Starting phenix.real_space_refine
on Wed Mar  5 17:50:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ex5_28651/03_2025/8ex5_28651.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ex5_28651/03_2025/8ex5_28651.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.47
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ex5_28651/03_2025/8ex5_28651.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ex5_28651/03_2025/8ex5_28651.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ex5_28651/03_2025/8ex5_28651.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ex5_28651/03_2025/8ex5_28651.cif"
  }
  resolution = 3.47
  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=   0.001 sd=   0.018
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      17      5.16       5
     C    2090      2.51       5
     N     524      2.21       5
     O     546      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 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: 3177
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3177
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 414, 3177
          Classifications: {'peptide': 414}
          Link IDs: {'PTRANS': 12, 'TRANS': 401}
          Chain breaks: 2
  Time building chain proxies: 3.20, per 1000 atoms: 1.01
  Number of scatterers: 3177
  At special positions: 0
  Unit cell: (70.092, 68.794, 79.827, 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      17     16.00
     O     546      8.00
     N     524      7.00
     C    2090      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: 0.76
  Conformation dependent library (CDL) restraints added in 358.5 milliseconds
  

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  756

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 0 sheets defined
      90.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 99 through 134
      removed outlier: 3.628A  pdb=" N   ALA A 103 " --> pdb=" O   GLU A  99 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   VAL A 122 " --> pdb=" O   ASP A 118 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   ALA A 123 " --> pdb=" O   ARG A 119 " (cutoff:3.500A)
      removed outlier: 5.889A  pdb=" N   LEU A 127 " --> pdb=" O   ALA A 123 " (cutoff:3.500A)
      removed outlier: 5.886A  pdb=" N   ASP A 128 " --> pdb=" O   GLY A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 165
      removed outlier: 3.726A  pdb=" N   ALA A 140 " --> pdb=" O   LYS A 136 " (cutoff:3.500A)
      Proline residue:  A 156  - end of helix
      removed outlier: 3.792A  pdb=" N   ARG A 164 " --> pdb=" O   TYR A 160 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   PHE A 165 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 186
    Processing helix  chain 'A' and resid 193 through 222
      Proline residue:  A 215  - end of helix
      removed outlier: 3.820A  pdb=" N   PHE A 222 " --> pdb=" O   ILE A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 256
      removed outlier: 4.259A  pdb=" N   ILE A 238 " --> pdb=" O   PHE A 234 " (cutoff:3.500A)
      Proline residue:  A 239  - end of helix
    Processing helix  chain 'A' and resid 265 through 281
      removed outlier: 4.435A  pdb=" N   LEU A 269 " --> pdb=" O   VAL A 265 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   VAL A 281 " --> pdb=" O   ILE A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 312
    Processing helix  chain 'A' and resid 312 through 348
      Proline residue:  A 337  - end of helix
    Processing helix  chain 'A' and resid 361 through 392
    Processing helix  chain 'A' and resid 394 through 417
      removed outlier: 3.635A  pdb=" N   LEU A 398 " --> pdb=" O   ARG A 394 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   CYS A 400 " --> pdb=" O   ASP A 396 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   GLY A 403 " --> pdb=" O   VAL A 399 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   PHE A 415 " --> pdb=" O   ILE A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 438
      removed outlier: 4.295A  pdb=" N   LEU A 435 " --> pdb=" O   VAL A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 450
      removed outlier: 3.583A  pdb=" N   ALA A 444 " --> pdb=" O   TRP A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 454
      No H-bonds generated for 'chain 'A' and resid 452 through 454'
    Processing helix  chain 'A' and resid 455 through 470
    Processing helix  chain 'A' and resid 474 through 488
    Processing helix  chain 'A' and resid 493 through 538
      removed outlier: 4.238A  pdb=" N   CYS A 508 " --> pdb=" O   ALA A 504 " (cutoff:3.500A)
      Proline residue:  A 509  - end of helix
      removed outlier: 5.161A  pdb=" N   VAL A 527 " --> pdb=" O   ALA A 523 " (cutoff:3.500A)
      removed outlier: 5.312A  pdb=" N   SER A 528 " --> pdb=" O   LEU A 524 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLN A 536 " --> pdb=" O   ARG A 532 " (cutoff:3.500A)

    274 hydrogen bonds defined for protein.
    822 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: 0.86

  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: 968
        1.34 -     1.46: 631
        1.46 -     1.58: 1626
        1.58 -     1.69: 0
        1.69 -     1.81: 26
  Bond restraints: 3251
  Sorted by residual:
  bond pdb=" C   CYS A 508 "
       pdb=" N   PRO A 509 "
    ideal  model  delta    sigma   weight residual
    1.333  1.356 -0.023 1.44e-02 4.82e+03 2.55e+00
  bond pdb=" C   SER A 266 "
       pdb=" N   PRO A 267 "
    ideal  model  delta    sigma   weight residual
    1.334  1.368 -0.034 2.34e-02 1.83e+03 2.14e+00
  bond pdb=" N   LYS A 224 "
       pdb=" CA  LYS A 224 "
    ideal  model  delta    sigma   weight residual
    1.457  1.476 -0.018 1.29e-02 6.01e+03 2.00e+00
  bond pdb=" CG  LEU A 171 "
       pdb=" CD2 LEU A 171 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.25e+00
  bond pdb=" CB  ILE A 107 "
       pdb=" CG2 ILE A 107 "
    ideal  model  delta    sigma   weight residual
    1.521  1.488  0.033 3.30e-02 9.18e+02 9.99e-01
  ... (remaining 3246 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 4132
        1.27 -     2.55: 227
        2.55 -     3.82: 35
        3.82 -     5.10: 16
        5.10 -     6.37: 6
  Bond angle restraints: 4416
  Sorted by residual:
  angle pdb=" N   ILE A 188 "
        pdb=" CA  ILE A 188 "
        pdb=" C   ILE A 188 "
      ideal   model   delta    sigma   weight residual
     108.95  112.36   -3.41 9.80e-01 1.04e+00 1.21e+01
  angle pdb=" N   VAL A 431 "
        pdb=" CA  VAL A 431 "
        pdb=" C   VAL A 431 "
      ideal   model   delta    sigma   weight residual
     112.80  108.88    3.92 1.15e+00 7.56e-01 1.16e+01
  angle pdb=" C   PHE A 177 "
        pdb=" N   TRP A 178 "
        pdb=" CA  TRP A 178 "
      ideal   model   delta    sigma   weight residual
     120.31  115.32    4.99 1.52e+00 4.33e-01 1.08e+01
  angle pdb=" N   TRP A 178 "
        pdb=" CA  TRP A 178 "
        pdb=" CB  TRP A 178 "
      ideal   model   delta    sigma   weight residual
     110.28  115.08   -4.80 1.55e+00 4.16e-01 9.58e+00
  angle pdb=" CA  TRP A 178 "
        pdb=" CB  TRP A 178 "
        pdb=" CG  TRP A 178 "
      ideal   model   delta    sigma   weight residual
     113.60  119.39   -5.79 1.90e+00 2.77e-01 9.28e+00
  ... (remaining 4411 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.94: 1714
       15.94 -    31.88: 125
       31.88 -    47.82: 26
       47.82 -    63.75: 6
       63.75 -    79.69: 1
  Dihedral angle restraints: 1872
    sinusoidal: 692
      harmonic: 1180
  Sorted by residual:
  dihedral pdb=" CA  THR A 223 "
           pdb=" C   THR A 223 "
           pdb=" N   LYS A 224 "
           pdb=" CA  LYS A 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.37  -23.63     0      5.00e+00 4.00e-02 2.23e+01
  dihedral pdb=" CA  GLU A 207 "
           pdb=" C   GLU A 207 "
           pdb=" N   ALA A 208 "
           pdb=" CA  ALA A 208 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.16   17.84     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CA  LEU A 221 "
           pdb=" C   LEU A 221 "
           pdb=" N   PHE A 222 "
           pdb=" CA  PHE A 222 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.50  -17.50     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 1869 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 313
       0.031 -    0.061: 146
       0.061 -    0.092: 39
       0.092 -    0.123: 18
       0.123 -    0.153: 5
  Chirality restraints: 521
  Sorted by residual:
  chirality pdb=" CA  GLU A 207 "
            pdb=" N   GLU A 207 "
            pdb=" C   GLU A 207 "
            pdb=" CB  GLU A 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.87e-01
  chirality pdb=" CA  PRO A 267 "
            pdb=" N   PRO A 267 "
            pdb=" C   PRO A 267 "
            pdb=" CB  PRO A 267 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.52e-01
  chirality pdb=" CA  SER A 475 "
            pdb=" N   SER A 475 "
            pdb=" C   SER A 475 "
            pdb=" CB  SER A 475 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.35e-01
  ... (remaining 518 not shown)

  Planarity restraints: 539
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 178 "    0.025 2.00e-02 2.50e+03   2.10e-02 1.10e+01
        pdb=" CG  TRP A 178 "   -0.058 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 178 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 178 "    0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 178 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 178 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 178 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 178 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 178 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 178 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 508 "   -0.033 5.00e-02 4.00e+02   5.08e-02 4.13e+00
        pdb=" N   PRO A 509 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 509 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 509 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 223 "   -0.007 2.00e-02 2.50e+03   1.45e-02 2.09e+00
        pdb=" C   THR A 223 "    0.025 2.00e-02 2.50e+03
        pdb=" O   THR A 223 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   LYS A 224 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 536 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 52
        2.69 -     3.24: 3428
        3.24 -     3.80: 5240
        3.80 -     4.35: 6680
        4.35 -     4.90: 11130
  Nonbonded interactions: 26530
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 186 "
            pdb=" O   LEU A 263 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" O   GLY A 206 "
            pdb=" OG  SER A 209 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" OD1 ASP A 118 "
            pdb=" OG  SER A 266 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   MET A 404 "
            pdb=" OG  SER A 407 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" NH1 ARG A 167 "
            pdb=" OG1 THR A 216 "
     model   vdw
     2.368 3.120
  ... (remaining 26525 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:             2.540
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.860
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6687
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      :  0.004   0.040   3251  Z= 0.287
  Angle     :  0.714   6.370   4416  Z= 0.423
  Chirality :  0.041   0.153    521
  Planarity :  0.005   0.051    539
  Dihedral  : 12.108  79.692   1116
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.42), residues: 408
  helix:  1.13 (0.27), residues: 353
  sheet:  None (None), residues: 0
  loop : -2.78 (0.82), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.003   TRP A 178 
 HIS   0.001   0.001   HIS A 260 
 PHE   0.023   0.002   PHE A 465 
 TYR   0.018   0.002   TYR A 426 
 ARG   0.005   0.001   ARG A 264 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A  182 THR cc_start: 0.7787 (m) cc_final: 0.6251 (t)
REVERT: A  447 LEU cc_start: 0.8555 (tt) cc_final: 0.8258 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.1304
  time to fit residues: 6.6652
Evaluate side-chains
  35 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0970
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
A 344 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.235576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.213842 restraints weight = 3653.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.4345 rms_B_bonded: 1.53
r_work: 0.4198 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.4198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6823
moved from start:          0.0767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3251  Z= 0.226
  Angle     :  0.599   6.231   4416  Z= 0.323
  Chirality :  0.042   0.154    521
  Planarity :  0.004   0.049    539
  Dihedral  :  4.961  20.893    444
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  6.87 %
    Favored  : 92.84 %
  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:  1.43 (0.41), residues: 408
  helix:  1.50 (0.27), residues: 353
  sheet:  None (None), residues: 0
  loop : -2.64 (0.77), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A 178 
 HIS   0.002   0.001   HIS A 468 
 PHE   0.014   0.002   PHE A 327 
 TYR   0.016   0.002   TYR A 426 
 ARG   0.004   0.000   ARG A 264 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 0.296 
Fit side-chains
REVERT: A  182 THR cc_start: 0.8040 (m) cc_final: 0.6331 (t)
REVERT: A  264 ARG cc_start: 0.4563 (mtp85) cc_final: 0.3547 (mtp-110)
REVERT: A  447 LEU cc_start: 0.8584 (tt) cc_final: 0.8307 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 41
  average time/residue: 0.1346
  time to fit residues: 7.0429
Evaluate side-chains
  40 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 5 optimal weight:    0.4980
   chunk 35 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0170
   chunk 31 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
A 344 GLN
A 535 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4566 r_free = 0.4566 target = 0.237373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.215429 restraints weight = 3654.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.4371 rms_B_bonded: 1.56
r_work: 0.4164 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.4164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6849
moved from start:          0.1102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3251  Z= 0.205
  Angle     :  0.561   6.242   4416  Z= 0.302
  Chirality :  0.041   0.140    521
  Planarity :  0.004   0.049    539
  Dihedral  :  4.770  21.188    444
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 10.15 %
    Favored  : 88.96 %
  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:  1.74 (0.41), residues: 408
  helix:  1.67 (0.27), residues: 356
  sheet:  None (None), residues: 0
  loop : -2.47 (0.81), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 178 
 HIS   0.002   0.001   HIS A 468 
 PHE   0.014   0.001   PHE A 327 
 TYR   0.014   0.002   TYR A 426 
 ARG   0.003   0.000   ARG A 264 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A  182 THR cc_start: 0.8056 (m) cc_final: 0.6319 (t)
REVERT: A  264 ARG cc_start: 0.4516 (mtp85) cc_final: 0.3358 (mtp-110)
REVERT: A  447 LEU cc_start: 0.8593 (tt) cc_final: 0.8315 (tp)
  outliers start: 3
  outliers final: 2
  residues processed: 41
  average time/residue: 0.1390
  time to fit residues: 7.3116
Evaluate side-chains
  40 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  178 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0670
   chunk 25 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
A 344 GLN
A 535 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4569 r_free = 0.4569 target = 0.237839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.215864 restraints weight = 3668.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.4376 rms_B_bonded: 1.54
r_work: 0.4173 rms_B_bonded: 4.65 restraints_weight: 0.5000
r_work (final): 0.4173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6837
moved from start:          0.1311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3251  Z= 0.202
  Angle     :  0.551   6.241   4416  Z= 0.296
  Chirality :  0.041   0.137    521
  Planarity :  0.004   0.050    539
  Dihedral  :  4.714  21.017    444
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 11.64 %
    Favored  : 87.46 %
  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:  1.98 (0.42), residues: 408
  helix:  1.81 (0.27), residues: 356
  sheet:  None (None), residues: 0
  loop : -2.23 (0.82), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 178 
 HIS   0.001   0.001   HIS A 468 
 PHE   0.030   0.002   PHE A 193 
 TYR   0.015   0.001   TYR A 426 
 ARG   0.003   0.000   ARG A 264 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.378 
Fit side-chains
REVERT: A  182 THR cc_start: 0.8067 (m) cc_final: 0.6356 (t)
REVERT: A  264 ARG cc_start: 0.4467 (mtp85) cc_final: 0.3221 (mtp-110)
REVERT: A  439 ASN cc_start: 0.7361 (p0) cc_final: 0.6627 (m-40)
REVERT: A  447 LEU cc_start: 0.8569 (tt) cc_final: 0.8302 (tp)
  outliers start: 3
  outliers final: 1
  residues processed: 41
  average time/residue: 0.1387
  time to fit residues: 7.3087
Evaluate side-chains
  38 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 37
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 31 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 344 GLN
A 535 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.235938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.213881 restraints weight = 3637.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.4359 rms_B_bonded: 1.52
r_work: 0.4160 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.4160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6871
moved from start:          0.1349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3251  Z= 0.233
  Angle     :  0.572   6.304   4416  Z= 0.306
  Chirality :  0.041   0.140    521
  Planarity :  0.004   0.050    539
  Dihedral  :  4.751  21.179    444
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 12.24 %
    Favored  : 86.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.42), residues: 408
  helix:  1.72 (0.27), residues: 358
  sheet:  None (None), residues: 0
  loop : -1.92 (0.85), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 178 
 HIS   0.002   0.001   HIS A 468 
 PHE   0.024   0.002   PHE A 193 
 TYR   0.016   0.002   TYR A 426 
 ARG   0.003   0.000   ARG A 264 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A  182 THR cc_start: 0.8083 (m) cc_final: 0.6426 (t)
REVERT: A  264 ARG cc_start: 0.4616 (mtp85) cc_final: 0.3217 (mtp-110)
REVERT: A  439 ASN cc_start: 0.7333 (p0) cc_final: 0.6765 (m-40)
REVERT: A  447 LEU cc_start: 0.8604 (tt) cc_final: 0.8341 (tp)
  outliers start: 3
  outliers final: 3
  residues processed: 41
  average time/residue: 0.1294
  time to fit residues: 7.0121
Evaluate side-chains
  41 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  178 TRP
Chi-restraints excluded: chain A residue  248 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 38 optimal weight:    0.0770
   chunk 1 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   chunk 6 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0980
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.3938

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

Flipped N/Q/H residues before XYZ refinement:
A 344 GLN
A 535 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.238012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.215852 restraints weight = 3640.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.4394 rms_B_bonded: 1.56
r_work: 0.4198 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.4198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6788
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3251  Z= 0.169
  Angle     :  0.521   5.776   4416  Z= 0.280
  Chirality :  0.040   0.133    521
  Planarity :  0.004   0.049    539
  Dihedral  :  4.566  20.329    444
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 13.13 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.34 (0.42), residues: 408
  helix:  2.00 (0.27), residues: 358
  sheet:  None (None), residues: 0
  loop : -1.78 (0.87), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 178 
 HIS   0.001   0.001   HIS A 468 
 PHE   0.021   0.002   PHE A 193 
 TYR   0.014   0.001   TYR A 426 
 ARG   0.003   0.000   ARG A 264 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A  182 THR cc_start: 0.7996 (m) cc_final: 0.6267 (t)
REVERT: A  264 ARG cc_start: 0.4592 (mtp85) cc_final: 0.3139 (mtp-110)
REVERT: A  439 ASN cc_start: 0.7185 (p0) cc_final: 0.6876 (m-40)
REVERT: A  447 LEU cc_start: 0.8534 (tt) cc_final: 0.8256 (tp)
REVERT: A  517 MET cc_start: 0.4545 (ttt) cc_final: 0.4249 (ttm)
  outliers start: 2
  outliers final: 2
  residues processed: 38
  average time/residue: 0.1463
  time to fit residues: 7.1574
Evaluate side-chains
  36 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 34
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  178 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 23 optimal weight:    0.0970
   chunk 8 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 27 optimal weight:    0.4980
   chunk 30 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
A 344 GLN
A 535 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.239156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.217003 restraints weight = 3673.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.4387 rms_B_bonded: 1.56
r_work: 0.4172 rms_B_bonded: 4.85 restraints_weight: 0.5000
r_work (final): 0.4172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6818
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3251  Z= 0.186
  Angle     :  0.532   6.114   4416  Z= 0.285
  Chirality :  0.040   0.134    521
  Planarity :  0.004   0.049    539
  Dihedral  :  4.520  20.116    444
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 13.13 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.42 (0.42), residues: 408
  helix:  2.02 (0.27), residues: 358
  sheet:  None (None), residues: 0
  loop : -1.45 (0.93), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 178 
 HIS   0.001   0.001   HIS A 132 
 PHE   0.020   0.002   PHE A 236 
 TYR   0.015   0.001   TYR A 426 
 ARG   0.002   0.000   ARG A 264 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A  182 THR cc_start: 0.8060 (m) cc_final: 0.6354 (t)
REVERT: A  264 ARG cc_start: 0.4719 (mtp85) cc_final: 0.3144 (mtp-110)
REVERT: A  439 ASN cc_start: 0.7274 (p0) cc_final: 0.6969 (m-40)
REVERT: A  447 LEU cc_start: 0.8545 (tt) cc_final: 0.8279 (tp)
REVERT: A  517 MET cc_start: 0.4512 (ttt) cc_final: 0.4169 (ttm)
REVERT: A  535 GLN cc_start: 0.5502 (mt0) cc_final: 0.5199 (mt0)
  outliers start: 4
  outliers final: 3
  residues processed: 40
  average time/residue: 0.1285
  time to fit residues: 6.9987
Evaluate side-chains
  38 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  178 TRP
Chi-restraints excluded: chain A residue  248 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 9 optimal weight:    0.0370
   chunk 11 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 39 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0970
   chunk 35 optimal weight:    0.5980
   chunk 0 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.3856

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

Flipped N/Q/H residues before XYZ refinement:
A 344 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4601 r_free = 0.4601 target = 0.241148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.219332 restraints weight = 3593.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.4408 rms_B_bonded: 1.53
r_work: 0.4206 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.4206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6773
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3251  Z= 0.168
  Angle     :  0.514   6.186   4416  Z= 0.274
  Chirality :  0.039   0.133    521
  Planarity :  0.004   0.049    539
  Dihedral  :  4.419  19.520    444
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 12.84 %
    Favored  : 85.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.58 (0.42), residues: 408
  helix:  2.13 (0.27), residues: 358
  sheet:  None (None), residues: 0
  loop : -1.42 (0.92), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 178 
 HIS   0.001   0.001   HIS A 132 
 PHE   0.020   0.002   PHE A 236 
 TYR   0.016   0.001   TYR A 426 
 ARG   0.002   0.000   ARG A 264 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A  182 THR cc_start: 0.7989 (m) cc_final: 0.6287 (t)
REVERT: A  264 ARG cc_start: 0.4691 (mtp85) cc_final: 0.3271 (mtm180)
REVERT: A  439 ASN cc_start: 0.7209 (p0) cc_final: 0.6999 (m-40)
REVERT: A  447 LEU cc_start: 0.8525 (tt) cc_final: 0.8268 (tp)
REVERT: A  517 MET cc_start: 0.4516 (ttt) cc_final: 0.4173 (ttm)
  outliers start: 4
  outliers final: 3
  residues processed: 43
  average time/residue: 0.1187
  time to fit residues: 6.7483
Evaluate side-chains
  39 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  178 TRP
Chi-restraints excluded: chain A residue  248 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 4 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 26 optimal weight:    0.4980
   chunk 8 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 344 GLN
A 535 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4575 r_free = 0.4575 target = 0.238060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.215815 restraints weight = 3654.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.4375 rms_B_bonded: 1.57
r_work: 0.4165 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.4165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6839
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3251  Z= 0.214
  Angle     :  0.552   6.229   4416  Z= 0.294
  Chirality :  0.040   0.138    521
  Planarity :  0.004   0.050    539
  Dihedral  :  4.517  19.146    444
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 13.13 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.34 (0.42), residues: 408
  helix:  1.97 (0.27), residues: 358
  sheet:  None (None), residues: 0
  loop : -1.60 (0.89), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 178 
 HIS   0.001   0.001   HIS A 468 
 PHE   0.020   0.002   PHE A 236 
 TYR   0.016   0.001   TYR A 426 
 ARG   0.003   0.000   ARG A 264 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A  182 THR cc_start: 0.8063 (m) cc_final: 0.6428 (t)
REVERT: A  264 ARG cc_start: 0.4823 (mtp85) cc_final: 0.3394 (mtm110)
REVERT: A  439 ASN cc_start: 0.7278 (p0) cc_final: 0.6947 (m-40)
REVERT: A  447 LEU cc_start: 0.8585 (tt) cc_final: 0.8324 (tp)
REVERT: A  517 MET cc_start: 0.4467 (ttt) cc_final: 0.4128 (ttm)
  outliers start: 5
  outliers final: 4
  residues processed: 40
  average time/residue: 0.1190
  time to fit residues: 6.4050
Evaluate side-chains
  39 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  178 TRP
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  248 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 29 optimal weight:    0.3980
   chunk 19 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 5 optimal weight:    0.3980
   chunk 11 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 344 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4577 r_free = 0.4577 target = 0.238361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.216054 restraints weight = 3620.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.4371 rms_B_bonded: 1.57
r_work: 0.4200 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.4200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6807
moved from start:          0.1808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3251  Z= 0.200
  Angle     :  0.543   6.316   4416  Z= 0.289
  Chirality :  0.040   0.144    521
  Planarity :  0.004   0.050    539
  Dihedral  :  4.510  18.477    444
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 12.84 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.35 (0.42), residues: 408
  helix:  2.01 (0.27), residues: 356
  sheet:  None (None), residues: 0
  loop : -1.71 (0.85), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 178 
 HIS   0.001   0.001   HIS A 468 
 PHE   0.021   0.002   PHE A 236 
 TYR   0.016   0.001   TYR A 426 
 ARG   0.003   0.000   ARG A 264 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A  182 THR cc_start: 0.8056 (m) cc_final: 0.6415 (t)
REVERT: A  264 ARG cc_start: 0.4824 (mtp85) cc_final: 0.3361 (mtm180)
REVERT: A  439 ASN cc_start: 0.7208 (p0) cc_final: 0.6918 (m-40)
REVERT: A  447 LEU cc_start: 0.8571 (tt) cc_final: 0.8306 (tp)
REVERT: A  517 MET cc_start: 0.4564 (ttt) cc_final: 0.4246 (ttm)
  outliers start: 5
  outliers final: 4
  residues processed: 40
  average time/residue: 0.1238
  time to fit residues: 6.6502
Evaluate side-chains
  40 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  178 TRP
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  248 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0970
   chunk 19 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 1 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
A 344 GLN
A 535 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.237923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.216152 restraints weight = 3551.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.4388 rms_B_bonded: 1.54
r_work: 0.4179 rms_B_bonded: 4.62 restraints_weight: 0.5000
r_work (final): 0.4179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6815
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3251  Z= 0.191
  Angle     :  0.538   6.256   4416  Z= 0.286
  Chirality :  0.040   0.143    521
  Planarity :  0.004   0.050    539
  Dihedral  :  4.484  18.181    444
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 13.73 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.42 (0.42), residues: 408
  helix:  2.05 (0.27), residues: 356
  sheet:  None (None), residues: 0
  loop : -1.68 (0.86), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 178 
 HIS   0.001   0.001   HIS A 468 
 PHE   0.021   0.002   PHE A 236 
 TYR   0.016   0.001   TYR A 426 
 ARG   0.003   0.000   ARG A 264 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1815.68 seconds
wall clock time: 32 minutes 7.26 seconds (1927.26 seconds total)