 308 "
            pdb=" N   SER A 308 "
            pdb=" C   SER A 308 "
            pdb=" CB  SER A 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.70e-01
  ... (remaining 1103 not shown)

  Planarity restraints: 1120
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B 548 "    0.009 2.00e-02 2.50e+03   1.80e-02 3.25e+00
        pdb=" CD  GLU B 548 "   -0.031 2.00e-02 2.50e+03
        pdb=" OE1 GLU B 548 "    0.011 2.00e-02 2.50e+03
        pdb=" OE2 GLU B 548 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 547 "    0.007 2.00e-02 2.50e+03   1.44e-02 2.07e+00
        pdb=" C   LYS A 547 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   LYS A 547 "    0.009 2.00e-02 2.50e+03
        pdb=" N   GLU A 548 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A  99 "   -0.023 5.00e-02 4.00e+02   3.52e-02 1.98e+00
        pdb=" N   PRO A 100 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 100 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 100 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1117 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 234
        2.72 -     3.27: 7187
        3.27 -     3.81: 11568
        3.81 -     4.36: 12791
        4.36 -     4.90: 22678
  Nonbonded interactions: 54458
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  79 "
            pdb=" O   MET B 142 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" O   SER A 119 "
            pdb=" OG  SER A 119 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" OH  TYR A  79 "
            pdb=" O   MET A 142 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" OE2 GLU B 370 "
            pdb=" OG  SER B 409 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OE2 GLU A 370 "
            pdb=" OG  SER A 409 "
     model   vdw
     2.234 3.040
  ... (remaining 54453 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             0.900
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.110
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  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:2.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
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   0.035   6794  Z= 0.129
  Angle     :  0.549   9.607   9222  Z= 0.293
  Chirality :  0.036   0.200   1106
  Planarity :  0.003   0.035   1120
  Dihedral  : 16.136  77.931   2404
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.47 %
    Favored  : 76.53 %
  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:  3.00 (0.30), residues: 838
  helix:  2.62 (0.21), residues: 612
  sheet:  None (None), residues: 0
  loop :  0.23 (0.47), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 134 
 HIS   0.009   0.002   HIS A 333 
 PHE   0.013   0.001   PHE B 390 
 TYR   0.017   0.002   TYR B  79 
 ARG   0.001   0.000   ARG B 312 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10107 (  467)
  hydrogen bonds       : angle       4.52647 ( 1329)
  SS BOND              : bond        0.00284 (    2)
  SS BOND              : angle       1.46700 (    4)
  covalent geometry    : bond        0.00297 ( 6792)
  covalent geometry    : angle       0.54867 ( 9218)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.773 
Fit side-chains
REVERT: A   93 ASN cc_start: 0.7604 (m110) cc_final: 0.7110 (m110)
REVERT: A  548 GLU cc_start: 0.7800 (mp0) cc_final: 0.7525 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1497
  time to fit residues: 20.9764
Evaluate side-chains
  92 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 63 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:   30.0000
   chunk 34 optimal weight:    0.7980
   chunk 65 optimal weight:    0.1980
   chunk 25 optimal weight:    2.9990
   chunk 40 optimal weight:    0.4980
   chunk 49 optimal weight:    2.9990
   chunk 76 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B  93 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.148493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.119023 restraints weight = 7508.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 1.89
r_work: 0.3132 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2997 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.0564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6794  Z= 0.128
  Angle     :  0.494   6.957   9222  Z= 0.263
  Chirality :  0.036   0.118   1106
  Planarity :  0.003   0.031   1120
  Dihedral  :  3.659  19.682    896
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 21.73 %
    Favored  : 75.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.14 (0.30), residues: 838
  helix:  2.67 (0.20), residues: 618
  sheet:  None (None), residues: 0
  loop :  0.37 (0.49), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 134 
 HIS   0.005   0.002   HIS B 333 
 PHE   0.013   0.001   PHE B 227 
 TYR   0.019   0.002   TYR A  79 
 ARG   0.002   0.000   ARG A 312 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03258 (  467)
  hydrogen bonds       : angle       3.77901 ( 1329)
  SS BOND              : bond        0.00144 (    2)
  SS BOND              : angle       1.44625 (    4)
  covalent geometry    : bond        0.00302 ( 6792)
  covalent geometry    : angle       0.49291 ( 9218)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.773 
Fit side-chains
REVERT: A   93 ASN cc_start: 0.7628 (m110) cc_final: 0.7036 (m110)
REVERT: A  133 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7231 (mp)
REVERT: B  133 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7200 (mp)
REVERT: B  414 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7926 (tp)
REVERT: B  548 GLU cc_start: 0.8135 (pm20) cc_final: 0.7897 (pm20)
  outliers start: 22
  outliers final: 6
  residues processed: 112
  average time/residue: 0.1770
  time to fit residues: 28.9390
Evaluate side-chains
  103 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  284 GLN
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  414 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 44 optimal weight:    0.5980
   chunk 55 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 80 optimal weight:    0.0010
   chunk 23 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.6586

-------------------------------------------------------------------------------
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 = 0.3590 r_free = 0.3590 target = 0.147773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.118550 restraints weight = 7552.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 1.87
r_work: 0.3119 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.0799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6794  Z= 0.132
  Angle     :  0.493   6.119   9222  Z= 0.261
  Chirality :  0.036   0.119   1106
  Planarity :  0.003   0.032   1120
  Dihedral  :  3.666  20.353    896
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 23.47 %
    Favored  : 74.13 %
  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:  3.13 (0.30), residues: 838
  helix:  2.68 (0.20), residues: 618
  sheet:  None (None), residues: 0
  loop :  0.30 (0.48), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 134 
 HIS   0.005   0.001   HIS A 333 
 PHE   0.013   0.001   PHE B 227 
 TYR   0.017   0.002   TYR A  79 
 ARG   0.001   0.000   ARG A 312 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03017 (  467)
  hydrogen bonds       : angle       3.67037 ( 1329)
  SS BOND              : bond        0.00308 (    2)
  SS BOND              : angle       1.45845 (    4)
  covalent geometry    : bond        0.00315 ( 6792)
  covalent geometry    : angle       0.49251 ( 9218)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 1.814 
Fit side-chains
REVERT: A   93 ASN cc_start: 0.7642 (m110) cc_final: 0.7027 (m110)
REVERT: A  133 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7208 (mp)
REVERT: B  133 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7211 (mp)
REVERT: B  414 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7903 (tp)
  outliers start: 18
  outliers final: 9
  residues processed: 108
  average time/residue: 0.2028
  time to fit residues: 31.8057
Evaluate side-chains
  105 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  284 GLN
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  284 GLN
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  518 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.147111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.117635 restraints weight = 7732.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 1.88
r_work: 0.3111 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.0906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6794  Z= 0.137
  Angle     :  0.494   6.072   9222  Z= 0.261
  Chirality :  0.036   0.123   1106
  Planarity :  0.003   0.032   1120
  Dihedral  :  3.684  20.447    896
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 22.93 %
    Favored  : 74.40 %
  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:  3.12 (0.30), residues: 838
  helix:  2.68 (0.20), residues: 618
  sheet:  None (None), residues: 0
  loop :  0.27 (0.48), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 134 
 HIS   0.007   0.001   HIS A 333 
 PHE   0.015   0.001   PHE A 390 
 TYR   0.017   0.002   TYR A  79 
 ARG   0.002   0.000   ARG A 312 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02955 (  467)
  hydrogen bonds       : angle       3.61859 ( 1329)
  SS BOND              : bond        0.00294 (    2)
  SS BOND              : angle       1.45722 (    4)
  covalent geometry    : bond        0.00332 ( 6792)
  covalent geometry    : angle       0.49287 ( 9218)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.839 
Fit side-chains
REVERT: A   93 ASN cc_start: 0.7690 (m110) cc_final: 0.7077 (m110)
REVERT: A  133 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7284 (mp)
REVERT: B  133 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7275 (mp)
REVERT: B  414 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7943 (tp)
  outliers start: 20
  outliers final: 11
  residues processed: 107
  average time/residue: 0.2056
  time to fit residues: 32.2145
Evaluate side-chains
  105 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 1.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  284 GLN
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain A residue  518 CYS
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  284 GLN
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  518 CYS
Chi-restraints excluded: chain B residue  530 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 73 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    1.3788

-------------------------------------------------------------------------------
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 = 0.3536 r_free = 0.3536 target = 0.142557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.113461 restraints weight = 7703.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 1.83
r_work: 0.3063 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2932 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.1069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6794  Z= 0.217
  Angle     :  0.557   6.561   9222  Z= 0.292
  Chirality :  0.038   0.135   1106
  Planarity :  0.004   0.035   1120
  Dihedral  :  3.896  22.111    896
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 23.47 %
    Favored  : 73.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.80 (0.29), residues: 838
  helix:  2.44 (0.20), residues: 618
  sheet:  None (None), residues: 0
  loop :  0.20 (0.48), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 134 
 HIS   0.005   0.001   HIS A 333 
 PHE   0.016   0.002   PHE B 227 
 TYR   0.017   0.002   TYR A  79 
 ARG   0.002   0.000   ARG A 312 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03298 (  467)
  hydrogen bonds       : angle       3.76988 ( 1329)
  SS BOND              : bond        0.00446 (    2)
  SS BOND              : angle       1.98795 (    4)
  covalent geometry    : bond        0.00537 ( 6792)
  covalent geometry    : angle       0.55538 ( 9218)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 96
  time to evaluate  : 1.005 
Fit side-chains
REVERT: A  133 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7325 (mp)
REVERT: A  310 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8104 (mm)
REVERT: A  333 HIS cc_start: 0.8136 (m90) cc_final: 0.7846 (m90)
REVERT: B  133 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7316 (mp)
REVERT: B  310 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8159 (mm)
REVERT: B  333 HIS cc_start: 0.8185 (m90) cc_final: 0.7835 (m90)
  outliers start: 26
  outliers final: 18
  residues processed: 118
  average time/residue: 0.1991
  time to fit residues: 33.9684
Evaluate side-chains
  118 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 1.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  284 GLN
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  518 CYS
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  284 GLN
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  308 SER
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  348 SER
Chi-restraints excluded: chain B residue  473 GLU
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  518 CYS
Chi-restraints excluded: chain B residue  530 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 68 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 73 optimal weight:    0.1980
   chunk 32 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 72 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 = 0.3570 r_free = 0.3570 target = 0.145864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.116626 restraints weight = 7533.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 1.88
r_work: 0.3100 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.1061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6794  Z= 0.133
  Angle     :  0.507   7.053   9222  Z= 0.267
  Chirality :  0.036   0.124   1106
  Planarity :  0.003   0.033   1120
  Dihedral  :  3.790  21.324    896
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 23.20 %
    Favored  : 73.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.02 (0.30), residues: 838
  helix:  2.61 (0.20), residues: 618
  sheet:  None (None), residues: 0
  loop :  0.25 (0.48), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 134 
 HIS   0.004   0.001   HIS A 333 
 PHE   0.018   0.001   PHE A 390 
 TYR   0.016   0.002   TYR A  79 
 ARG   0.001   0.000   ARG B 312 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02984 (  467)
  hydrogen bonds       : angle       3.64061 ( 1329)
  SS BOND              : bond        0.00273 (    2)
  SS BOND              : angle       1.53892 (    4)
  covalent geometry    : bond        0.00323 ( 6792)
  covalent geometry    : angle       0.50644 ( 9218)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 94
  time to evaluate  : 1.797 
Fit side-chains
REVERT: A  133 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7247 (mp)
REVERT: A  310 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8081 (mm)
REVERT: A  333 HIS cc_start: 0.8182 (m90) cc_final: 0.7851 (m90)
REVERT: A  348 SER cc_start: 0.9203 (OUTLIER) cc_final: 0.8830 (m)
REVERT: A  353 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8158 (mp)
REVERT: A  548 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7603 (mp0)
REVERT: B  133 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7230 (mp)
REVERT: B  310 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8179 (mm)
REVERT: B  414 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7814 (tp)
  outliers start: 26
  outliers final: 13
  residues processed: 113
  average time/residue: 0.2871
  time to fit residues: 49.2720
Evaluate side-chains
  112 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 1.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  518 CYS
Chi-restraints excluded: chain A residue  548 GLU
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  154 TYR
Chi-restraints excluded: chain B residue  284 GLN
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  308 SER
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  518 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 43 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 77 optimal weight:    0.4980
   chunk 40 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 55 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3568 r_free = 0.3568 target = 0.145454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.116076 restraints weight = 7552.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 1.87
r_work: 0.3097 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.1101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6794  Z= 0.142
  Angle     :  0.514   7.369   9222  Z= 0.270
  Chirality :  0.036   0.128   1106
  Planarity :  0.003   0.032   1120
  Dihedral  :  3.763  21.466    896
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 23.33 %
    Favored  : 72.80 %
  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:  3.05 (0.30), residues: 838
  helix:  2.62 (0.20), residues: 618
  sheet:  None (None), residues: 0
  loop :  0.28 (0.48), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 134 
 HIS   0.004   0.001   HIS A 333 
 PHE   0.017   0.002   PHE A 390 
 TYR   0.016   0.002   TYR A  79 
 ARG   0.002   0.000   ARG B 312 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02957 (  467)
  hydrogen bonds       : angle       3.61066 ( 1329)
  SS BOND              : bond        0.00322 (    2)
  SS BOND              : angle       1.57531 (    4)
  covalent geometry    : bond        0.00345 ( 6792)
  covalent geometry    : angle       0.51291 ( 9218)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 92
  time to evaluate  : 2.060 
Fit side-chains
REVERT: A  133 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7194 (mp)
REVERT: A  310 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8022 (mm)
REVERT: A  333 HIS cc_start: 0.8242 (m90) cc_final: 0.7979 (m-70)
REVERT: A  348 SER cc_start: 0.9164 (OUTLIER) cc_final: 0.8802 (m)
REVERT: A  548 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7527 (mp0)
REVERT: B  133 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7184 (mp)
REVERT: B  310 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8116 (mm)
REVERT: B  348 SER cc_start: 0.9059 (OUTLIER) cc_final: 0.8786 (m)
REVERT: B  414 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7765 (tp)
REVERT: B  549 PHE cc_start: 0.7337 (m-10) cc_final: 0.7004 (m-10)
  outliers start: 29
  outliers final: 17
  residues processed: 115
  average time/residue: 0.2107
  time to fit residues: 37.0741
Evaluate side-chains
  117 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 92
  time to evaluate  : 1.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  154 TYR
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  518 CYS
Chi-restraints excluded: chain A residue  548 GLU
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  154 TYR
Chi-restraints excluded: chain B residue  284 GLN
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  308 SER
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  348 SER
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  518 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 69 optimal weight:    0.5980
   chunk 81 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0070
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
A 289 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.147220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.117987 restraints weight = 7590.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 1.89
r_work: 0.3117 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2982 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.1130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6794  Z= 0.119
  Angle     :  0.500   7.683   9222  Z= 0.262
  Chirality :  0.036   0.129   1106
  Planarity :  0.003   0.031   1120
  Dihedral  :  3.716  20.884    896
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 23.87 %
    Favored  : 72.53 %
  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:  3.24 (0.30), residues: 838
  helix:  2.76 (0.20), residues: 618
  sheet:  None (None), residues: 0
  loop :  0.36 (0.49), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 134 
 HIS   0.007   0.001   HIS A 333 
 PHE   0.017   0.001   PHE A 390 
 TYR   0.015   0.002   TYR A  79 
 ARG   0.001   0.000   ARG A 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02830 (  467)
  hydrogen bonds       : angle       3.53243 ( 1329)
  SS BOND              : bond        0.00245 (    2)
  SS BOND              : angle       1.38841 (    4)
  covalent geometry    : bond        0.00284 ( 6792)
  covalent geometry    : angle       0.49904 ( 9218)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 0.742 
Fit side-chains
REVERT: A   93 ASN cc_start: 0.7619 (m110) cc_final: 0.7032 (m110)
REVERT: A  133 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7147 (mp)
REVERT: A  310 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8054 (mm)
REVERT: A  548 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7503 (mp0)
REVERT: B  133 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7133 (mp)
REVERT: B  310 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8137 (mm)
REVERT: B  348 SER cc_start: 0.9171 (OUTLIER) cc_final: 0.8792 (m)
REVERT: B  414 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7769 (tp)
REVERT: B  548 GLU cc_start: 0.8228 (pm20) cc_final: 0.7776 (pm20)
  outliers start: 27
  outliers final: 16
  residues processed: 112
  average time/residue: 0.2560
  time to fit residues: 42.7619
Evaluate side-chains
  111 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 1.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  154 TYR
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  518 CYS
Chi-restraints excluded: chain A residue  548 GLU
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  154 TYR
Chi-restraints excluded: chain B residue  284 GLN
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  308 SER
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  348 SER
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  518 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 62 optimal weight:    0.0050
   chunk 19 optimal weight:    0.9980
   chunk 4 optimal weight:    5.9990
   chunk 35 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 75 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.6794

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

Flipped N/Q/H residues before XYZ refinement:
B 289 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.146262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.116954 restraints weight = 7590.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 1.88
r_work: 0.3110 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.1172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6794  Z= 0.135
  Angle     :  0.513   8.216   9222  Z= 0.269
  Chirality :  0.036   0.130   1106
  Planarity :  0.003   0.031   1120
  Dihedral  :  3.749  21.179    896
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 24.13 %
    Favored  : 72.27 %
  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:  3.26 (0.30), residues: 838
  helix:  2.77 (0.20), residues: 618
  sheet:  None (None), residues: 0
  loop :  0.38 (0.49), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 134 
 HIS   0.005   0.001   HIS A 333 
 PHE   0.017   0.001   PHE A 390 
 TYR   0.016   0.002   TYR A  79 
 ARG   0.002   0.000   ARG A 312 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02897 (  467)
  hydrogen bonds       : angle       3.54406 ( 1329)
  SS BOND              : bond        0.00320 (    2)
  SS BOND              : angle       1.50074 (    4)
  covalent geometry    : bond        0.00327 ( 6792)
  covalent geometry    : angle       0.51197 ( 9218)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 91
  time to evaluate  : 1.577 
Fit side-chains
REVERT: A   93 ASN cc_start: 0.7615 (m110) cc_final: 0.6987 (m110)
REVERT: A  310 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8105 (mm)
REVERT: A  548 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7575 (mp0)
REVERT: B  133 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7178 (mp)
REVERT: B  310 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8123 (mm)
REVERT: B  348 SER cc_start: 0.9171 (OUTLIER) cc_final: 0.8793 (m)
REVERT: B  414 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7744 (tp)
REVERT: B  548 GLU cc_start: 0.8311 (pm20) cc_final: 0.7822 (pm20)
  outliers start: 27
  outliers final: 19
  residues processed: 110
  average time/residue: 0.1590
  time to fit residues: 26.0197
Evaluate side-chains
  114 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 89
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  154 TYR
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  284 GLN
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain A residue  518 CYS
Chi-restraints excluded: chain A residue  548 GLU
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  154 TYR
Chi-restraints excluded: chain B residue  284 GLN
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  308 SER
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  348 SER
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  518 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 41 optimal weight:    0.3980
   chunk 48 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0980
   chunk 54 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3590 r_free = 0.3590 target = 0.147549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.118371 restraints weight = 7641.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 1.90
r_work: 0.3126 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.1220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6794  Z= 0.119
  Angle     :  0.504   8.526   9222  Z= 0.264
  Chirality :  0.036   0.131   1106
  Planarity :  0.003   0.031   1120
  Dihedral  :  3.683  20.752    896
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 24.00 %
    Favored  : 72.53 %
  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:  3.35 (0.30), residues: 838
  helix:  2.84 (0.20), residues: 618
  sheet:  None (None), residues: 0
  loop :  0.39 (0.49), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 134 
 HIS   0.004   0.001   HIS A 333 
 PHE   0.017   0.001   PHE A 390 
 TYR   0.015   0.002   TYR A  79 
 ARG   0.001   0.000   ARG A 312 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02784 (  467)
  hydrogen bonds       : angle       3.48423 ( 1329)
  SS BOND              : bond        0.00264 (    2)
  SS BOND              : angle       1.35366 (    4)
  covalent geometry    : bond        0.00285 ( 6792)
  covalent geometry    : angle       0.50356 ( 9218)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 89
  time to evaluate  : 0.730 
Fit side-chains
REVERT: A   93 ASN cc_start: 0.7632 (m110) cc_final: 0.6972 (m110)
REVERT: A  310 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8065 (mm)
REVERT: A  348 SER cc_start: 0.9159 (OUTLIER) cc_final: 0.8823 (m)
REVERT: A  548 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7619 (mp0)
REVERT: B  133 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.7092 (mp)
REVERT: B  310 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8118 (mm)
REVERT: B  348 SER cc_start: 0.9158 (OUTLIER) cc_final: 0.8785 (m)
REVERT: B  414 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7755 (tp)
REVERT: B  548 GLU cc_start: 0.8333 (pm20) cc_final: 0.7853 (pm20)
  outliers start: 26
  outliers final: 17
  residues processed: 108
  average time/residue: 0.1352
  time to fit residues: 21.6441
Evaluate side-chains
  113 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  154 TYR
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain A residue  518 CYS
Chi-restraints excluded: chain A residue  548 GLU
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  154 TYR
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  308 SER
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  348 SER
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  518 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 53 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 75 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0170
   chunk 57 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 73 optimal weight:    0.0970
   chunk 78 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 4 optimal weight:    9.9990
   overall best weight:    0.3816

-------------------------------------------------------------------------------
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 = 0.148199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.119763 restraints weight = 7745.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 1.89
r_work: 0.3136 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2998 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.1355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6794  Z= 0.107
  Angle     :  0.490   8.196   9222  Z= 0.257
  Chirality :  0.036   0.151   1106
  Planarity :  0.003   0.030   1120
  Dihedral  :  3.592  20.051    896
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 24.40 %
    Favored  : 72.53 %
  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:  3.49 (0.30), residues: 838
  helix:  2.95 (0.20), residues: 618
  sheet:  None (None), residues: 0
  loop :  0.44 (0.50), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 134 
 HIS   0.004   0.001   HIS A 333 
 PHE   0.017   0.001   PHE A 390 
 TYR   0.015   0.001   TYR A  79 
 ARG   0.002   0.000   ARG B 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02658 (  467)
  hydrogen bonds       : angle       3.40126 ( 1329)
  SS BOND              : bond        0.00233 (    2)
  SS BOND              : angle       1.20896 (    4)
  covalent geometry    : bond        0.00251 ( 6792)
  covalent geometry    : angle       0.48964 ( 9218)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4294.62 seconds
wall clock time: 78 minutes 45.81 seconds (4725.81 seconds total)