Starting phenix.real_space_refine
on Fri Aug 22 17:25:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w9v_37382/08_2025/8w9v_37382.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w9v_37382/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w9v_37382/08_2025/8w9v_37382.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w9v_37382/08_2025/8w9v_37382.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w9v_37382/08_2025/8w9v_37382.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w9v_37382/08_2025/8w9v_37382.map"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.53, per 1000 atoms: 0.23
  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: 0.57
  Conformation dependent library (CDL) restraints added in 369.7 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 0.20
  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: 1.04

  Time building geometry restraints manager: 0.80 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: 0.01
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:             0.860
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.810
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   15.240
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG A 447 
 TYR   0.016   0.002   TYR A  50 
 PHE   0.011   0.001   PHE A 198 
 TRP   0.004   0.001   TRP A  45 
 HIS   0.004   0.001   HIS A 368 

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

*********************** 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  : 0.309 
Fit side-chains
  outliers start: 7
  outliers final: 7
  residues processed: 87
  average time/residue: 0.5112
  time to fit residues: 46.9672
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  : 0.257 
-------------------------------------------------------------------------------
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 49 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    8.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.3980
   chunk 45 optimal weight:    8.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    1.4184

-------------------------------------------------------------------------------
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
B 424 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.108493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.090769 restraints weight = 8244.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.2953 rms_B_bonded: 1.36
r_work: 0.2867 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2763 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.0739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   6718  Z= 0.151
  Angle     :  0.494   5.758   9134  Z= 0.257
  Chirality :  0.039   0.131   1110
  Planarity :  0.004   0.049   1108
  Dihedral  :  4.887  54.184    904
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.82
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.07 (0.28), residues: 840
  helix:  2.10 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop : -0.51 (0.37), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 450 
 TYR   0.015   0.002   TYR A  50 
 PHE   0.012   0.001   PHE A 198 
 TRP   0.005   0.001   TRP B  45 
 HIS   0.005   0.001   HIS A 368 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 6718)
  covalent geometry    : angle       0.49370 ( 9134)
  hydrogen bonds       : bond        0.03745 (  449)
  hydrogen bonds       : angle       4.04212 ( 1317)

*********************** 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
  107 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 81
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  354 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8120 (mt0)
REVERT: A  434 ASN cc_start: 0.8795 (m-40) cc_final: 0.8545 (m110)
REVERT: B  185 ARG cc_start: 0.7137 (mtt90) cc_final: 0.6425 (mmm-85)
REVERT: B  299 ARG cc_start: 0.7502 (mtm180) cc_final: 0.6986 (mtm180)
REVERT: B  434 ASN cc_start: 0.8777 (m-40) cc_final: 0.8569 (m110)
  outliers start: 26
  outliers final: 12
  residues processed: 92
  average time/residue: 0.4987
  time to fit residues: 48.4715
Evaluate side-chains
  96 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 45 optimal weight:    7.9990
   chunk 80 optimal weight:    3.9990
   chunk 64 optimal weight:    0.0020
   overall best weight:    0.7388

-------------------------------------------------------------------------------
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 = 0.3209 r_free = 0.3209 target = 0.110812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.093229 restraints weight = 8221.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 1.36
r_work: 0.2889 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2785 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.0968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6718  Z= 0.101
  Angle     :  0.447   5.135   9134  Z= 0.231
  Chirality :  0.037   0.121   1110
  Planarity :  0.004   0.047   1108
  Dihedral  :  4.163  46.599    898
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 12.93 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.48 (0.28), residues: 840
  helix:  2.45 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop : -0.47 (0.36), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 185 
 TYR   0.014   0.001   TYR A  50 
 PHE   0.010   0.001   PHE A 198 
 TRP   0.003   0.001   TRP B 287 
 HIS   0.003   0.001   HIS B 368 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 6718)
  covalent geometry    : angle       0.44674 ( 9134)
  hydrogen bonds       : bond        0.02984 (  449)
  hydrogen bonds       : angle       3.72998 ( 1317)

*********************** 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
  106 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 81
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A  434 ASN cc_start: 0.8752 (m-40) cc_final: 0.8504 (m110)
REVERT: B   57 LEU cc_start: 0.8380 (mm) cc_final: 0.8046 (mt)
REVERT: B  185 ARG cc_start: 0.7074 (mtt90) cc_final: 0.6345 (mmm-85)
REVERT: B  299 ARG cc_start: 0.7443 (mtm180) cc_final: 0.6975 (mtm180)
REVERT: B  434 ASN cc_start: 0.8752 (m-40) cc_final: 0.8531 (m110)
REVERT: B  450 ARG cc_start: 0.7841 (ttm170) cc_final: 0.6977 (ttp-110)
REVERT: B  529 LYS cc_start: 0.8491 (mttp) cc_final: 0.8258 (mmtp)
  outliers start: 25
  outliers final: 17
  residues processed: 93
  average time/residue: 0.4590
  time to fit residues: 45.2617
Evaluate side-chains
  96 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
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  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 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  301 MET
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
Chi-restraints excluded: chain B residue  461 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 15 optimal weight:    0.5980
   chunk 3 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9980
   chunk 76 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 35 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.8382

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.112348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.095231 restraints weight = 8179.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 1.28
r_work: 0.2927 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2825 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.1025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6718  Z= 0.105
  Angle     :  0.443   5.442   9134  Z= 0.228
  Chirality :  0.037   0.122   1110
  Planarity :  0.004   0.048   1108
  Dihedral  :  4.171  46.723    898
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 13.33 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.58 (0.28), residues: 840
  helix:  2.54 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop : -0.47 (0.35), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 185 
 TYR   0.014   0.002   TYR A  50 
 PHE   0.011   0.001   PHE A 198 
 TRP   0.003   0.001   TRP A 502 
 HIS   0.004   0.001   HIS A 368 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 6718)
  covalent geometry    : angle       0.44338 ( 9134)
  hydrogen bonds       : bond        0.02881 (  449)
  hydrogen bonds       : angle       3.63852 ( 1317)

*********************** 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
  110 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 83
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  434 ASN cc_start: 0.8747 (m-40) cc_final: 0.8492 (m110)
REVERT: B   57 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7940 (mt)
REVERT: B  185 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6309 (mmm-85)
REVERT: B  299 ARG cc_start: 0.7336 (mtm180) cc_final: 0.6868 (mtm180)
REVERT: B  434 ASN cc_start: 0.8726 (m-40) cc_final: 0.8490 (m110)
REVERT: B  450 ARG cc_start: 0.7757 (ttm170) cc_final: 0.6871 (ttp-110)
REVERT: B  461 MET cc_start: 0.8905 (mmm) cc_final: 0.8661 (OUTLIER)
REVERT: B  529 LYS cc_start: 0.8481 (mttp) cc_final: 0.8241 (mmtp)
  outliers start: 27
  outliers final: 17
  residues processed: 95
  average time/residue: 0.4801
  time to fit residues: 48.3298
Evaluate side-chains
  100 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
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  354 GLN
Chi-restraints excluded: chain A residue  365 ASN
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  510 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  301 MET
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  511 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 35 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9990
   chunk 67 optimal weight:    4.9990
   chunk 18 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   chunk 61 optimal weight:    0.3980
   chunk 38 optimal weight:    5.9990
   chunk 3 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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 = 0.3243 r_free = 0.3243 target = 0.113021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.095816 restraints weight = 8293.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3011 rms_B_bonded: 1.29
r_work: 0.2929 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2828 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.1099

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= 0.100
  Angle     :  0.436   5.927   9134  Z= 0.225
  Chirality :  0.037   0.122   1110
  Planarity :  0.004   0.048   1108
  Dihedral  :  4.127  46.986    898
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 12.93 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.72 (0.28), residues: 840
  helix:  2.66 (0.20), residues: 600
  sheet:  None (None), residues: 0
  loop : -0.48 (0.35), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 185 
 TYR   0.014   0.001   TYR A  50 
 PHE   0.011   0.001   PHE A 198 
 TRP   0.003   0.001   TRP A 502 
 HIS   0.004   0.001   HIS A 368 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 6718)
  covalent geometry    : angle       0.43629 ( 9134)
  hydrogen bonds       : bond        0.02777 (  449)
  hydrogen bonds       : angle       3.55784 ( 1317)

*********************** 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
  111 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 83
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A  434 ASN cc_start: 0.8743 (m-40) cc_final: 0.8473 (m110)
REVERT: B   57 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7886 (mt)
REVERT: B  185 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6308 (mmm-85)
REVERT: B  299 ARG cc_start: 0.7291 (mtm180) cc_final: 0.6819 (mtm180)
REVERT: B  434 ASN cc_start: 0.8707 (m-40) cc_final: 0.8475 (m110)
REVERT: B  450 ARG cc_start: 0.7784 (ttm170) cc_final: 0.6878 (ttp-110)
REVERT: B  529 LYS cc_start: 0.8499 (mttp) cc_final: 0.8260 (mmtp)
  outliers start: 28
  outliers final: 22
  residues processed: 96
  average time/residue: 0.4881
  time to fit residues: 49.7095
Evaluate side-chains
  106 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 82
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
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  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  510 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  185 ARG
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  301 MET
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  511 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 71 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 22 optimal weight:    0.4980
   chunk 79 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 80 optimal weight:    5.9990
   chunk 34 optimal weight:    0.3980
   chunk 15 optimal weight:    6.9990
   overall best weight:    0.6380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.111679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.094027 restraints weight = 8290.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 1.36
r_work: 0.2899 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2797 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.1188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6718  Z= 0.092
  Angle     :  0.424   5.045   9134  Z= 0.221
  Chirality :  0.036   0.119   1110
  Planarity :  0.004   0.048   1108
  Dihedral  :  4.065  46.726    898
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 13.47 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.87 (0.28), residues: 840
  helix:  2.78 (0.20), residues: 600
  sheet:  None (None), residues: 0
  loop : -0.47 (0.35), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 185 
 TYR   0.013   0.001   TYR A  50 
 PHE   0.010   0.001   PHE A 198 
 TRP   0.003   0.001   TRP A 502 
 HIS   0.003   0.001   HIS A 368 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 ( 6718)
  covalent geometry    : angle       0.42431 ( 9134)
  hydrogen bonds       : bond        0.02646 (  449)
  hydrogen bonds       : angle       3.47381 ( 1317)

*********************** 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
  111 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 85
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A  292 LEU cc_start: 0.7927 (mp) cc_final: 0.7717 (tt)
REVERT: A  299 ARG cc_start: 0.7500 (mtm180) cc_final: 0.7073 (mtm180)
REVERT: A  434 ASN cc_start: 0.8763 (m-40) cc_final: 0.8514 (m110)
REVERT: B   57 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7991 (mt)
REVERT: B  185 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6318 (mmm-85)
REVERT: B  299 ARG cc_start: 0.7384 (mtm180) cc_final: 0.6919 (mtm180)
REVERT: B  434 ASN cc_start: 0.8729 (m-40) cc_final: 0.8514 (m110)
REVERT: B  450 ARG cc_start: 0.7839 (ttm170) cc_final: 0.6938 (ttp-110)
REVERT: B  529 LYS cc_start: 0.8497 (mttp) cc_final: 0.8252 (mmtp)
  outliers start: 26
  outliers final: 19
  residues processed: 95
  average time/residue: 0.5190
  time to fit residues: 52.2708
Evaluate side-chains
  104 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
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  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   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  301 MET
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 8 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 64 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.9186

-------------------------------------------------------------------------------
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 = 0.3210 r_free = 0.3210 target = 0.110789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.093110 restraints weight = 8270.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 1.36
r_work: 0.2882 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2778 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.1175

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= 0.107
  Angle     :  0.443   6.639   9134  Z= 0.228
  Chirality :  0.037   0.124   1110
  Planarity :  0.004   0.048   1108
  Dihedral  :  4.130  47.080    898
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 14.13 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.83 (0.28), residues: 840
  helix:  2.75 (0.20), residues: 600
  sheet:  None (None), residues: 0
  loop : -0.47 (0.35), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 185 
 TYR   0.015   0.002   TYR A  50 
 PHE   0.011   0.001   PHE A 198 
 TRP   0.003   0.001   TRP A 502 
 HIS   0.004   0.001   HIS A 368 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 6718)
  covalent geometry    : angle       0.44297 ( 9134)
  hydrogen bonds       : bond        0.02759 (  449)
  hydrogen bonds       : angle       3.49752 ( 1317)

*********************** 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
  108 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A  292 LEU cc_start: 0.7981 (mp) cc_final: 0.7776 (tt)
REVERT: A  299 ARG cc_start: 0.7494 (mtm180) cc_final: 0.7075 (mtm180)
REVERT: A  306 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7571 (mp0)
REVERT: A  434 ASN cc_start: 0.8775 (m-40) cc_final: 0.8531 (m110)
REVERT: B  185 ARG cc_start: 0.7111 (mtt90) cc_final: 0.6381 (mmm-85)
REVERT: B  299 ARG cc_start: 0.7400 (mtm180) cc_final: 0.6939 (mtm180)
REVERT: B  434 ASN cc_start: 0.8728 (m-40) cc_final: 0.8510 (m110)
REVERT: B  450 ARG cc_start: 0.7871 (ttm170) cc_final: 0.6966 (ttp-110)
REVERT: B  529 LYS cc_start: 0.8508 (mttp) cc_final: 0.8280 (mmtp)
  outliers start: 23
  outliers final: 20
  residues processed: 97
  average time/residue: 0.5184
  time to fit residues: 53.1118
Evaluate side-chains
  104 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
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  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  510 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  301 MET
Chi-restraints excluded: chain B residue  422 LEU
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  510 LEU
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 15 optimal weight:    5.9990
   chunk 9 optimal weight:    9.9990
   chunk 59 optimal weight:    0.6980
   chunk 54 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 69 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    0.7780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.111161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.093463 restraints weight = 8321.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.2977 rms_B_bonded: 1.36
r_work: 0.2890 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2787 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.1210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6718  Z= 0.099
  Angle     :  0.432   5.048   9134  Z= 0.225
  Chirality :  0.037   0.121   1110
  Planarity :  0.004   0.048   1108
  Dihedral  :  4.115  47.169    898
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 14.13 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.88 (0.28), residues: 840
  helix:  2.79 (0.20), residues: 600
  sheet:  None (None), residues: 0
  loop : -0.46 (0.35), residues: 240

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 6718)
  covalent geometry    : angle       0.43219 ( 9134)
  hydrogen bonds       : bond        0.02677 (  449)
  hydrogen bonds       : angle       3.46470 ( 1317)

*********************** 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: 24
    poor density    : 81
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A  299 ARG cc_start: 0.7483 (mtm180) cc_final: 0.7076 (mtm180)
REVERT: A  306 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7601 (mp0)
REVERT: A  434 ASN cc_start: 0.8769 (m-40) cc_final: 0.8529 (m110)
REVERT: B  185 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6335 (mmm-85)
REVERT: B  299 ARG cc_start: 0.7388 (mtm180) cc_final: 0.6923 (mtm180)
REVERT: B  434 ASN cc_start: 0.8734 (m-40) cc_final: 0.8502 (m110)
REVERT: B  450 ARG cc_start: 0.7857 (ttm170) cc_final: 0.6953 (ttp-110)
REVERT: B  529 LYS cc_start: 0.8497 (mttp) cc_final: 0.8267 (mmtp)
  outliers start: 24
  outliers final: 20
  residues processed: 94
  average time/residue: 0.5239
  time to fit residues: 52.1138
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  : 0.247 
-------------------------------------------------------------------------------
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  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  510 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  301 MET
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 21 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 62 optimal weight:    6.9990
   chunk 24 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 51 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.111046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.093346 restraints weight = 8313.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 1.38
r_work: 0.2880 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.2776 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.1217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6718  Z= 0.109
  Angle     :  0.461   8.770   9134  Z= 0.234
  Chirality :  0.037   0.123   1110
  Planarity :  0.004   0.048   1108
  Dihedral  :  4.163  47.571    898
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 14.00 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.83 (0.28), residues: 840
  helix:  2.75 (0.20), residues: 600
  sheet:  None (None), residues: 0
  loop : -0.46 (0.35), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 185 
 TYR   0.015   0.002   TYR A  50 
 PHE   0.012   0.001   PHE A 198 
 TRP   0.003   0.001   TRP B 502 
 HIS   0.004   0.001   HIS A 368 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 6718)
  covalent geometry    : angle       0.46133 ( 9134)
  hydrogen bonds       : bond        0.02748 (  449)
  hydrogen bonds       : angle       3.48490 ( 1317)

*********************** 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
  106 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 82
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A  299 ARG cc_start: 0.7482 (mtm180) cc_final: 0.7071 (mtm180)
REVERT: A  306 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7562 (mp0)
REVERT: A  434 ASN cc_start: 0.8769 (m-40) cc_final: 0.8521 (m110)
REVERT: B  185 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6333 (mmm-85)
REVERT: B  299 ARG cc_start: 0.7396 (mtm180) cc_final: 0.6896 (mtm180)
REVERT: B  434 ASN cc_start: 0.8740 (m-40) cc_final: 0.8522 (m110)
REVERT: B  450 ARG cc_start: 0.7851 (ttm170) cc_final: 0.6953 (ttp-110)
REVERT: B  529 LYS cc_start: 0.8499 (mttp) cc_final: 0.8267 (mmtp)
  outliers start: 24
  outliers final: 23
  residues processed: 95
  average time/residue: 0.4721
  time to fit residues: 47.5054
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  : 0.311 
-------------------------------------------------------------------------------
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  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  510 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   63 ILE
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  301 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 73 optimal weight:    5.9990
   chunk 45 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 75 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.3197 r_free = 0.3197 target = 0.109819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.092135 restraints weight = 8327.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 1.36
r_work: 0.2871 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2767 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.1208

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= 0.123
  Angle     :  0.456   5.071   9134  Z= 0.237
  Chirality :  0.037   0.127   1110
  Planarity :  0.004   0.048   1108
  Dihedral  :  4.265  48.766    898
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 14.53 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.73 (0.28), residues: 840
  helix:  2.67 (0.20), residues: 600
  sheet:  None (None), residues: 0
  loop : -0.49 (0.35), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 185 
 TYR   0.015   0.002   TYR B  50 
 PHE   0.012   0.001   PHE A 198 
 TRP   0.004   0.001   TRP A 502 
 HIS   0.004   0.001   HIS A 368 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 6718)
  covalent geometry    : angle       0.45585 ( 9134)
  hydrogen bonds       : bond        0.02848 (  449)
  hydrogen bonds       : angle       3.52401 ( 1317)

********************** 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  : 0.227 
Fit side-chains
REVERT: A  299 ARG cc_start: 0.7492 (mtm180) cc_final: 0.7088 (mtm180)
REVERT: A  306 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7633 (mp0)
REVERT: A  434 ASN cc_start: 0.8795 (m-40) cc_final: 0.8545 (m110)
REVERT: A  532 LYS cc_start: 0.7555 (mmtm) cc_final: 0.7009 (mmtp)
REVERT: B  185 ARG cc_start: 0.7101 (mtt90) cc_final: 0.6309 (mmm-85)
REVERT: B  299 ARG cc_start: 0.7401 (mtm180) cc_final: 0.6931 (mtm180)
REVERT: B  434 ASN cc_start: 0.8745 (m-40) cc_final: 0.8513 (m110)
REVERT: B  450 ARG cc_start: 0.7867 (ttm170) cc_final: 0.7002 (ttp-110)
REVERT: B  529 LYS cc_start: 0.8521 (mttp) cc_final: 0.8287 (mmtp)
  outliers start: 22
  outliers final: 19
  residues processed: 92
  average time/residue: 0.4413
  time to fit residues: 43.0105
Evaluate side-chains
  101 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 81
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
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  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  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 51 optimal weight:    7.9990
   chunk 36 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 53 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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 = 0.3173 r_free = 0.3173 target = 0.108141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.090497 restraints weight = 8308.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 1.36
r_work: 0.2848 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2744 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.1189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6718  Z= 0.164
  Angle     :  0.492   7.008   9134  Z= 0.254
  Chirality :  0.039   0.135   1110
  Planarity :  0.004   0.048   1108
  Dihedral  :  4.476  51.055    898
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 14.80 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.50 (0.28), residues: 840
  helix:  2.48 (0.20), residues: 600
  sheet:  None (None), residues: 0
  loop : -0.53 (0.35), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 367 
 TYR   0.015   0.002   TYR A  50 
 PHE   0.013   0.001   PHE A 198 
 TRP   0.005   0.001   TRP B 502 
 HIS   0.005   0.001   HIS B 368 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 6718)
  covalent geometry    : angle       0.49207 ( 9134)
  hydrogen bonds       : bond        0.03136 (  449)
  hydrogen bonds       : angle       3.64443 ( 1317)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2045.47 seconds
wall clock time: 35 minutes 44.48 seconds (2144.48 seconds total)