Starting phenix.real_space_refine
on Wed Jun  4 14:05:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qcx_18336/06_2025/8qcx_18336.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qcx_18336/06_2025/8qcx_18336.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qcx_18336/06_2025/8qcx_18336.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qcx_18336/06_2025/8qcx_18336.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qcx_18336/06_2025/8qcx_18336.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qcx_18336/06_2025/8qcx_18336.cif"
  }
  resolution = 3.1
  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=   0.004 sd=   0.194
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      19      5.16       5
     C    2182      2.51       5
     N     521      2.21       5
     O     561      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 3283
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3283
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 422, 3283
          Classifications: {'peptide': 422}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 406}
          Chain breaks: 1
  Time building chain proxies: 2.49, per 1000 atoms: 0.76
  Number of scatterers: 3283
  At special positions: 0
  Unit cell: (84.804, 56.154, 65.322, 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      19     16.00
     O     561      8.00
     N     521      7.00
     C    2182      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: 0.74
  Conformation dependent library (CDL) restraints added in 447.7 milliseconds
  

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  772

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 0 sheets defined
      92.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 82 through 104
      removed outlier: 4.291A  pdb=" N   ALA A  86 " --> pdb=" O   ARG A  82 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ILE A 103 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 117
      removed outlier: 4.113A  pdb=" N   HIS A 114 " --> pdb=" O   ASN A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 169
      removed outlier: 3.782A  pdb=" N   LEU A 126 " --> pdb=" O   ALA A 122 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   SER A 127 " --> pdb=" O   ILE A 123 " (cutoff:3.500A)
      removed outlier: 4.879A  pdb=" N   TYR A 130 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   MET A 131 " --> pdb=" O   SER A 127 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   TYR A 134 " --> pdb=" O   TYR A 130 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ILE A 135 " --> pdb=" O   MET A 131 " (cutoff:3.500A)
      Proline residue:  A 136  - end of helix
      removed outlier: 5.098A  pdb=" N   LEU A 139 " --> pdb=" O   ILE A 135 " (cutoff:3.500A)
      Proline residue:  A 140  - end of helix
      removed outlier: 7.639A  pdb=" N   LEU A 150 " --> pdb=" O   GLU A 146 " (cutoff:3.500A)
      removed outlier: 9.190A  pdb=" N   ARG A 151 " --> pdb=" O   LYS A 147 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   THR A 152 " --> pdb=" O   PHE A 148 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ILE A 153 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   LEU A 169 " --> pdb=" O   ALA A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 172
      No H-bonds generated for 'chain 'A' and resid 170 through 172'
    Processing helix  chain 'A' and resid 176 through 196
      removed outlier: 3.585A  pdb=" N   THR A 180 " --> pdb=" O   LEU A 176 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   VAL A 192 " --> pdb=" O   SER A 188 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   PHE A 193 " --> pdb=" O   VAL A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 206
      removed outlier: 3.650A  pdb=" N   ILE A 201 " --> pdb=" O   MET A 197 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   ALA A 202 " --> pdb=" O   PRO A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 209
      No H-bonds generated for 'chain 'A' and resid 207 through 209'
    Processing helix  chain 'A' and resid 210 through 232
      removed outlier: 3.626A  pdb=" N   ILE A 226 " --> pdb=" O   ASN A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 237
    Processing helix  chain 'A' and resid 242 through 271
      removed outlier: 3.807A  pdb=" N   TYR A 248 " --> pdb=" O   ASP A 244 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   HIS A 249 " --> pdb=" O   GLU A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 291
    Processing helix  chain 'A' and resid 296 through 307
      removed outlier: 3.614A  pdb=" N   ARG A 303 " --> pdb=" O   GLY A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 330
    Processing helix  chain 'A' and resid 330 through 339
      removed outlier: 3.552A  pdb=" N   HIS A 338 " --> pdb=" O   MET A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 372
      removed outlier: 3.704A  pdb=" N   VAL A 362 " --> pdb=" O   MET A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 396
    Processing helix  chain 'A' and resid 397 through 399
      No H-bonds generated for 'chain 'A' and resid 397 through 399'
    Processing helix  chain 'A' and resid 400 through 430
      removed outlier: 3.831A  pdb=" N   VAL A 404 " --> pdb=" O   HIS A 400 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LEU A 419 " --> pdb=" O   MET A 415 " (cutoff:3.500A)
      Proline residue:  A 420  - end of helix
    Processing helix  chain 'A' and resid 434 through 465
    Processing helix  chain 'A' and resid 465 through 486
      removed outlier: 3.703A  pdb=" N   GLY A 469 " --> pdb=" O   GLY A 465 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU A 473 " --> pdb=" O   GLY A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 502

    272 hydrogen bonds defined for protein.
    816 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: 0.95

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 984
        1.34 -     1.46: 811
        1.46 -     1.58: 1539
        1.58 -     1.69: 0
        1.69 -     1.81: 31
  Bond restraints: 3365
  Sorted by residual:
  bond pdb=" N   LYS A 273 "
       pdb=" CA  LYS A 273 "
    ideal  model  delta    sigma   weight residual
    1.452  1.495 -0.042 1.22e-02 6.72e+03 1.21e+01
  bond pdb=" N   VAL A 271 "
       pdb=" CA  VAL A 271 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.25e-02 6.40e+03 9.67e+00
  bond pdb=" N   ASN A 307 "
       pdb=" CA  ASN A 307 "
    ideal  model  delta    sigma   weight residual
    1.461  1.492 -0.030 1.30e-02 5.92e+03 5.43e+00
  bond pdb=" N   SER A 127 "
       pdb=" CA  SER A 127 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.030 1.32e-02 5.74e+03 5.29e+00
  bond pdb=" N   GLN A 284 "
       pdb=" CA  GLN A 284 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.026 1.23e-02 6.61e+03 4.40e+00
  ... (remaining 3360 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 4450
        1.21 -     2.42: 88
        2.42 -     3.64: 24
        3.64 -     4.85: 17
        4.85 -     6.06: 3
  Bond angle restraints: 4582
  Sorted by residual:
  angle pdb=" CA  LYS A 273 "
        pdb=" C   LYS A 273 "
        pdb=" O   LYS A 273 "
      ideal   model   delta    sigma   weight residual
     121.88  117.31    4.57 1.30e+00 5.92e-01 1.24e+01
  angle pdb=" N   GLN A 284 "
        pdb=" CA  GLN A 284 "
        pdb=" C   GLN A 284 "
      ideal   model   delta    sigma   weight residual
     111.36  107.61    3.75 1.09e+00 8.42e-01 1.18e+01
  angle pdb=" CA  PRO A 198 "
        pdb=" N   PRO A 198 "
        pdb=" CD  PRO A 198 "
      ideal   model   delta    sigma   weight residual
     112.00  107.23    4.77 1.40e+00 5.10e-01 1.16e+01
  angle pdb=" N   SER A 127 "
        pdb=" CA  SER A 127 "
        pdb=" C   SER A 127 "
      ideal   model   delta    sigma   weight residual
     113.50  109.40    4.10 1.23e+00 6.61e-01 1.11e+01
  angle pdb=" CA  LYS A 273 "
        pdb=" C   LYS A 273 "
        pdb=" N   GLU A 274 "
      ideal   model   delta    sigma   weight residual
     115.63  119.70   -4.07 1.36e+00 5.41e-01 8.97e+00
  ... (remaining 4577 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.06: 1726
       16.06 -    32.12: 169
       32.12 -    48.18: 35
       48.18 -    64.24: 4
       64.24 -    80.30: 3
  Dihedral angle restraints: 1937
    sinusoidal: 726
      harmonic: 1211
  Sorted by residual:
  dihedral pdb=" CA  MET A 197 "
           pdb=" C   MET A 197 "
           pdb=" N   PRO A 198 "
           pdb=" CA  PRO A 198 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.42   19.58     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  TYR A  94 "
           pdb=" C   TYR A  94 "
           pdb=" N   SER A  95 "
           pdb=" CA  SER A  95 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.34   16.66     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CB  GLU A 245 "
           pdb=" CG  GLU A 245 "
           pdb=" CD  GLU A 245 "
           pdb=" OE1 GLU A 245 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -80.30   80.30     1      3.00e+01 1.11e-03 8.87e+00
  ... (remaining 1934 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 430
       0.046 -    0.092: 100
       0.092 -    0.138: 11
       0.138 -    0.184: 0
       0.184 -    0.230: 2
  Chirality restraints: 543
  Sorted by residual:
  chirality pdb=" CA  ASN A 307 "
            pdb=" N   ASN A 307 "
            pdb=" C   ASN A 307 "
            pdb=" CB  ASN A 307 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" CB  VAL A 271 "
            pdb=" CA  VAL A 271 "
            pdb=" CG1 VAL A 271 "
            pdb=" CG2 VAL A 271 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 9.51e-01
  chirality pdb=" CA  PHE A 272 "
            pdb=" N   PHE A 272 "
            pdb=" C   PHE A 272 "
            pdb=" CB  PHE A 272 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.62   -0.11 2.00e-01 2.50e+01 3.23e-01
  ... (remaining 540 not shown)

  Planarity restraints: 555
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 197 "   -0.082 5.00e-02 4.00e+02   1.22e-01 2.39e+01
        pdb=" N   PRO A 198 "    0.211 5.00e-02 4.00e+02
        pdb=" CA  PRO A 198 "   -0.063 5.00e-02 4.00e+02
        pdb=" CD  PRO A 198 "   -0.066 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 431 "    0.022 5.00e-02 4.00e+02   3.37e-02 1.82e+00
        pdb=" N   PRO A 432 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 432 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 432 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 233 "   -0.021 5.00e-02 4.00e+02   3.17e-02 1.61e+00
        pdb=" N   PRO A 234 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO A 234 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 234 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 552 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 860
        2.80 -     3.33: 3407
        3.33 -     3.85: 5408
        3.85 -     4.37: 6569
        4.37 -     4.90: 11128
  Nonbonded interactions: 27372
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 391 "
            pdb=" OG1 THR A 395 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OE1 GLU A 342 "
            pdb=" ND2 ASN A 345 "
     model   vdw
     2.310 3.120
  nonbonded pdb=" NE1 TRP A 166 "
            pdb=" OG1 THR A 262 "
     model   vdw
     2.359 3.120
  nonbonded pdb=" OG  SER A  99 "
            pdb=" OD1 ASN A 222 "
     model   vdw
     2.361 3.040
  nonbonded pdb=" OD2 ASP A 490 "
            pdb=" NH2 ARG A 492 "
     model   vdw
     2.386 3.120
  ... (remaining 27367 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.880
  Find NCS groups from input model:        0.020
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
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   0.042   3365  Z= 0.151
  Angle     :  0.505   6.060   4582  Z= 0.287
  Chirality :  0.038   0.230    543
  Planarity :  0.006   0.122    555
  Dihedral  : 13.428  80.295   1165
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.06 (0.41), residues: 418
  helix:  0.99 (0.27), residues: 357
  sheet:  None (None), residues: 0
  loop : -0.54 (0.90), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 102 
 HIS   0.001   0.000   HIS A 175 
 PHE   0.007   0.001   PHE A 425 
 TYR   0.011   0.001   TYR A  94 
 ARG   0.002   0.000   ARG A 303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24594 (  272)
  hydrogen bonds       : angle       7.45008 (  816)
  covalent geometry    : bond        0.00264 ( 3365)
  covalent geometry    : angle       0.50487 ( 4582)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.333 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.1302
  time to fit residues: 8.3492
Evaluate side-chains
  43 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 21 optimal weight:   20.0000
   chunk 32 optimal weight:    2.9990
   chunk 12 optimal weight:    0.1980
   chunk 20 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  98 ASN
A 104 GLN
A 332 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.143415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.114297 restraints weight = 4051.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 2.16
r_work: 0.2931 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2792 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.1850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3365  Z= 0.149
  Angle     :  0.563   7.202   4582  Z= 0.305
  Chirality :  0.039   0.142    543
  Planarity :  0.006   0.082    555
  Dihedral  :  3.898  17.504    452
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  7.37 %
    Favored  : 91.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.24 (0.41), residues: 418
  helix:  1.84 (0.27), residues: 359
  sheet:  None (None), residues: 0
  loop : -0.66 (0.91), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 102 
 HIS   0.002   0.000   HIS A 338 
 PHE   0.012   0.001   PHE A 472 
 TYR   0.025   0.002   TYR A  94 
 ARG   0.003   0.000   ARG A 493 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05788 (  272)
  hydrogen bonds       : angle       4.68474 (  816)
  covalent geometry    : bond        0.00297 ( 3365)
  covalent geometry    : angle       0.56281 ( 4582)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A  367 TRP cc_start: 0.8340 (t-100) cc_final: 0.8108 (t-100)
REVERT: A  411 MET cc_start: 0.8460 (ttp) cc_final: 0.8242 (ttp)
REVERT: A  428 GLU cc_start: 0.8577 (tp30) cc_final: 0.8249 (tp30)
  outliers start: 4
  outliers final: 1
  residues processed: 55
  average time/residue: 0.1109
  time to fit residues: 8.1138
Evaluate side-chains
  47 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 46
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  363 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 37 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 20 optimal weight:    0.2980
   chunk 10 optimal weight:    0.0870
   chunk 36 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.5958

-------------------------------------------------------------------------------
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 = 0.3724 r_free = 0.3724 target = 0.144836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.114984 restraints weight = 3972.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3087 rms_B_bonded: 2.14
r_work: 0.2960 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2819 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.2295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3365  Z= 0.127
  Angle     :  0.534   7.159   4582  Z= 0.281
  Chirality :  0.038   0.148    543
  Planarity :  0.005   0.069    555
  Dihedral  :  3.907  17.967    452
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  9.92 %
    Favored  : 88.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.52 (0.41), residues: 418
  helix:  2.05 (0.27), residues: 359
  sheet:  None (None), residues: 0
  loop : -0.66 (0.92), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 102 
 HIS   0.002   0.000   HIS A 338 
 PHE   0.013   0.001   PHE A 220 
 TYR   0.026   0.001   TYR A  94 
 ARG   0.001   0.000   ARG A 303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04709 (  272)
  hydrogen bonds       : angle       4.32380 (  816)
  covalent geometry    : bond        0.00258 ( 3365)
  covalent geometry    : angle       0.53439 ( 4582)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  197 MET cc_start: 0.8744 (ptt) cc_final: 0.8479 (ptt)
REVERT: A  251 SER cc_start: 0.8318 (t) cc_final: 0.7727 (p)
REVERT: A  263 LEU cc_start: 0.8667 (tp) cc_final: 0.8258 (mt)
REVERT: A  367 TRP cc_start: 0.8321 (t-100) cc_final: 0.8116 (t-100)
REVERT: A  384 MET cc_start: 0.8887 (mmm) cc_final: 0.8604 (mmm)
REVERT: A  428 GLU cc_start: 0.8519 (tp30) cc_final: 0.8102 (tp30)
  outliers start: 5
  outliers final: 2
  residues processed: 55
  average time/residue: 0.1129
  time to fit residues: 8.2760
Evaluate side-chains
  51 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 49
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 MET
Chi-restraints excluded: chain A residue  475 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 21 optimal weight:    7.9990
   chunk 41 optimal weight:    6.9990
   chunk 1 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 13 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0040
   chunk 24 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    1.5396

-------------------------------------------------------------------------------
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 = 0.3712 r_free = 0.3712 target = 0.143648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.113530 restraints weight = 4069.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 2.16
r_work: 0.2891 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2749 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.2395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3365  Z= 0.175
  Angle     :  0.578   7.478   4582  Z= 0.302
  Chirality :  0.040   0.163    543
  Planarity :  0.005   0.062    555
  Dihedral  :  4.059  17.960    452
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 10.48 %
    Favored  : 87.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.44 (0.41), residues: 418
  helix:  1.99 (0.27), residues: 357
  sheet:  None (None), residues: 0
  loop : -0.58 (0.87), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  85 
 HIS   0.003   0.001   HIS A 338 
 PHE   0.015   0.002   PHE A 413 
 TYR   0.028   0.002   TYR A  94 
 ARG   0.001   0.000   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04770 (  272)
  hydrogen bonds       : angle       4.31847 (  816)
  covalent geometry    : bond        0.00418 ( 3365)
  covalent geometry    : angle       0.57833 ( 4582)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A  272 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.6941 (t80)
  outliers start: 8
  outliers final: 5
  residues processed: 54
  average time/residue: 0.1066
  time to fit residues: 7.7288
Evaluate side-chains
  54 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 MET
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  475 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 41 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 16 optimal weight:    4.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3700 r_free = 0.3700 target = 0.143089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.113157 restraints weight = 4037.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 2.14
r_work: 0.2918 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2777 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3365  Z= 0.133
  Angle     :  0.541   6.572   4582  Z= 0.283
  Chirality :  0.038   0.153    543
  Planarity :  0.005   0.062    555
  Dihedral  :  4.031  17.812    452
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.88 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.61 (0.41), residues: 418
  helix:  2.08 (0.27), residues: 360
  sheet:  None (None), residues: 0
  loop : -0.50 (0.90), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  85 
 HIS   0.002   0.000   HIS A 338 
 PHE   0.015   0.001   PHE A 220 
 TYR   0.024   0.001   TYR A  94 
 ARG   0.001   0.000   ARG A 493 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04396 (  272)
  hydrogen bonds       : angle       4.20545 (  816)
  covalent geometry    : bond        0.00298 ( 3365)
  covalent geometry    : angle       0.54108 ( 4582)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A  263 LEU cc_start: 0.8530 (tp) cc_final: 0.8171 (mt)
REVERT: A  272 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.6931 (t80)
REVERT: A  384 MET cc_start: 0.8916 (mmm) cc_final: 0.8673 (mmm)
  outliers start: 7
  outliers final: 4
  residues processed: 54
  average time/residue: 0.1096
  time to fit residues: 7.9407
Evaluate side-chains
  54 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 MET
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  475 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.3691 r_free = 0.3691 target = 0.142366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.112321 restraints weight = 4161.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 2.16
r_work: 0.2905 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2766 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3365  Z= 0.144
  Angle     :  0.547   6.711   4582  Z= 0.285
  Chirality :  0.038   0.158    543
  Planarity :  0.005   0.058    555
  Dihedral  :  4.044  17.678    452
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.16 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.68 (0.41), residues: 418
  helix:  2.10 (0.27), residues: 366
  sheet:  None (None), residues: 0
  loop : -0.56 (0.95), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 367 
 HIS   0.002   0.001   HIS A 338 
 PHE   0.015   0.002   PHE A 413 
 TYR   0.025   0.001   TYR A  94 
 ARG   0.001   0.000   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04367 (  272)
  hydrogen bonds       : angle       4.17070 (  816)
  covalent geometry    : bond        0.00333 ( 3365)
  covalent geometry    : angle       0.54706 ( 4582)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.367 
Fit side-chains
REVERT: A  272 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.6905 (t80)
REVERT: A  384 MET cc_start: 0.8911 (mmm) cc_final: 0.8666 (mmm)
  outliers start: 7
  outliers final: 5
  residues processed: 52
  average time/residue: 0.1219
  time to fit residues: 8.5966
Evaluate side-chains
  54 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 MET
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  475 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 13 optimal weight:    8.9990
   chunk 4 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3706 r_free = 0.3706 target = 0.143568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.113575 restraints weight = 4075.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 2.15
r_work: 0.2954 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2813 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3365  Z= 0.132
  Angle     :  0.535   6.540   4582  Z= 0.278
  Chirality :  0.038   0.155    543
  Planarity :  0.005   0.056    555
  Dihedral  :  4.029  17.395    452
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 15.30 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.82 (0.41), residues: 418
  helix:  2.19 (0.27), residues: 366
  sheet:  None (None), residues: 0
  loop : -0.48 (0.96), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 337 
 HIS   0.002   0.000   HIS A 338 
 PHE   0.016   0.001   PHE A 220 
 TYR   0.025   0.001   TYR A  94 
 ARG   0.001   0.000   ARG A 492 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04208 (  272)
  hydrogen bonds       : angle       4.11900 (  816)
  covalent geometry    : bond        0.00298 ( 3365)
  covalent geometry    : angle       0.53455 ( 4582)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.355 
Fit side-chains
REVERT: A  272 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.6943 (t80)
REVERT: A  384 MET cc_start: 0.8912 (mmm) cc_final: 0.8677 (mmm)
REVERT: A  495 LYS cc_start: 0.7065 (mttp) cc_final: 0.6849 (mtmt)
  outliers start: 6
  outliers final: 3
  residues processed: 54
  average time/residue: 0.1101
  time to fit residues: 7.9624
Evaluate side-chains
  53 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 49
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 MET
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  475 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 18 optimal weight:    0.4980
   chunk 29 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 20 optimal weight:    9.9990
   chunk 25 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 13 optimal weight:   10.0000
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.139174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.109465 restraints weight = 4025.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 2.16
r_work: 0.2941 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2798 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.2815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3365  Z= 0.126
  Angle     :  0.527   6.507   4582  Z= 0.276
  Chirality :  0.038   0.154    543
  Planarity :  0.005   0.055    555
  Dihedral  :  4.015  17.319    452
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.73 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.91 (0.41), residues: 418
  helix:  2.25 (0.27), residues: 366
  sheet:  None (None), residues: 0
  loop : -0.43 (0.96), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 337 
 HIS   0.001   0.000   HIS A 338 
 PHE   0.015   0.001   PHE A 220 
 TYR   0.025   0.001   TYR A  94 
 ARG   0.001   0.000   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04110 (  272)
  hydrogen bonds       : angle       4.08661 (  816)
  covalent geometry    : bond        0.00279 ( 3365)
  covalent geometry    : angle       0.52742 ( 4582)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A  272 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.6885 (t80)
REVERT: A  384 MET cc_start: 0.8926 (mmm) cc_final: 0.8698 (mmm)
REVERT: A  495 LYS cc_start: 0.7059 (mttp) cc_final: 0.6844 (mtmt)
  outliers start: 7
  outliers final: 4
  residues processed: 55
  average time/residue: 0.1266
  time to fit residues: 9.3740
Evaluate side-chains
  54 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 MET
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  475 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 9 optimal weight:    0.4980
   chunk 3 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 28 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3713 r_free = 0.3713 target = 0.144322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.114695 restraints weight = 4086.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 2.16
r_work: 0.2936 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2795 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.2880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3365  Z= 0.127
  Angle     :  0.533   6.771   4582  Z= 0.277
  Chirality :  0.038   0.156    543
  Planarity :  0.005   0.054    555
  Dihedral  :  4.010  17.321    452
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 15.86 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.94 (0.41), residues: 418
  helix:  2.27 (0.27), residues: 367
  sheet:  None (None), residues: 0
  loop : -0.43 (0.98), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 337 
 HIS   0.001   0.000   HIS A 338 
 PHE   0.015   0.001   PHE A 220 
 TYR   0.025   0.001   TYR A  94 
 ARG   0.001   0.000   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04089 (  272)
  hydrogen bonds       : angle       4.07988 (  816)
  covalent geometry    : bond        0.00285 ( 3365)
  covalent geometry    : angle       0.53272 ( 4582)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A  272 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.6872 (t80)
REVERT: A  384 MET cc_start: 0.8913 (mmm) cc_final: 0.8683 (mmm)
REVERT: A  495 LYS cc_start: 0.7066 (mttp) cc_final: 0.6853 (mtmt)
  outliers start: 6
  outliers final: 4
  residues processed: 54
  average time/residue: 0.1058
  time to fit residues: 7.7248
Evaluate side-chains
  54 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 MET
Chi-restraints excluded: chain A residue  216 SER
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  475 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0000
   chunk 38 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.7386

-------------------------------------------------------------------------------
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 = 0.3750 r_free = 0.3750 target = 0.147217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.117939 restraints weight = 3995.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3075 rms_B_bonded: 2.13
r_work: 0.2947 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2805 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.2904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3365  Z= 0.124
  Angle     :  0.525   6.622   4582  Z= 0.273
  Chirality :  0.038   0.154    543
  Planarity :  0.004   0.053    555
  Dihedral  :  3.993  17.223    452
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 16.15 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.99 (0.42), residues: 418
  helix:  2.30 (0.27), residues: 367
  sheet:  None (None), residues: 0
  loop : -0.38 (0.99), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 337 
 HIS   0.002   0.000   HIS A 338 
 PHE   0.016   0.001   PHE A 220 
 TYR   0.025   0.001   TYR A  94 
 ARG   0.001   0.000   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04029 (  272)
  hydrogen bonds       : angle       4.07417 (  816)
  covalent geometry    : bond        0.00275 ( 3365)
  covalent geometry    : angle       0.52472 ( 4582)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.377 
Fit side-chains
REVERT: A  272 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.6886 (t80)
REVERT: A  298 LEU cc_start: 0.6349 (OUTLIER) cc_final: 0.5950 (tp)
REVERT: A  384 MET cc_start: 0.8892 (mmm) cc_final: 0.8667 (mmm)
REVERT: A  495 LYS cc_start: 0.7099 (mttp) cc_final: 0.6895 (mtmt)
  outliers start: 5
  outliers final: 3
  residues processed: 54
  average time/residue: 0.1010
  time to fit residues: 7.3998
Evaluate side-chains
  55 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 MET
Chi-restraints excluded: chain A residue  216 SER
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  475 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 16 optimal weight:    0.4980
   chunk 4 optimal weight:    0.6980
   chunk 20 optimal weight:    0.4980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3690 r_free = 0.3690 target = 0.143056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.113006 restraints weight = 4050.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 2.18
r_work: 0.2954 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2813 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.2994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3365  Z= 0.118
  Angle     :  0.518   6.597   4582  Z= 0.269
  Chirality :  0.037   0.153    543
  Planarity :  0.004   0.053    555
  Dihedral  :  3.964  17.154    452
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 16.15 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.06 (0.42), residues: 418
  helix:  2.34 (0.27), residues: 367
  sheet:  None (None), residues: 0
  loop : -0.39 (0.99), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 337 
 HIS   0.001   0.000   HIS A 338 
 PHE   0.015   0.001   PHE A 220 
 TYR   0.025   0.001   TYR A  94 
 ARG   0.001   0.000   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03941 (  272)
  hydrogen bonds       : angle       4.03447 (  816)
  covalent geometry    : bond        0.00256 ( 3365)
  covalent geometry    : angle       0.51771 ( 4582)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1852.32 seconds
wall clock time: 32 minutes 38.53 seconds (1958.53 seconds total)