Starting phenix.real_space_refine
on Wed Mar  5 22:03:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kdp_37142/03_2025/8kdp_37142.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kdp_37142/03_2025/8kdp_37142.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kdp_37142/03_2025/8kdp_37142.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kdp_37142/03_2025/8kdp_37142.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kdp_37142/03_2025/8kdp_37142.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kdp_37142/03_2025/8kdp_37142.cif"
  }
  resolution = 4.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      22      5.16       5
     C    2626      2.51       5
     N     614      2.21       5
     O     656      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 3918
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 409
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 409
          Classifications: {'peptide': 52}
          Link IDs: {'PTRANS': 2, 'TRANS': 49}
    Chain: "B"
      Number of atoms: 3509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 454, 3509
          Classifications: {'peptide': 454}
          Link IDs: {'PTRANS': 23, 'TRANS': 430}
          Chain breaks: 1
  Time building chain proxies: 2.67, per 1000 atoms: 0.68
  Number of scatterers: 3918
  At special positions: 0
  Unit cell: (78.2595, 85.932, 79.794, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      22     16.00
     O     656      8.00
     N     614      7.00
     C    2626      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 210 " - pdb=" SG  CYS B 164 " distance=2.14

  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: 0.87
  Conformation dependent library (CDL) restraints added in 445.3 milliseconds
  

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  932

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 0 sheets defined
      85.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 165 through 174
      removed outlier: 3.618A  pdb=" N   LEU A 170 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   VAL A 172 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLY A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 207
    Processing helix  chain 'B' and resid 51 through 65
      removed outlier: 4.322A  pdb=" N   GLY B  65 " --> pdb=" O   GLY B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 71
    Processing helix  chain 'B' and resid 72 through 77
      removed outlier: 4.101A  pdb=" N   LEU B  76 " --> pdb=" O   PRO B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 110
      removed outlier: 4.198A  pdb=" N   VAL B  87 " --> pdb=" O   GLY B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 125
      removed outlier: 3.737A  pdb=" N   VAL B 123 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 139
      removed outlier: 3.549A  pdb=" N   ALA B 129 " --> pdb=" O   GLY B 125 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ILE B 135 " --> pdb=" O   LEU B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 158
    Processing helix  chain 'B' and resid 159 through 161
      No H-bonds generated for 'chain 'B' and resid 159 through 161'
    Processing helix  chain 'B' and resid 167 through 189
      removed outlier: 3.874A  pdb=" N   LEU B 173 " --> pdb=" O   GLU B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 222
    Processing helix  chain 'B' and resid 239 through 255
      removed outlier: 4.674A  pdb=" N   LEU B 245 " --> pdb=" O   GLY B 241 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   PHE B 252 " --> pdb=" O   TYR B 248 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   ALA B 253 " --> pdb=" O   SER B 249 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   TYR B 254 " --> pdb=" O   GLY B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 264
      removed outlier: 3.860A  pdb=" N   LEU B 260 " --> pdb=" O   TRP B 257 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ASN B 261 " --> pdb=" O   ASN B 258 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   PHE B 262 " --> pdb=" O   TYR B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 298
      Proline residue:  B 275  - end of helix
      Proline residue:  B 283  - end of helix
    Processing helix  chain 'B' and resid 301 through 307
    Processing helix  chain 'B' and resid 310 through 321
      removed outlier: 3.544A  pdb=" N   ASP B 314 " --> pdb=" O   ALA B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 356
      removed outlier: 3.579A  pdb=" N   SER B 338 " --> pdb=" O   SER B 334 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASN B 340 " --> pdb=" O   PHE B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 365
    Processing helix  chain 'B' and resid 373 through 386
    Processing helix  chain 'B' and resid 387 through 390
    Processing helix  chain 'B' and resid 393 through 399
      removed outlier: 3.802A  pdb=" N   ILE B 397 " --> pdb=" O   ILE B 393 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ASN B 398 " --> pdb=" O   PHE B 394 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   PHE B 399 " --> pdb=" O   SER B 395 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 393 through 399'
    Processing helix  chain 'B' and resid 400 through 422
      removed outlier: 3.942A  pdb=" N   ASN B 404 " --> pdb=" O   PHE B 400 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   TRP B 405 " --> pdb=" O   SER B 401 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   HIS B 420 " --> pdb=" O   ILE B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 454
      removed outlier: 4.888A  pdb=" N   SER B 450 " --> pdb=" O   LEU B 446 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   PHE B 451 " --> pdb=" O   ILE B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 466
      removed outlier: 4.053A  pdb=" N   LEU B 466 " --> pdb=" O   PHE B 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 476
      removed outlier: 3.869A  pdb=" N   VAL B 471 " --> pdb=" O   SER B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 501
      removed outlier: 3.833A  pdb=" N   GLY B 488 " --> pdb=" O   TRP B 484 " (cutoff:3.500A)

    290 hydrogen bonds defined for protein.
    849 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: 1.12

  Time building geometry restraints manager: 1.06 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 704
        1.33 -     1.47: 1446
        1.47 -     1.60: 1840
        1.60 -     1.74: 0
        1.74 -     1.87: 31
  Bond restraints: 4021
  Sorted by residual:
  bond pdb=" C   ALA B 310 "
       pdb=" O   ALA B 310 "
    ideal  model  delta    sigma   weight residual
    1.235  1.196  0.039 1.26e-02 6.30e+03 9.79e+00
  bond pdb=" C   ARG B 141 "
       pdb=" O   ARG B 141 "
    ideal  model  delta    sigma   weight residual
    1.244  1.213  0.031 1.00e-02 1.00e+04 9.53e+00
  bond pdb=" C   VAL B 166 "
       pdb=" N   PRO B 167 "
    ideal  model  delta    sigma   weight residual
    1.332  1.366 -0.034 1.12e-02 7.97e+03 8.98e+00
  bond pdb=" C   GLY B 114 "
       pdb=" O   GLY B 114 "
    ideal  model  delta    sigma   weight residual
    1.235  1.199  0.036 1.23e-02 6.61e+03 8.45e+00
  bond pdb=" CG  MET A 196 "
       pdb=" SD  MET A 196 "
    ideal  model  delta    sigma   weight residual
    1.803  1.870 -0.067 2.50e-02 1.60e+03 7.25e+00
  ... (remaining 4016 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 4197
        1.85 -     3.69: 1081
        3.69 -     5.54: 188
        5.54 -     7.39: 21
        7.39 -     9.23: 3
  Bond angle restraints: 5490
  Sorted by residual:
  angle pdb=" CA  PHE B 399 "
        pdb=" CB  PHE B 399 "
        pdb=" CG  PHE B 399 "
      ideal   model   delta    sigma   weight residual
     113.80  123.03   -9.23 1.00e+00 1.00e+00 8.52e+01
  angle pdb=" CA  HIS B 319 "
        pdb=" CB  HIS B 319 "
        pdb=" CG  HIS B 319 "
      ideal   model   delta    sigma   weight residual
     113.80  107.02    6.78 1.00e+00 1.00e+00 4.60e+01
  angle pdb=" CA  HIS B 367 "
        pdb=" CB  HIS B 367 "
        pdb=" CG  HIS B 367 "
      ideal   model   delta    sigma   weight residual
     113.80  107.47    6.33 1.00e+00 1.00e+00 4.01e+01
  angle pdb=" CA  ASP B 198 "
        pdb=" CB  ASP B 198 "
        pdb=" CG  ASP B 198 "
      ideal   model   delta    sigma   weight residual
     112.60  118.88   -6.28 1.00e+00 1.00e+00 3.95e+01
  angle pdb=" CA  ASN B  49 "
        pdb=" CB  ASN B  49 "
        pdb=" CG  ASN B  49 "
      ideal   model   delta    sigma   weight residual
     112.60  118.08   -5.48 1.00e+00 1.00e+00 3.00e+01
  ... (remaining 5485 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.62: 2147
       17.62 -    35.23: 153
       35.23 -    52.84: 19
       52.84 -    70.45: 4
       70.45 -    88.06: 1
  Dihedral angle restraints: 2324
    sinusoidal: 873
      harmonic: 1451
  Sorted by residual:
  dihedral pdb=" CA  ALA B 310 "
           pdb=" C   ALA B 310 "
           pdb=" N   VAL B 311 "
           pdb=" CA  VAL B 311 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.35  -34.65     0      5.00e+00 4.00e-02 4.80e+01
  dihedral pdb=" CA  PHE B 389 "
           pdb=" C   PHE B 389 "
           pdb=" N   SER B 390 "
           pdb=" CA  SER B 390 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.89  -30.11     0      5.00e+00 4.00e-02 3.63e+01
  dihedral pdb=" CA  VAL B 476 "
           pdb=" C   VAL B 476 "
           pdb=" N   TRP B 477 "
           pdb=" CA  TRP B 477 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.84  -27.16     0      5.00e+00 4.00e-02 2.95e+01
  ... (remaining 2321 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 344
       0.058 -    0.115: 208
       0.115 -    0.173: 88
       0.173 -    0.230: 18
       0.230 -    0.288: 6
  Chirality restraints: 664
  Sorted by residual:
  chirality pdb=" CA  ASP B 116 "
            pdb=" N   ASP B 116 "
            pdb=" C   ASP B 116 "
            pdb=" CB  ASP B 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.07e+00
  chirality pdb=" CA  TYR B 155 "
            pdb=" N   TYR B 155 "
            pdb=" C   TYR B 155 "
            pdb=" CB  TYR B 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.29 2.00e-01 2.50e+01 2.03e+00
  chirality pdb=" CA  TYR B 387 "
            pdb=" N   TYR B 387 "
            pdb=" C   TYR B 387 "
            pdb=" CB  TYR B 387 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.74e+00
  ... (remaining 661 not shown)

  Planarity restraints: 658
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 399 "    0.034 2.00e-02 2.50e+03   2.05e-02 7.38e+00
        pdb=" CG  PHE B 399 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 399 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 399 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 399 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 399 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 399 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 427 "    0.215 9.50e-02 1.11e+02   9.65e-02 5.85e+00
        pdb=" NE  ARG B 427 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 427 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 427 "    0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 427 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 419 "    0.208 9.50e-02 1.11e+02   9.35e-02 5.46e+00
        pdb=" NE  ARG B 419 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 419 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 419 "   -0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 419 "    0.009 2.00e-02 2.50e+03
  ... (remaining 655 not shown)

  Histogram of nonbonded interaction distances:
        2.56 -     3.03: 2206
        3.03 -     3.49: 4342
        3.49 -     3.96: 6262
        3.96 -     4.43: 7198
        4.43 -     4.90: 11259
  Nonbonded interactions: 31267
  Sorted by model distance:
  nonbonded pdb=" O   GLN B 304 "
            pdb=" OG  SER B 308 "
     model   vdw
     2.557 3.040
  nonbonded pdb=" O   VAL B 331 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.575 3.040
  nonbonded pdb=" O   SER B 347 "
            pdb=" OG  SER B 376 "
     model   vdw
     2.613 3.040
  nonbonded pdb=" O   PHE B 233 "
            pdb=" OG1 THR B 236 "
     model   vdw
     2.618 3.040
  nonbonded pdb=" O   SER B 113 "
            pdb=" OG  SER B 113 "
     model   vdw
     2.628 3.040
  ... (remaining 31262 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.110
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.220
  Find NCS groups from input model:        0.040
  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:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
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      :  0.011   0.067   4021  Z= 0.702
  Angle     :  1.670   9.231   5490  Z= 1.135
  Chirality :  0.083   0.288    664
  Planarity :  0.010   0.097    658
  Dihedral  : 12.569  88.063   1389
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 0.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  6.57 %
    Favored  : 93.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.42 %

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: -1.96 (0.32), residues: 500
  helix: -1.28 (0.22), residues: 373
  sheet:  None (None), residues: 0
  loop : -0.69 (0.53), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.005   TRP A 193 
 HIS   0.007   0.002   HIS B 367 
 PHE   0.034   0.005   PHE B 399 
 TYR   0.028   0.006   TYR B 146 
 ARG   0.006   0.001   ARG B 427 

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 175
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 ARG cc_start: 0.7064 (mtm110) cc_final: 0.6408 (ttt-90)
REVERT: A  206 ARG cc_start: 0.9104 (ttm170) cc_final: 0.8677 (mpt180)
REVERT: B   78 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8299 (mp0)
REVERT: B   95 PHE cc_start: 0.7162 (t80) cc_final: 0.6764 (t80)
REVERT: B  112 LYS cc_start: 0.8029 (mtmt) cc_final: 0.7633 (mmmt)
REVERT: B  116 ASP cc_start: 0.8746 (p0) cc_final: 0.8463 (p0)
REVERT: B  120 MET cc_start: 0.9011 (ttm) cc_final: 0.8767 (ttm)
REVERT: B  146 TYR cc_start: 0.8646 (t80) cc_final: 0.8401 (t80)
REVERT: B  242 ASN cc_start: 0.7079 (m-40) cc_final: 0.6867 (t0)
REVERT: B  293 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8367 (t0)
REVERT: B  297 PHE cc_start: 0.8713 (m-10) cc_final: 0.7923 (m-80)
REVERT: B  309 GLU cc_start: 0.9359 (mt-10) cc_final: 0.8755 (tp30)
REVERT: B  365 MET cc_start: 0.8812 (mmt) cc_final: 0.8556 (mmm)
REVERT: B  472 TYR cc_start: 0.8156 (t80) cc_final: 0.7762 (t80)
REVERT: B  501 GLN cc_start: 0.8554 (tt0) cc_final: 0.7502 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 175
  average time/residue: 0.1531
  time to fit residues: 33.1656
Evaluate side-chains
  127 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:   20.0000
   chunk 37 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 23 optimal weight:   10.0000
   chunk 29 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
B 145 GLN
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.095521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.077443 restraints weight = 8830.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.080341 restraints weight = 4745.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.082340 restraints weight = 3065.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.3107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4021  Z= 0.250
  Angle     :  0.668   6.150   5490  Z= 0.347
  Chirality :  0.045   0.204    664
  Planarity :  0.004   0.028    658
  Dihedral  :  5.411  23.444    533
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  3.52 %
    Favored  : 95.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.38), residues: 500
  helix:  1.16 (0.27), residues: 374
  sheet:  None (None), residues: 0
  loop : -0.26 (0.57), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 477 
 HIS   0.008   0.002   HIS B 319 
 PHE   0.028   0.002   PHE B 399 
 TYR   0.016   0.002   TYR B 155 
 ARG   0.002   0.000   ARG B 355 

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 150
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 GLU cc_start: 0.8497 (mp0) cc_final: 0.8197 (mp0)
REVERT: A  182 ARG cc_start: 0.7962 (mtm110) cc_final: 0.6643 (ttt-90)
REVERT: B   78 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7045 (mp0)
REVERT: B  120 MET cc_start: 0.8861 (ttm) cc_final: 0.8520 (ttm)
REVERT: B  146 TYR cc_start: 0.8538 (t80) cc_final: 0.8294 (t80)
REVERT: B  242 ASN cc_start: 0.7030 (m-40) cc_final: 0.6823 (t0)
REVERT: B  249 SER cc_start: 0.8859 (m) cc_final: 0.8584 (t)
REVERT: B  305 MET cc_start: 0.8250 (mtp) cc_final: 0.8029 (mtp)
REVERT: B  365 MET cc_start: 0.8684 (mmt) cc_final: 0.7799 (mmm)
REVERT: B  410 LEU cc_start: 0.8538 (mt) cc_final: 0.8287 (mp)
REVERT: B  474 PHE cc_start: 0.8480 (t80) cc_final: 0.8244 (t80)
REVERT: B  499 LEU cc_start: 0.8859 (tp) cc_final: 0.8657 (tp)
REVERT: B  501 GLN cc_start: 0.7902 (tt0) cc_final: 0.7370 (mp10)
  outliers start: 3
  outliers final: 0
  residues processed: 151
  average time/residue: 0.1533
  time to fit residues: 28.9909
Evaluate side-chains
  115 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 47 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 39 optimal weight:   10.0000
   chunk 10 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 46 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 15 optimal weight:    6.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
B 186 ASN
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.096490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.078101 restraints weight = 8808.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.080940 restraints weight = 4612.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.083021 restraints weight = 2976.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.3984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4021  Z= 0.252
  Angle     :  0.663   8.181   5490  Z= 0.334
  Chirality :  0.045   0.167    664
  Planarity :  0.004   0.033    658
  Dihedral  :  5.040  19.166    533
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.29 %
    Favored  : 96.48 %
  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:  1.76 (0.39), residues: 500
  helix:  1.80 (0.28), residues: 362
  sheet:  None (None), residues: 0
  loop : -0.47 (0.56), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 193 
 HIS   0.005   0.002   HIS B 319 
 PHE   0.021   0.002   PHE A 189 
 TYR   0.021   0.002   TYR B 103 
 ARG   0.003   0.000   ARG B 141 

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 GLU cc_start: 0.8433 (mp0) cc_final: 0.8230 (mp0)
REVERT: A  182 ARG cc_start: 0.7914 (mtm110) cc_final: 0.6674 (ttt-90)
REVERT: A  187 LEU cc_start: 0.7797 (mm) cc_final: 0.7347 (mm)
REVERT: B   78 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7112 (mp0)
REVERT: B  120 MET cc_start: 0.8872 (ttm) cc_final: 0.8581 (ttm)
REVERT: B  197 GLN cc_start: 0.7904 (tp40) cc_final: 0.7602 (tp40)
REVERT: B  242 ASN cc_start: 0.7146 (m-40) cc_final: 0.6767 (t0)
REVERT: B  365 MET cc_start: 0.8583 (mmt) cc_final: 0.7541 (mmm)
REVERT: B  501 GLN cc_start: 0.7817 (tt0) cc_final: 0.7357 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1586
  time to fit residues: 25.1740
Evaluate side-chains
  100 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   chunk 22 optimal weight:    4.9990
   chunk 5 optimal weight:   10.0000
   chunk 39 optimal weight:    6.9990
   chunk 3 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 45 optimal weight:   10.0000
   chunk 8 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 497 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 = 0.3260 r_free = 0.3260 target = 0.096978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.079882 restraints weight = 8717.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.082722 restraints weight = 4387.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.084711 restraints weight = 2774.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.4340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4021  Z= 0.216
  Angle     :  0.602   6.369   5490  Z= 0.302
  Chirality :  0.042   0.168    664
  Planarity :  0.004   0.029    658
  Dihedral  :  4.740  18.719    533
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.76 %
    Favored  : 96.01 %
  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:  1.87 (0.39), residues: 500
  helix:  1.88 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -0.48 (0.56), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 193 
 HIS   0.005   0.002   HIS B 319 
 PHE   0.024   0.002   PHE B 451 
 TYR   0.012   0.001   TYR B 155 
 ARG   0.003   0.000   ARG B 348 

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 120
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 GLU cc_start: 0.8641 (mp0) cc_final: 0.8339 (mp0)
REVERT: A  182 ARG cc_start: 0.7948 (mtm110) cc_final: 0.6734 (ttt-90)
REVERT: A  187 LEU cc_start: 0.7914 (mm) cc_final: 0.7382 (mm)
REVERT: B   54 ASN cc_start: 0.7199 (m-40) cc_final: 0.6972 (m-40)
REVERT: B   78 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7059 (mp0)
REVERT: B  120 MET cc_start: 0.8849 (ttm) cc_final: 0.8448 (ttm)
REVERT: B  242 ASN cc_start: 0.6944 (m-40) cc_final: 0.6647 (t0)
REVERT: B  365 MET cc_start: 0.8422 (mmt) cc_final: 0.7564 (mmm)
REVERT: B  407 CYS cc_start: 0.8259 (m) cc_final: 0.8014 (t)
REVERT: B  410 LEU cc_start: 0.8497 (mt) cc_final: 0.8270 (mp)
REVERT: B  501 GLN cc_start: 0.7833 (tt0) cc_final: 0.7239 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 121
  average time/residue: 0.1406
  time to fit residues: 21.4023
Evaluate side-chains
  100 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 30 optimal weight:    9.9990
   chunk 11 optimal weight:    3.9990
   chunk 13 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 497 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 = 0.3272 r_free = 0.3272 target = 0.097701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.080092 restraints weight = 8860.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.082894 restraints weight = 4467.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.084754 restraints weight = 2852.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.4664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4021  Z= 0.225
  Angle     :  0.613   6.719   5490  Z= 0.304
  Chirality :  0.043   0.161    664
  Planarity :  0.004   0.030    658
  Dihedral  :  4.639  18.595    533
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  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:  1.77 (0.38), residues: 500
  helix:  1.76 (0.27), residues: 367
  sheet:  None (None), residues: 0
  loop : -0.44 (0.55), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 193 
 HIS   0.006   0.002   HIS B 319 
 PHE   0.025   0.002   PHE B 451 
 TYR   0.014   0.001   TYR B 289 
 ARG   0.003   0.000   ARG B 348 

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 GLU cc_start: 0.8704 (mp0) cc_final: 0.8355 (mp0)
REVERT: A  182 ARG cc_start: 0.7901 (mtm110) cc_final: 0.6535 (ttt-90)
REVERT: A  187 LEU cc_start: 0.8180 (mm) cc_final: 0.7761 (mm)
REVERT: A  196 MET cc_start: 0.8749 (ttm) cc_final: 0.8546 (ttm)
REVERT: B   54 ASN cc_start: 0.7199 (m-40) cc_final: 0.6979 (m-40)
REVERT: B   78 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7176 (mp0)
REVERT: B  120 MET cc_start: 0.8864 (ttm) cc_final: 0.8458 (ttm)
REVERT: B  173 LEU cc_start: 0.9049 (tp) cc_final: 0.8701 (tp)
REVERT: B  177 LEU cc_start: 0.8501 (mp) cc_final: 0.8213 (mt)
REVERT: B  242 ASN cc_start: 0.6926 (m-40) cc_final: 0.6711 (t0)
REVERT: B  254 TYR cc_start: 0.7187 (m-80) cc_final: 0.6871 (m-80)
REVERT: B  267 MET cc_start: 0.8581 (mmm) cc_final: 0.8365 (mmm)
REVERT: B  365 MET cc_start: 0.8459 (mmt) cc_final: 0.7659 (mmm)
REVERT: B  407 CYS cc_start: 0.8254 (m) cc_final: 0.7937 (t)
REVERT: B  501 GLN cc_start: 0.7891 (tt0) cc_final: 0.7234 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1397
  time to fit residues: 21.8578
Evaluate side-chains
  107 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 38 optimal weight:    9.9990
   chunk 42 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 17 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   chunk 7 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 27 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 ASN ** 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 = 0.3305 r_free = 0.3305 target = 0.099910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.082870 restraints weight = 8566.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.085720 restraints weight = 4348.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.087797 restraints weight = 2740.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.5034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4021  Z= 0.178
  Angle     :  0.589   8.694   5490  Z= 0.288
  Chirality :  0.042   0.188    664
  Planarity :  0.004   0.030    658
  Dihedral  :  4.399  17.703    533
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.38), residues: 500
  helix:  1.95 (0.28), residues: 367
  sheet:  None (None), residues: 0
  loop : -0.51 (0.54), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP B 477 
 HIS   0.005   0.001   HIS B 319 
 PHE   0.022   0.001   PHE B 451 
 TYR   0.015   0.001   TYR B 146 
 ARG   0.003   0.000   ARG B 348 

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 GLU cc_start: 0.8429 (mp0) cc_final: 0.8204 (mp0)
REVERT: A  182 ARG cc_start: 0.8090 (mtm110) cc_final: 0.6740 (ttt-90)
REVERT: A  187 LEU cc_start: 0.8238 (mm) cc_final: 0.7789 (mm)
REVERT: B   78 GLU cc_start: 0.7486 (mm-30) cc_final: 0.6938 (mp0)
REVERT: B   97 ILE cc_start: 0.8567 (mt) cc_final: 0.8354 (tt)
REVERT: B  120 MET cc_start: 0.8432 (ttm) cc_final: 0.8105 (ttm)
REVERT: B  146 TYR cc_start: 0.8511 (t80) cc_final: 0.8299 (t80)
REVERT: B  213 LEU cc_start: 0.8523 (pp) cc_final: 0.8192 (mt)
REVERT: B  242 ASN cc_start: 0.6731 (m-40) cc_final: 0.6481 (t0)
REVERT: B  365 MET cc_start: 0.8503 (mmt) cc_final: 0.7803 (mmm)
REVERT: B  501 GLN cc_start: 0.7860 (tt0) cc_final: 0.7255 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1446
  time to fit residues: 23.0530
Evaluate side-chains
  102 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 37 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 29 optimal weight:   10.0000
   chunk 25 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 41 optimal weight:    6.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** B  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 ASN ** 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 = 0.3266 r_free = 0.3266 target = 0.098262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.080947 restraints weight = 8926.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.083842 restraints weight = 4541.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.085716 restraints weight = 2894.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.5137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4021  Z= 0.206
  Angle     :  0.605   6.750   5490  Z= 0.300
  Chirality :  0.044   0.175    664
  Planarity :  0.004   0.030    658
  Dihedral  :  4.516  18.317    533
  Min Nonbonded Distance : 2.657

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  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:  1.76 (0.38), residues: 500
  helix:  1.80 (0.27), residues: 369
  sheet:  None (None), residues: 0
  loop : -0.62 (0.54), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 477 
 HIS   0.005   0.001   HIS B 319 
 PHE   0.023   0.002   PHE B 451 
 TYR   0.012   0.001   TYR B 103 
 ARG   0.004   0.001   ARG A 206 

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 GLU cc_start: 0.8677 (mp0) cc_final: 0.8298 (mp0)
REVERT: A  182 ARG cc_start: 0.7803 (mtm110) cc_final: 0.6600 (ttt-90)
REVERT: A  187 LEU cc_start: 0.8102 (mm) cc_final: 0.7617 (mm)
REVERT: B   78 GLU cc_start: 0.7794 (mm-30) cc_final: 0.6982 (mp0)
REVERT: B   97 ILE cc_start: 0.8563 (mt) cc_final: 0.8294 (tt)
REVERT: B  120 MET cc_start: 0.8535 (ttm) cc_final: 0.8036 (ttm)
REVERT: B  146 TYR cc_start: 0.8600 (t80) cc_final: 0.8335 (t80)
REVERT: B  178 CYS cc_start: 0.8812 (t) cc_final: 0.8608 (t)
REVERT: B  213 LEU cc_start: 0.8547 (pp) cc_final: 0.8235 (mt)
REVERT: B  242 ASN cc_start: 0.6751 (m-40) cc_final: 0.6486 (t0)
REVERT: B  365 MET cc_start: 0.8439 (mmt) cc_final: 0.7668 (mmm)
REVERT: B  501 GLN cc_start: 0.8024 (tt0) cc_final: 0.7249 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1374
  time to fit residues: 20.2886
Evaluate side-chains
  105 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 5 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   chunk 24 optimal weight:    9.9990
   chunk 30 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 13 optimal weight:   10.0000
   chunk 16 optimal weight:    0.0870
   chunk 1 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.3562

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

Flipped N/Q/H residues before XYZ refinement:
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 ASN ** 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 = 0.3300 r_free = 0.3300 target = 0.099986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.082893 restraints weight = 8636.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.085675 restraints weight = 4406.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.087548 restraints weight = 2797.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.5302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4021  Z= 0.197
  Angle     :  0.603   6.032   5490  Z= 0.296
  Chirality :  0.043   0.166    664
  Planarity :  0.004   0.032    658
  Dihedral  :  4.420  17.763    533
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.38), residues: 500
  helix:  1.84 (0.27), residues: 369
  sheet:  None (None), residues: 0
  loop : -0.57 (0.54), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 477 
 HIS   0.005   0.001   HIS B 319 
 PHE   0.021   0.002   PHE B 451 
 TYR   0.016   0.001   TYR B 103 
 ARG   0.004   0.001   ARG B 427 

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 GLU cc_start: 0.8445 (mp0) cc_final: 0.8235 (mp0)
REVERT: A  182 ARG cc_start: 0.7893 (mtm110) cc_final: 0.6698 (ttt-90)
REVERT: A  187 LEU cc_start: 0.8240 (mm) cc_final: 0.7762 (mm)
REVERT: B   78 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7479 (mp0)
REVERT: B   97 ILE cc_start: 0.8617 (mt) cc_final: 0.8292 (tt)
REVERT: B  120 MET cc_start: 0.8415 (ttm) cc_final: 0.8134 (ttm)
REVERT: B  146 TYR cc_start: 0.8553 (t80) cc_final: 0.8228 (t80)
REVERT: B  178 CYS cc_start: 0.8860 (t) cc_final: 0.8657 (t)
REVERT: B  213 LEU cc_start: 0.8570 (pp) cc_final: 0.8222 (mt)
REVERT: B  218 GLN cc_start: 0.8475 (tp40) cc_final: 0.8225 (tp40)
REVERT: B  300 LEU cc_start: 0.8901 (mt) cc_final: 0.8695 (mt)
REVERT: B  305 MET cc_start: 0.8433 (mtp) cc_final: 0.8219 (mtp)
REVERT: B  365 MET cc_start: 0.8419 (mmt) cc_final: 0.7661 (mmm)
REVERT: B  501 GLN cc_start: 0.7959 (tt0) cc_final: 0.7262 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1436
  time to fit residues: 22.3982
Evaluate side-chains
  102 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 12 optimal weight:    0.8980
   chunk 33 optimal weight:    7.9990
   chunk 37 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 46 optimal weight:    0.0010
   chunk 43 optimal weight:    0.8980
   chunk 34 optimal weight:    6.9990
   overall best weight:    0.7188

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

Flipped N/Q/H residues before XYZ refinement:
** B  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 242 ASN
** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.101683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.084875 restraints weight = 8577.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.087634 restraints weight = 4317.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.089671 restraints weight = 2698.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.5529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   4021  Z= 0.189
  Angle     :  0.617   9.263   5490  Z= 0.300
  Chirality :  0.042   0.161    664
  Planarity :  0.004   0.033    658
  Dihedral  :  4.374  17.466    533
  Min Nonbonded Distance : 2.660

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.38), residues: 500
  helix:  1.79 (0.27), residues: 369
  sheet:  None (None), residues: 0
  loop : -0.56 (0.54), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 477 
 HIS   0.004   0.001   HIS B 319 
 PHE   0.021   0.001   PHE B 451 
 TYR   0.020   0.001   TYR B 103 
 ARG   0.005   0.001   ARG B 427 

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
REVERT: A  168 GLU cc_start: 0.8404 (mp0) cc_final: 0.8179 (mp0)
REVERT: A  182 ARG cc_start: 0.7824 (mtm110) cc_final: 0.6646 (ttt-90)
REVERT: A  187 LEU cc_start: 0.8334 (mm) cc_final: 0.7885 (mm)
REVERT: B   78 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7570 (mp0)
REVERT: B  120 MET cc_start: 0.8556 (ttm) cc_final: 0.8263 (ttm)
REVERT: B  146 TYR cc_start: 0.8576 (t80) cc_final: 0.8231 (t80)
REVERT: B  173 LEU cc_start: 0.9032 (tp) cc_final: 0.8826 (tp)
REVERT: B  213 LEU cc_start: 0.8614 (pp) cc_final: 0.8235 (mt)
REVERT: B  218 GLN cc_start: 0.8519 (tp40) cc_final: 0.8265 (tp40)
REVERT: B  254 TYR cc_start: 0.7705 (m-80) cc_final: 0.7337 (m-80)
REVERT: B  305 MET cc_start: 0.8458 (mtp) cc_final: 0.8192 (mtp)
REVERT: B  365 MET cc_start: 0.8385 (mmt) cc_final: 0.7643 (mmm)
REVERT: B  501 GLN cc_start: 0.8007 (tt0) cc_final: 0.7248 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1395
  time to fit residues: 22.0400
Evaluate side-chains
  102 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 41 optimal weight:    0.5980
   chunk 46 optimal weight:    0.0370
   chunk 10 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 42 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9990
   chunk 48 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
** B  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 ASN ** 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 = 0.3350 r_free = 0.3350 target = 0.103044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.086402 restraints weight = 8731.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.089244 restraints weight = 4419.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.091281 restraints weight = 2747.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.5848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   4021  Z= 0.184
  Angle     :  0.619  10.450   5490  Z= 0.302
  Chirality :  0.043   0.161    664
  Planarity :  0.004   0.031    658
  Dihedral  :  4.312  17.392    533
  Min Nonbonded Distance : 2.660

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.38), residues: 500
  helix:  1.72 (0.27), residues: 372
  sheet:  None (None), residues: 0
  loop : -0.59 (0.54), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 477 
 HIS   0.004   0.001   HIS B 319 
 PHE   0.024   0.001   PHE A 189 
 TYR   0.022   0.001   TYR B 103 
 ARG   0.004   0.001   ARG B 427 

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 ARG cc_start: 0.7864 (mtm110) cc_final: 0.6904 (ttt-90)
REVERT: A  187 LEU cc_start: 0.8293 (mm) cc_final: 0.7838 (mm)
REVERT: B  120 MET cc_start: 0.8447 (ttm) cc_final: 0.8211 (ttm)
REVERT: B  146 TYR cc_start: 0.8511 (t80) cc_final: 0.8203 (t80)
REVERT: B  178 CYS cc_start: 0.8720 (t) cc_final: 0.8496 (t)
REVERT: B  213 LEU cc_start: 0.8651 (pp) cc_final: 0.8242 (mt)
REVERT: B  218 GLN cc_start: 0.8384 (tp40) cc_final: 0.8149 (tp40)
REVERT: B  254 TYR cc_start: 0.7718 (m-80) cc_final: 0.7322 (m-80)
REVERT: B  365 MET cc_start: 0.8349 (mmt) cc_final: 0.7706 (mmm)
REVERT: B  410 LEU cc_start: 0.8676 (mt) cc_final: 0.8425 (mp)
REVERT: B  477 TRP cc_start: 0.6274 (t60) cc_final: 0.5981 (t60)
REVERT: B  501 GLN cc_start: 0.7932 (tt0) cc_final: 0.7275 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1284
  time to fit residues: 20.2589
Evaluate side-chains
  104 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 35 optimal weight:    9.9990
   chunk 33 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 46 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
** B  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 ASN ** 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 = 0.3331 r_free = 0.3331 target = 0.101977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.085090 restraints weight = 8598.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.087979 restraints weight = 4382.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.089987 restraints weight = 2753.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.5910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   4021  Z= 0.189
  Angle     :  0.629   7.678   5490  Z= 0.304
  Chirality :  0.043   0.163    664
  Planarity :  0.004   0.032    658
  Dihedral  :  4.365  17.496    533
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.38), residues: 500
  helix:  1.72 (0.27), residues: 371
  sheet:  None (None), residues: 0
  loop : -0.60 (0.54), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 477 
 HIS   0.004   0.001   HIS B 319 
 PHE   0.022   0.001   PHE A 189 
 TYR   0.020   0.001   TYR B 103 
 ARG   0.004   0.001   ARG B 427 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1349.14 seconds
wall clock time: 24 minutes 18.73 seconds (1458.73 seconds total)