Starting phenix.real_space_refine
on Sat May 10 14:27:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w9v_37382/05_2025/8w9v_37382.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w9v_37382/05_2025/8w9v_37382.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w9v_37382/05_2025/8w9v_37382.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w9v_37382/05_2025/8w9v_37382.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w9v_37382/05_2025/8w9v_37382.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w9v_37382/05_2025/8w9v_37382.cif"
  }
  resolution = 2.9
  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=   0.006
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
     K       6      8.98       5
     S      46      5.16       5
     C    4324      2.51       5
     N    1054      2.21       5
     O    1144      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6574
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 3284
          Classifications: {'peptide': 426}
          Link IDs: {'PTRANS': 19, 'TRANS': 406}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 3284
          Classifications: {'peptide': 426}
          Link IDs: {'PTRANS': 19, 'TRANS': 406}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {'  K': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {'  K': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 4.62, per 1000 atoms: 0.70
  Number of scatterers: 6574
  At special positions: 0
  Unit cell: (102.3, 86.49, 87.42, 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)
     K       6     19.00
     S      46     16.00
     O    1144      8.00
     N    1054      7.00
     C    4324      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.63
  Conformation dependent library (CDL) restraints added in 979.6 milliseconds
  

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1588

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 0 sheets defined
      75.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 42 through 65
    Processing helix  chain 'A' and resid 75 through 88
      removed outlier: 3.509A  pdb=" N   MET A  79 " --> pdb=" O   PRO A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 115
    Processing helix  chain 'A' and resid 116 through 127
    Processing helix  chain 'A' and resid 179 through 216
    Processing helix  chain 'A' and resid 216 through 227
      Proline residue:  A 222  - end of helix
    Processing helix  chain 'A' and resid 229 through 244
    Processing helix  chain 'A' and resid 254 through 258
      removed outlier: 3.712A  pdb=" N   SER A 258 " --> pdb=" O   VAL A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 275
    Processing helix  chain 'A' and resid 277 through 293
    Processing helix  chain 'A' and resid 295 through 304
    Processing helix  chain 'A' and resid 315 through 341
    Processing helix  chain 'A' and resid 344 through 348
      removed outlier: 3.758A  pdb=" N   ASP A 348 " --> pdb=" O   SER A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 367
      removed outlier: 3.739A  pdb=" N   ARG A 367 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 393
    Processing helix  chain 'A' and resid 422 through 427
    Processing helix  chain 'A' and resid 429 through 445
    Processing helix  chain 'A' and resid 445 through 452
    Processing helix  chain 'A' and resid 457 through 470
    Processing helix  chain 'A' and resid 479 through 485
    Processing helix  chain 'A' and resid 498 through 503
    Processing helix  chain 'A' and resid 504 through 520
    Processing helix  chain 'A' and resid 520 through 525
    Processing helix  chain 'B' and resid 42 through 65
    Processing helix  chain 'B' and resid 75 through 88
      removed outlier: 3.502A  pdb=" N   MET B  79 " --> pdb=" O   PRO B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 115
    Processing helix  chain 'B' and resid 116 through 127
    Processing helix  chain 'B' and resid 179 through 216
      removed outlier: 3.527A  pdb=" N   HIS B 202 " --> pdb=" O   PHE B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 227
      Proline residue:  B 222  - end of helix
    Processing helix  chain 'B' and resid 229 through 243
    Processing helix  chain 'B' and resid 254 through 258
      removed outlier: 3.713A  pdb=" N   SER B 258 " --> pdb=" O   VAL B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 275
      removed outlier: 3.519A  pdb=" N   GLN B 270 " --> pdb=" O   LEU B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 293
      removed outlier: 3.582A  pdb=" N   LEU B 292 " --> pdb=" O   PHE B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 304
    Processing helix  chain 'B' and resid 315 through 341
    Processing helix  chain 'B' and resid 344 through 348
      removed outlier: 3.775A  pdb=" N   ASP B 348 " --> pdb=" O   SER B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 367
      removed outlier: 3.540A  pdb=" N   THR B 356 " --> pdb=" O   SER B 352 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ARG B 367 " --> pdb=" O   VAL B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 393
    Processing helix  chain 'B' and resid 422 through 427
    Processing helix  chain 'B' and resid 429 through 445
    Processing helix  chain 'B' and resid 445 through 452
    Processing helix  chain 'B' and resid 457 through 470
    Processing helix  chain 'B' and resid 479 through 485
    Processing helix  chain 'B' and resid 498 through 503
    Processing helix  chain 'B' and resid 504 through 520
    Processing helix  chain 'B' and resid 520 through 525

    449 hydrogen bonds defined for protein.
    1317 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: 1.64

  Time building geometry restraints manager: 1.89 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1036
        1.32 -     1.45: 1764
        1.45 -     1.57: 3844
        1.57 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 6718
  Sorted by residual:
  bond pdb=" C   ASN A 253 "
       pdb=" O   ASN A 253 "
    ideal  model  delta    sigma   weight residual
    1.235  1.201  0.034 1.26e-02 6.30e+03 7.28e+00
  bond pdb=" C   ASN B 253 "
       pdb=" O   ASN B 253 "
    ideal  model  delta    sigma   weight residual
    1.235  1.211  0.024 1.26e-02 6.30e+03 3.58e+00
  bond pdb=" CB  PRO B 430 "
       pdb=" CG  PRO B 430 "
    ideal  model  delta    sigma   weight residual
    1.492  1.566 -0.074 5.00e-02 4.00e+02 2.16e+00
  bond pdb=" N   LEU A 292 "
       pdb=" CA  LEU A 292 "
    ideal  model  delta    sigma   weight residual
    1.460  1.474 -0.014 1.22e-02 6.72e+03 1.41e+00
  bond pdb=" CA  ASN A 253 "
       pdb=" C   ASN A 253 "
    ideal  model  delta    sigma   weight residual
    1.523  1.508  0.015 1.34e-02 5.57e+03 1.30e+00
  ... (remaining 6713 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 8941
        1.32 -     2.63: 138
        2.63 -     3.95: 37
        3.95 -     5.26: 17
        5.26 -     6.58: 1
  Bond angle restraints: 9134
  Sorted by residual:
  angle pdb=" N   THR B 276 "
        pdb=" CA  THR B 276 "
        pdb=" C   THR B 276 "
      ideal   model   delta    sigma   weight residual
     111.14  115.20   -4.06 1.08e+00 8.57e-01 1.41e+01
  angle pdb=" CA  PRO B 430 "
        pdb=" N   PRO B 430 "
        pdb=" CD  PRO B 430 "
      ideal   model   delta    sigma   weight residual
     112.00  108.11    3.89 1.40e+00 5.10e-01 7.70e+00
  angle pdb=" C   THR B  88 "
        pdb=" N   VAL B  89 "
        pdb=" CA  VAL B  89 "
      ideal   model   delta    sigma   weight residual
     121.97  126.41   -4.44 1.80e+00 3.09e-01 6.07e+00
  angle pdb=" O   THR A  88 "
        pdb=" C   THR A  88 "
        pdb=" N   VAL A  89 "
      ideal   model   delta    sigma   weight residual
     122.42  126.18   -3.76 1.61e+00 3.86e-01 5.45e+00
  angle pdb=" C   THR A  88 "
        pdb=" N   VAL A  89 "
        pdb=" CA  VAL A  89 "
      ideal   model   delta    sigma   weight residual
     121.97  126.09   -4.12 1.80e+00 3.09e-01 5.23e+00
  ... (remaining 9129 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.84: 3400
       13.84 -    27.68: 390
       27.68 -    41.52: 107
       41.52 -    55.36: 57
       55.36 -    69.20: 4
  Dihedral angle restraints: 3958
    sinusoidal: 1500
      harmonic: 2458
  Sorted by residual:
  dihedral pdb=" CA  ASN B 365 "
           pdb=" C   ASN B 365 "
           pdb=" N   ALA B 366 "
           pdb=" CA  ALA B 366 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.57   16.43     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CA  ASN B 275 "
           pdb=" CB  ASN B 275 "
           pdb=" CG  ASN B 275 "
           pdb=" OD1 ASN B 275 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -159.20   69.20     2      2.00e+01 2.50e-03 1.05e+01
  dihedral pdb=" CA  ASN A 365 "
           pdb=" C   ASN A 365 "
           pdb=" N   ALA A 366 "
           pdb=" CA  ALA A 366 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.64   15.36     0      5.00e+00 4.00e-02 9.43e+00
  ... (remaining 3955 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 945
       0.052 -    0.104: 147
       0.104 -    0.156: 16
       0.156 -    0.208: 0
       0.208 -    0.260: 2
  Chirality restraints: 1110
  Sorted by residual:
  chirality pdb=" CA  ASN A 253 "
            pdb=" N   ASN A 253 "
            pdb=" C   ASN A 253 "
            pdb=" CB  ASN A 253 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.69e+00
  chirality pdb=" CA  ASN B 253 "
            pdb=" N   ASN B 253 "
            pdb=" C   ASN B 253 "
            pdb=" CB  ASN B 253 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  ILE B 374 "
            pdb=" N   ILE B 374 "
            pdb=" C   ILE B 374 "
            pdb=" CB  ILE B 374 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.78e-01
  ... (remaining 1107 not shown)

  Planarity restraints: 1108
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 429 "    0.047 5.00e-02 4.00e+02   7.04e-02 7.92e+00
        pdb=" N   PRO B 430 "   -0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO B 430 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 430 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 252 "   -0.008 2.00e-02 2.50e+03   1.60e-02 2.55e+00
        pdb=" C   GLU A 252 "    0.028 2.00e-02 2.50e+03
        pdb=" O   GLU A 252 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ASN A 253 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 252 "    0.008 2.00e-02 2.50e+03   1.59e-02 2.52e+00
        pdb=" C   GLU B 252 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   GLU B 252 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ASN B 253 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1105 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.81: 1912
        2.81 -     3.39: 7634
        3.39 -     3.98: 13246
        3.98 -     4.56: 19207
        4.56 -     5.14: 26759
  Nonbonded interactions: 68758
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN B 424 "
            pdb=" OG  SER B 526 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OE1 GLN A 424 "
            pdb=" OG  SER A 526 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" O   PRO A 430 "
            pdb=" ND2 ASN A 434 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" O   PHE A 361 "
            pdb=" ND2 ASN A 365 "
     model   vdw
     2.268 3.120
  nonbonded pdb=" OH  TYR B 197 "
            pdb=" O   ALA B 273 "
     model   vdw
     2.272 3.040
  ... (remaining 68753 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:             0.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.460
  Find NCS groups from input model:        0.190
  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:12.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
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   0.074   6718  Z= 0.135
  Angle     :  0.480   6.581   9134  Z= 0.253
  Chirality :  0.038   0.260   1110
  Planarity :  0.004   0.070   1108
  Dihedral  : 14.065  69.196   2370
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 15.07 %
    Favored  : 84.00 %
  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:  1.62 (0.28), residues: 840
  helix:  1.69 (0.21), residues: 596
  sheet:  None (None), residues: 0
  loop : -0.38 (0.38), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  45 
 HIS   0.004   0.001   HIS A 368 
 PHE   0.011   0.001   PHE A 198 
 TYR   0.016   0.002   TYR A  50 
 ARG   0.002   0.000   ARG A 447 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15674 (  449)
  hydrogen bonds       : angle       5.39373 ( 1317)
  covalent geometry    : bond        0.00303 ( 6718)
  covalent geometry    : angle       0.47964 ( 9134)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.730 
Fit side-chains
  outliers start: 7
  outliers final: 7
  residues processed: 87
  average time/residue: 1.2793
  time to fit residues: 117.7395
Evaluate side-chains
  84 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  457 SER
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  457 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 63 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 34 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 253 ASN
A 270 GLN
A 424 GLN
B 253 ASN
** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 424 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.108676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.091003 restraints weight = 8169.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 1.36
r_work: 0.2872 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2768 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.0777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6718  Z= 0.144
  Angle     :  0.490   5.848   9134  Z= 0.254
  Chirality :  0.038   0.131   1110
  Planarity :  0.004   0.049   1108
  Dihedral  :  4.844  53.869    904
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 12.40 %
    Favored  : 84.13 %
  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:  2.10 (0.28), residues: 840
  helix:  2.12 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop : -0.51 (0.37), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  45 
 HIS   0.005   0.001   HIS A 368 
 PHE   0.012   0.001   PHE A 198 
 TYR   0.015   0.002   TYR A  50 
 ARG   0.001   0.000   ARG A 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03608 (  449)
  hydrogen bonds       : angle       4.01080 ( 1317)
  covalent geometry    : bond        0.00336 ( 6718)
  covalent geometry    : angle       0.48974 ( 9134)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 82
  time to evaluate  : 0.756 
Fit side-chains
REVERT: A  185 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.6923 (mmm160)
REVERT: A  354 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8127 (mt0)
REVERT: A  434 ASN cc_start: 0.8804 (m-40) cc_final: 0.8570 (m110)
REVERT: B  185 ARG cc_start: 0.7153 (mtt90) cc_final: 0.6447 (mmm-85)
REVERT: B  299 ARG cc_start: 0.7570 (mtm180) cc_final: 0.7062 (mtm180)
  outliers start: 26
  outliers final: 13
  residues processed: 93
  average time/residue: 1.0497
  time to fit residues: 103.6441
Evaluate side-chains
  96 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  185 ARG
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  354 GLN
Chi-restraints excluded: chain A residue  365 ASN
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  304 ASN
Chi-restraints excluded: chain B residue  345 SER
Chi-restraints excluded: chain B residue  348 ASP
Chi-restraints excluded: chain B residue  426 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   chunk 42 optimal weight:    5.9990
   chunk 82 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
B 275 ASN
B 368 HIS
B 434 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.107321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.089640 restraints weight = 8343.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.2922 rms_B_bonded: 1.36
r_work: 0.2833 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2729 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.0920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6718  Z= 0.165
  Angle     :  0.494   5.379   9134  Z= 0.255
  Chirality :  0.039   0.134   1110
  Planarity :  0.004   0.048   1108
  Dihedral  :  4.462  49.549    898
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 12.53 %
    Favored  : 83.33 %
  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:  2.14 (0.28), residues: 840
  helix:  2.17 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop : -0.53 (0.36), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  45 
 HIS   0.005   0.001   HIS A 368 
 PHE   0.013   0.001   PHE A 198 
 TYR   0.015   0.002   TYR A  50 
 ARG   0.002   0.000   ARG B 367 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03477 (  449)
  hydrogen bonds       : angle       3.92249 ( 1317)
  covalent geometry    : bond        0.00390 ( 6718)
  covalent geometry    : angle       0.49424 ( 9134)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 82
  time to evaluate  : 0.683 
Fit side-chains
REVERT: A  185 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.6904 (mmm160)
REVERT: A  354 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8058 (mt0)
REVERT: A  434 ASN cc_start: 0.8824 (m-40) cc_final: 0.8577 (m110)
REVERT: B  185 ARG cc_start: 0.7171 (mtt90) cc_final: 0.6435 (mmm-85)
REVERT: B  299 ARG cc_start: 0.7511 (mtm180) cc_final: 0.7049 (mtm180)
REVERT: B  461 MET cc_start: 0.9044 (mmm) cc_final: 0.8782 (OUTLIER)
REVERT: B  529 LYS cc_start: 0.8568 (mttp) cc_final: 0.8341 (mmtp)
  outliers start: 31
  outliers final: 16
  residues processed: 95
  average time/residue: 0.9708
  time to fit residues: 98.1696
Evaluate side-chains
  98 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  185 ARG
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  354 GLN
Chi-restraints excluded: chain A residue  365 ASN
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  304 ASN
Chi-restraints excluded: chain B residue  345 SER
Chi-restraints excluded: chain B residue  426 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 78 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 74 optimal weight:    6.9990
   chunk 33 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 368 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.111346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.094203 restraints weight = 8268.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.2977 rms_B_bonded: 1.28
r_work: 0.2894 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2792 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.1028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6718  Z= 0.105
  Angle     :  0.449   5.461   9134  Z= 0.232
  Chirality :  0.037   0.123   1110
  Planarity :  0.004   0.048   1108
  Dihedral  :  4.318  49.644    898
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 13.20 %
    Favored  : 82.80 %
  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:  2.44 (0.28), residues: 840
  helix:  2.43 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop : -0.52 (0.35), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  45 
 HIS   0.004   0.001   HIS A 368 
 PHE   0.011   0.001   PHE A 198 
 TYR   0.013   0.001   TYR A  50 
 ARG   0.001   0.000   ARG B 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02944 (  449)
  hydrogen bonds       : angle       3.72858 ( 1317)
  covalent geometry    : bond        0.00235 ( 6718)
  covalent geometry    : angle       0.44913 ( 9134)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 85
  time to evaluate  : 0.790 
Fit side-chains
REVERT: A  185 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6755 (mmm160)
REVERT: A  301 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7852 (ttm)
REVERT: A  434 ASN cc_start: 0.8755 (m-40) cc_final: 0.8482 (m110)
REVERT: A  529 LYS cc_start: 0.8539 (mttp) cc_final: 0.8318 (mmtp)
REVERT: B  185 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6246 (mmm-85)
REVERT: B  299 ARG cc_start: 0.7348 (mtm180) cc_final: 0.6878 (mtm180)
REVERT: B  434 ASN cc_start: 0.8758 (m-40) cc_final: 0.8537 (m110)
REVERT: B  461 MET cc_start: 0.8955 (mmm) cc_final: 0.8748 (mmm)
REVERT: B  529 LYS cc_start: 0.8529 (mttp) cc_final: 0.8290 (mmtp)
  outliers start: 30
  outliers final: 18
  residues processed: 96
  average time/residue: 1.0328
  time to fit residues: 105.8140
Evaluate side-chains
  103 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  185 ARG
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  301 MET
Chi-restraints excluded: chain A residue  354 GLN
Chi-restraints excluded: chain A residue  365 ASN
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  185 ARG
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  304 ASN
Chi-restraints excluded: chain B residue  345 SER
Chi-restraints excluded: chain B residue  348 ASP
Chi-restraints excluded: chain B residue  426 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 15 optimal weight:    6.9990
   chunk 71 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 56 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 72 optimal weight:    0.4980
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 270 GLN
A 368 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.111428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.094300 restraints weight = 8160.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 1.27
r_work: 0.2897 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2795 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.1089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6718  Z= 0.103
  Angle     :  0.444   6.023   9134  Z= 0.229
  Chirality :  0.037   0.122   1110
  Planarity :  0.004   0.048   1108
  Dihedral  :  4.251  49.473    898
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 13.73 %
    Favored  : 82.53 %
  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:  2.55 (0.28), residues: 840
  helix:  2.53 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop : -0.54 (0.35), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  45 
 HIS   0.004   0.001   HIS A 368 
 PHE   0.011   0.001   PHE A 198 
 TYR   0.014   0.001   TYR A  50 
 ARG   0.001   0.000   ARG B 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02842 (  449)
  hydrogen bonds       : angle       3.64186 ( 1317)
  covalent geometry    : bond        0.00231 ( 6718)
  covalent geometry    : angle       0.44410 ( 9134)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 84
  time to evaluate  : 0.727 
Fit side-chains
REVERT: A  185 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6731 (mmm160)
REVERT: A  301 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7847 (ttm)
REVERT: A  434 ASN cc_start: 0.8732 (m-40) cc_final: 0.8465 (m110)
REVERT: A  529 LYS cc_start: 0.8524 (mttp) cc_final: 0.8293 (mmtp)
REVERT: B   57 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7944 (mt)
REVERT: B  185 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6341 (mmm-85)
REVERT: B  299 ARG cc_start: 0.7321 (mtm180) cc_final: 0.6854 (mtm180)
REVERT: B  434 ASN cc_start: 0.8725 (m-40) cc_final: 0.8496 (m110)
REVERT: B  461 MET cc_start: 0.8927 (mmm) cc_final: 0.8696 (mmm)
REVERT: B  529 LYS cc_start: 0.8511 (mttp) cc_final: 0.8275 (mmtp)
  outliers start: 28
  outliers final: 18
  residues processed: 95
  average time/residue: 0.9881
  time to fit residues: 99.8839
Evaluate side-chains
  105 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  185 ARG
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  301 MET
Chi-restraints excluded: chain A residue  354 GLN
Chi-restraints excluded: chain A residue  365 ASN
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  185 ARG
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  304 ASN
Chi-restraints excluded: chain B residue  348 ASP
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  511 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 35 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 70 optimal weight:    5.9990
   chunk 13 optimal weight:    0.4980
   chunk 82 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0570
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
A 368 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.112750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.095623 restraints weight = 8194.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.2996 rms_B_bonded: 1.28
r_work: 0.2914 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2814 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.1200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6718  Z= 0.089
  Angle     :  0.422   5.036   9134  Z= 0.220
  Chirality :  0.036   0.119   1110
  Planarity :  0.004   0.048   1108
  Dihedral  :  4.130  48.784    898
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 13.60 %
    Favored  : 82.53 %
  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:  2.80 (0.28), residues: 840
  helix:  2.74 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop : -0.52 (0.35), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 287 
 HIS   0.002   0.000   HIS B 368 
 PHE   0.010   0.001   PHE A 361 
 TYR   0.013   0.001   TYR A  50 
 ARG   0.001   0.000   ARG A 447 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02632 (  449)
  hydrogen bonds       : angle       3.50194 ( 1317)
  covalent geometry    : bond        0.00195 ( 6718)
  covalent geometry    : angle       0.42191 ( 9134)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 84
  time to evaluate  : 0.721 
Fit side-chains
REVERT: A  292 LEU cc_start: 0.7899 (mp) cc_final: 0.7650 (tt)
REVERT: A  299 ARG cc_start: 0.7455 (mtm180) cc_final: 0.7018 (mtm180)
REVERT: A  301 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7856 (ttm)
REVERT: A  434 ASN cc_start: 0.8729 (m-40) cc_final: 0.8473 (m110)
REVERT: A  529 LYS cc_start: 0.8470 (mttp) cc_final: 0.8220 (mmtp)
REVERT: A  532 LYS cc_start: 0.7491 (mmtm) cc_final: 0.6958 (mmtp)
REVERT: B   57 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7952 (mt)
REVERT: B  185 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6342 (mmm-85)
REVERT: B  299 ARG cc_start: 0.7330 (mtm180) cc_final: 0.6861 (mtm180)
REVERT: B  434 ASN cc_start: 0.8742 (m-40) cc_final: 0.8502 (m110)
REVERT: B  461 MET cc_start: 0.8934 (mmm) cc_final: 0.8699 (mmm)
REVERT: B  529 LYS cc_start: 0.8503 (mttp) cc_final: 0.8275 (mmtp)
  outliers start: 29
  outliers final: 17
  residues processed: 95
  average time/residue: 0.9536
  time to fit residues: 96.4846
Evaluate side-chains
  102 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  301 MET
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain A residue  354 GLN
Chi-restraints excluded: chain A residue  365 ASN
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  436 ILE
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  185 ARG
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  304 ASN
Chi-restraints excluded: chain B residue  348 ASP
Chi-restraints excluded: chain B residue  422 LEU
Chi-restraints excluded: chain B residue  426 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 70 optimal weight:    5.9990
   chunk 83 optimal weight:    3.9990
   chunk 55 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 270 GLN
A 368 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.111212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.093435 restraints weight = 8349.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 1.36
r_work: 0.2882 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2780 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.1199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6718  Z= 0.105
  Angle     :  0.442   6.752   9134  Z= 0.228
  Chirality :  0.037   0.124   1110
  Planarity :  0.004   0.048   1108
  Dihedral  :  4.161  48.316    898
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 14.40 %
    Favored  : 82.13 %
  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:  2.79 (0.28), residues: 840
  helix:  2.72 (0.20), residues: 600
  sheet:  None (None), residues: 0
  loop : -0.49 (0.35), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 502 
 HIS   0.003   0.000   HIS B 368 
 PHE   0.011   0.001   PHE A 198 
 TYR   0.014   0.001   TYR A  50 
 ARG   0.004   0.000   ARG A 185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02745 (  449)
  hydrogen bonds       : angle       3.51077 ( 1317)
  covalent geometry    : bond        0.00239 ( 6718)
  covalent geometry    : angle       0.44180 ( 9134)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 0.669 
Fit side-chains
REVERT: A  292 LEU cc_start: 0.7960 (mp) cc_final: 0.7719 (tt)
REVERT: A  299 ARG cc_start: 0.7506 (mtm180) cc_final: 0.7082 (mtm180)
REVERT: A  434 ASN cc_start: 0.8771 (m-40) cc_final: 0.8530 (m110)
REVERT: B  185 ARG cc_start: 0.7115 (mtt90) cc_final: 0.6383 (mmm-85)
REVERT: B  299 ARG cc_start: 0.7375 (mtm180) cc_final: 0.6910 (mtm180)
REVERT: B  434 ASN cc_start: 0.8768 (m-40) cc_final: 0.8533 (m110)
REVERT: B  529 LYS cc_start: 0.8545 (mttp) cc_final: 0.8325 (mmtp)
  outliers start: 26
  outliers final: 20
  residues processed: 96
  average time/residue: 0.9294
  time to fit residues: 95.2459
Evaluate side-chains
  102 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  301 MET
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain A residue  354 GLN
Chi-restraints excluded: chain A residue  365 ASN
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  348 ASP
Chi-restraints excluded: chain B residue  422 LEU
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  511 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 56 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0980
   chunk 50 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 81 optimal weight:    0.9990
   chunk 54 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 368 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.113239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.096051 restraints weight = 8163.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.3001 rms_B_bonded: 1.28
r_work: 0.2919 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.1239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6718  Z= 0.094
  Angle     :  0.429   5.038   9134  Z= 0.224
  Chirality :  0.036   0.121   1110
  Planarity :  0.004   0.047   1108
  Dihedral  :  4.117  47.890    898
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 14.80 %
    Favored  : 81.87 %
  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:  2.86 (0.28), residues: 840
  helix:  2.78 (0.20), residues: 600
  sheet:  None (None), residues: 0
  loop : -0.49 (0.35), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 502 
 HIS   0.003   0.000   HIS B 368 
 PHE   0.011   0.001   PHE A 198 
 TYR   0.014   0.001   TYR A  50 
 ARG   0.004   0.000   ARG A 185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02641 (  449)
  hydrogen bonds       : angle       3.47102 ( 1317)
  covalent geometry    : bond        0.00210 ( 6718)
  covalent geometry    : angle       0.42937 ( 9134)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 80
  time to evaluate  : 0.666 
Fit side-chains
REVERT: A  292 LEU cc_start: 0.7964 (mp) cc_final: 0.7761 (tt)
REVERT: A  299 ARG cc_start: 0.7423 (mtm180) cc_final: 0.7007 (mtm180)
REVERT: A  306 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7549 (mp0)
REVERT: A  434 ASN cc_start: 0.8734 (m-40) cc_final: 0.8486 (m110)
REVERT: A  532 LYS cc_start: 0.7517 (mmtm) cc_final: 0.6970 (mmtp)
REVERT: B  185 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.6289 (mmm-85)
REVERT: B  299 ARG cc_start: 0.7341 (mtm180) cc_final: 0.6871 (mtm180)
REVERT: B  434 ASN cc_start: 0.8740 (m-40) cc_final: 0.8511 (m110)
REVERT: B  529 LYS cc_start: 0.8515 (mttp) cc_final: 0.8294 (mmtp)
  outliers start: 25
  outliers final: 21
  residues processed: 95
  average time/residue: 0.9928
  time to fit residues: 100.3392
Evaluate side-chains
  103 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  301 MET
Chi-restraints excluded: chain A residue  306 GLU
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain A residue  354 GLN
Chi-restraints excluded: chain A residue  365 ASN
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  436 ILE
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  185 ARG
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  348 ASP
Chi-restraints excluded: chain B residue  422 LEU
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  511 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 68 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 76 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 56 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 368 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.111245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.093549 restraints weight = 8293.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.2976 rms_B_bonded: 1.36
r_work: 0.2889 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2787 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.1237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6718  Z= 0.101
  Angle     :  0.443   7.114   9134  Z= 0.228
  Chirality :  0.037   0.122   1110
  Planarity :  0.004   0.047   1108
  Dihedral  :  4.127  47.754    898
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 14.80 %
    Favored  : 82.00 %
  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:  2.84 (0.28), residues: 840
  helix:  2.76 (0.20), residues: 600
  sheet:  None (None), residues: 0
  loop : -0.49 (0.35), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 502 
 HIS   0.003   0.001   HIS B 368 
 PHE   0.011   0.001   PHE A 198 
 TYR   0.014   0.001   TYR A  50 
 ARG   0.004   0.000   ARG A 185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02682 (  449)
  hydrogen bonds       : angle       3.47288 ( 1317)
  covalent geometry    : bond        0.00228 ( 6718)
  covalent geometry    : angle       0.44277 ( 9134)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 81
  time to evaluate  : 0.747 
Fit side-chains
REVERT: A  299 ARG cc_start: 0.7484 (mtm180) cc_final: 0.7080 (mtm180)
REVERT: A  306 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7589 (mp0)
REVERT: A  434 ASN cc_start: 0.8763 (m-40) cc_final: 0.8520 (m110)
REVERT: A  532 LYS cc_start: 0.7526 (mmtm) cc_final: 0.6978 (mmtp)
REVERT: B  185 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6340 (mmm-85)
REVERT: B  299 ARG cc_start: 0.7380 (mtm180) cc_final: 0.6880 (mtm180)
REVERT: B  434 ASN cc_start: 0.8762 (m-40) cc_final: 0.8540 (m110)
REVERT: B  529 LYS cc_start: 0.8528 (mttp) cc_final: 0.8308 (mmtp)
  outliers start: 24
  outliers final: 20
  residues processed: 96
  average time/residue: 0.9568
  time to fit residues: 97.6098
Evaluate side-chains
  101 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 79
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  270 GLN
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  306 GLU
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain A residue  354 GLN
Chi-restraints excluded: chain A residue  365 ASN
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  436 ILE
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  185 ARG
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  422 LEU
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  511 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 25 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 368 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.109206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.091512 restraints weight = 8317.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 1.36
r_work: 0.2856 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2751 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.1203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6718  Z= 0.134
  Angle     :  0.477   9.850   9134  Z= 0.243
  Chirality :  0.038   0.129   1110
  Planarity :  0.004   0.048   1108
  Dihedral  :  4.306  49.127    898
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 15.07 %
    Favored  : 82.00 %
  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:  2.64 (0.28), residues: 840
  helix:  2.60 (0.20), residues: 600
  sheet:  None (None), residues: 0
  loop : -0.52 (0.35), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 502 
 HIS   0.004   0.001   HIS B 368 
 PHE   0.013   0.001   PHE A 198 
 TYR   0.016   0.002   TYR B  50 
 ARG   0.004   0.000   ARG A 185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02935 (  449)
  hydrogen bonds       : angle       3.56083 ( 1317)
  covalent geometry    : bond        0.00311 ( 6718)
  covalent geometry    : angle       0.47704 ( 9134)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 81
  time to evaluate  : 0.666 
Fit side-chains
REVERT: A  299 ARG cc_start: 0.7502 (mtm180) cc_final: 0.7102 (mtm180)
REVERT: A  306 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7588 (mp0)
REVERT: A  434 ASN cc_start: 0.8790 (m-40) cc_final: 0.8526 (m110)
REVERT: A  532 LYS cc_start: 0.7517 (mmtm) cc_final: 0.6975 (mmtp)
REVERT: B  185 ARG cc_start: 0.7139 (mtt90) cc_final: 0.6343 (mmm-85)
REVERT: B  299 ARG cc_start: 0.7398 (mtm180) cc_final: 0.6932 (mtm180)
REVERT: B  434 ASN cc_start: 0.8791 (m-40) cc_final: 0.8568 (m110)
REVERT: B  529 LYS cc_start: 0.8558 (mttp) cc_final: 0.8328 (mmtp)
  outliers start: 22
  outliers final: 19
  residues processed: 93
  average time/residue: 1.0018
  time to fit residues: 99.1100
Evaluate side-chains
  99 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  270 GLN
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  301 MET
Chi-restraints excluded: chain A residue  306 GLU
Chi-restraints excluded: chain A residue  365 ASN
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  348 ASP
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  511 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 62 optimal weight:    7.9990
   chunk 41 optimal weight:    3.9990
   chunk 34 optimal weight:    0.3980
   chunk 1 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 368 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.109638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.092026 restraints weight = 8348.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 1.36
r_work: 0.2858 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2754 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.1207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6718  Z= 0.129
  Angle     :  0.468   7.107   9134  Z= 0.241
  Chirality :  0.038   0.129   1110
  Planarity :  0.004   0.048   1108
  Dihedral  :  4.335  49.985    898
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 15.47 %
    Favored  : 81.87 %
  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:  2.62 (0.28), residues: 840
  helix:  2.59 (0.20), residues: 600
  sheet:  None (None), residues: 0
  loop : -0.54 (0.35), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 502 
 HIS   0.004   0.001   HIS B 368 
 PHE   0.012   0.001   PHE A 198 
 TYR   0.014   0.002   TYR B  50 
 ARG   0.004   0.000   ARG A 185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02895 (  449)
  hydrogen bonds       : angle       3.56067 ( 1317)
  covalent geometry    : bond        0.00299 ( 6718)
  covalent geometry    : angle       0.46751 ( 9134)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4093.62 seconds
wall clock time: 71 minutes 40.60 seconds (4300.60 seconds total)