Starting phenix.real_space_refine
on Mon Feb 10 23:07:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xpz_33386/02_2025/7xpz_33386.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xpz_33386/02_2025/7xpz_33386.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xpz_33386/02_2025/7xpz_33386.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xpz_33386/02_2025/7xpz_33386.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xpz_33386/02_2025/7xpz_33386.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xpz_33386/02_2025/7xpz_33386.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      10      5.16       5
     C    2148      2.51       5
     N     530      2.21       5
     O     539      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 3227
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 402, 3227
          Classifications: {'peptide': 402}
          Link IDs: {'PTRANS': 14, 'TRANS': 387}
          Chain breaks: 1
  Time building chain proxies: 3.07, per 1000 atoms: 0.95
  Number of scatterers: 3227
  At special positions: 0
  Unit cell: (81, 75, 63, 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      10     16.00
     O     539      8.00
     N     530      7.00
     C    2148      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: 0.79
  Conformation dependent library (CDL) restraints added in 397.6 milliseconds
  

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  762

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 0 sheets defined
      76.1% 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 28 through 39
      removed outlier: 3.576A  pdb=" N   PHE A  34 " --> pdb=" O   CYS A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 53
    Processing helix  chain 'A' and resid 60 through 67
      removed outlier: 3.550A  pdb=" N   THR A  65 " --> pdb=" O   ARG A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 79
      removed outlier: 3.672A  pdb=" N   LEU A  72 " --> pdb=" O   ILE A  68 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   SER A  73 " --> pdb=" O   THR A  69 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   TYR A  76 " --> pdb=" O   LEU A  72 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   LEU A  77 " --> pdb=" O   SER A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 90
      removed outlier: 3.937A  pdb=" N   ASP A  88 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   TYR A  89 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU A  90 " --> pdb=" O   LEU A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 110
      removed outlier: 3.540A  pdb=" N   GLY A 100 " --> pdb=" O   LEU A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 132
      removed outlier: 3.623A  pdb=" N   MET A 119 " --> pdb=" O   SER A 115 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU A 121 " --> pdb=" O   ALA A 117 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   VAL A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   THR A 129 " --> pdb=" O   PHE A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 144
      removed outlier: 4.340A  pdb=" N   TYR A 136 " --> pdb=" O   ALA A 132 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   SER A 137 " --> pdb=" O   ARG A 133 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ILE A 140 " --> pdb=" O   TYR A 136 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   PHE A 141 " --> pdb=" O   SER A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 177
      removed outlier: 3.820A  pdb=" N   VAL A 152 " --> pdb=" O   ARG A 148 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLY A 154 " --> pdb=" O   GLN A 150 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ALA A 159 " --> pdb=" O   TYR A 155 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU A 161 " --> pdb=" O   ARG A 157 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   LEU A 162 " --> pdb=" O   ALA A 158 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   SER A 168 " --> pdb=" O   VAL A 164 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   VAL A 175 " --> pdb=" O   GLY A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 192
      removed outlier: 3.577A  pdb=" N   ALA A 191 " --> pdb=" O   TYR A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 202
      removed outlier: 3.735A  pdb=" N   PHE A 202 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 257
    Processing helix  chain 'A' and resid 260 through 264
    Processing helix  chain 'A' and resid 266 through 277
      removed outlier: 3.642A  pdb=" N   SER A 271 " --> pdb=" O   LEU A 267 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   LEU A 272 " --> pdb=" O   ARG A 268 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   VAL A 275 " --> pdb=" O   SER A 271 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   PHE A 276 " --> pdb=" O   LEU A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 286
    Processing helix  chain 'A' and resid 287 through 296
      removed outlier: 3.600A  pdb=" N   ASN A 293 " --> pdb=" O   HIS A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 323
      removed outlier: 3.919A  pdb=" N   SER A 313 " --> pdb=" O   ALA A 309 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   SER A 321 " --> pdb=" O   GLY A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 333
      removed outlier: 3.853A  pdb=" N   ALA A 332 " --> pdb=" O   ILE A 329 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   ARG A 333 " --> pdb=" O   ARG A 330 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 329 through 333'
    Processing helix  chain 'A' and resid 334 through 354
      removed outlier: 3.915A  pdb=" N   THR A 343 " --> pdb=" O   ILE A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 361
    Processing helix  chain 'A' and resid 362 through 377
      removed outlier: 3.594A  pdb=" N   ALA A 367 " --> pdb=" O   TRP A 363 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ALA A 368 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   PHE A 369 " --> pdb=" O   CYS A 365 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   PHE A 372 " --> pdb=" O   ALA A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 387
    Processing helix  chain 'A' and resid 392 through 400
      removed outlier: 3.881A  pdb=" N   ALA A 397 " --> pdb=" O   LYS A 393 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   LEU A 398 " --> pdb=" O   GLU A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 419
    Processing helix  chain 'A' and resid 427 through 442
      removed outlier: 3.868A  pdb=" N   LEU A 434 " --> pdb=" O   LYS A 430 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   VAL A 437 " --> pdb=" O   GLN A 433 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   TYR A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)

    163 hydrogen bonds defined for protein.
    480 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: 0.78

  Time building geometry restraints manager: 0.94 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: 962
        1.34 -     1.46: 827
        1.46 -     1.57: 1511
        1.57 -     1.69: 0
        1.69 -     1.81: 16
  Bond restraints: 3316
  Sorted by residual:
  bond pdb=" C   THR A  93 "
       pdb=" N   PRO A  94 "
    ideal  model  delta    sigma   weight residual
    1.336  1.350 -0.014 1.23e-02 6.61e+03 1.38e+00
  bond pdb=" CB  PRO A  70 "
       pdb=" CG  PRO A  70 "
    ideal  model  delta    sigma   weight residual
    1.492  1.437  0.055 5.00e-02 4.00e+02 1.19e+00
  bond pdb=" CB  PRO A 381 "
       pdb=" CG  PRO A 381 "
    ideal  model  delta    sigma   weight residual
    1.492  1.439  0.053 5.00e-02 4.00e+02 1.11e+00
  bond pdb=" CB  PRO A  94 "
       pdb=" CG  PRO A  94 "
    ideal  model  delta    sigma   weight residual
    1.492  1.440  0.052 5.00e-02 4.00e+02 1.08e+00
  bond pdb=" CB  PRO A  50 "
       pdb=" CG  PRO A  50 "
    ideal  model  delta    sigma   weight residual
    1.492  1.443  0.049 5.00e-02 4.00e+02 9.47e-01
  ... (remaining 3311 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 4266
        1.40 -     2.79: 206
        2.79 -     4.19: 31
        4.19 -     5.58: 12
        5.58 -     6.98: 5
  Bond angle restraints: 4520
  Sorted by residual:
  angle pdb=" C   VAL A 250 "
        pdb=" N   LEU A 251 "
        pdb=" CA  LEU A 251 "
      ideal   model   delta    sigma   weight residual
     123.05  128.86   -5.81 1.57e+00 4.06e-01 1.37e+01
  angle pdb=" N   ALA A 252 "
        pdb=" CA  ALA A 252 "
        pdb=" C   ALA A 252 "
      ideal   model   delta    sigma   weight residual
     113.18  108.52    4.66 1.33e+00 5.65e-01 1.23e+01
  angle pdb=" N   SER A 301 "
        pdb=" CA  SER A 301 "
        pdb=" C   SER A 301 "
      ideal   model   delta    sigma   weight residual
     110.80  117.03   -6.23 2.13e+00 2.20e-01 8.57e+00
  angle pdb=" CA  THR A  69 "
        pdb=" C   THR A  69 "
        pdb=" N   PRO A  70 "
      ideal   model   delta    sigma   weight residual
     118.44  122.92   -4.48 1.59e+00 3.96e-01 7.94e+00
  angle pdb=" C   VAL A 418 "
        pdb=" N   SER A 419 "
        pdb=" CA  SER A 419 "
      ideal   model   delta    sigma   weight residual
     121.54  116.19    5.35 1.91e+00 2.74e-01 7.85e+00
  ... (remaining 4515 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.48: 1743
       15.48 -    30.95: 132
       30.95 -    46.42: 27
       46.42 -    61.90: 6
       61.90 -    77.37: 2
  Dihedral angle restraints: 1910
    sinusoidal: 725
      harmonic: 1185
  Sorted by residual:
  dihedral pdb=" CA  ASN A 300 "
           pdb=" C   ASN A 300 "
           pdb=" N   SER A 301 "
           pdb=" CA  SER A 301 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.80  -25.20     0      5.00e+00 4.00e-02 2.54e+01
  dihedral pdb=" CA  THR A 298 "
           pdb=" C   THR A 298 "
           pdb=" N   THR A 299 "
           pdb=" CA  THR A 299 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.29   21.71     0      5.00e+00 4.00e-02 1.89e+01
  dihedral pdb=" CA  ARG A  91 "
           pdb=" C   ARG A  91 "
           pdb=" N   TYR A  92 "
           pdb=" CA  TYR A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.01   20.99     0      5.00e+00 4.00e-02 1.76e+01
  ... (remaining 1907 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 302
       0.037 -    0.073: 170
       0.073 -    0.110: 46
       0.110 -    0.146: 8
       0.146 -    0.183: 2
  Chirality restraints: 528
  Sorted by residual:
  chirality pdb=" CA  THR A  49 "
            pdb=" N   THR A  49 "
            pdb=" C   THR A  49 "
            pdb=" CB  THR A  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.18 2.00e-01 2.50e+01 8.37e-01
  chirality pdb=" CA  THR A  93 "
            pdb=" N   THR A  93 "
            pdb=" C   THR A  93 "
            pdb=" CB  THR A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.35    0.17 2.00e-01 2.50e+01 7.48e-01
  chirality pdb=" CA  THR A  69 "
            pdb=" N   THR A  69 "
            pdb=" C   THR A  69 "
            pdb=" CB  THR A  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.14 2.00e-01 2.50e+01 5.16e-01
  ... (remaining 525 not shown)

  Planarity restraints: 546
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  81 "    0.050 5.00e-02 4.00e+02   7.45e-02 8.89e+00
        pdb=" N   PRO A  82 "   -0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO A  82 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A  82 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  69 "    0.049 5.00e-02 4.00e+02   7.26e-02 8.43e+00
        pdb=" N   PRO A  70 "   -0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO A  70 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A  70 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 380 "   -0.047 5.00e-02 4.00e+02   7.07e-02 8.00e+00
        pdb=" N   PRO A 381 "    0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO A 381 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 381 "   -0.040 5.00e-02 4.00e+02
  ... (remaining 543 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 1104
        2.83 -     3.35: 2879
        3.35 -     3.86: 5331
        3.86 -     4.38: 6586
        4.38 -     4.90: 10693
  Nonbonded interactions: 26593
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 304 "
            pdb=" OH  TYR A 366 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O   THR A 404 "
            pdb=" OG1 THR A 408 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" OD2 ASP A  56 "
            pdb=" OG  SER A 183 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" OH  TYR A 139 "
            pdb=" O   LYS A 204 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" OG  SER A 271 "
            pdb=" OD1 ASN A 403 "
     model   vdw
     2.337 3.040
  ... (remaining 26588 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:             1.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.830
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
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      :  0.005   0.055   3316  Z= 0.343
  Angle     :  0.732   6.979   4520  Z= 0.426
  Chirality :  0.046   0.183    528
  Planarity :  0.008   0.075    546
  Dihedral  : 12.260  77.370   1148
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  9.51 %
    Favored  : 89.91 %
  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: -6.77 (0.22), residues: 398
  helix: -4.54 (0.11), residues: 308
  sheet:  None (None), residues: 0
  loop : -2.98 (0.52), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 274 
 HIS   0.001   0.000   HIS A 358 
 PHE   0.009   0.001   PHE A 276 
 TYR   0.010   0.002   TYR A  92 
 ARG   0.002   0.000   ARG A 264 

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A   22 LEU cc_start: 0.6860 (tp) cc_final: 0.6364 (pp)
REVERT: A   26 ARG cc_start: 0.6911 (tpt-90) cc_final: 0.6414 (ttm170)
REVERT: A   40 GLN cc_start: 0.7794 (mm110) cc_final: 0.7521 (mm-40)
REVERT: A   92 TYR cc_start: 0.8170 (m-80) cc_final: 0.7871 (m-80)
REVERT: A  122 MET cc_start: 0.8952 (tmm) cc_final: 0.8715 (tmm)
REVERT: A  310 ASP cc_start: 0.7621 (t0) cc_final: 0.7286 (t0)
  outliers start: 2
  outliers final: 1
  residues processed: 57
  average time/residue: 0.2029
  time to fit residues: 13.7606
Evaluate side-chains
  43 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 12 optimal weight:    0.1980
   chunk 19 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0970
   chunk 36 optimal weight:    0.2980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.3578

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

Flipped N/Q/H residues before XYZ refinement:
A 118 HIS
A 377 GLN
A 433 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.114345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.097605 restraints weight = 4426.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3120 rms_B_bonded: 2.03
r_work: 0.3015 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3316  Z= 0.168
  Angle     :  0.544   5.654   4520  Z= 0.290
  Chirality :  0.037   0.113    528
  Planarity :  0.006   0.046    546
  Dihedral  :  5.431  34.845    451
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 11.82 %
    Favored  : 86.17 %
  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: -4.56 (0.32), residues: 398
  helix: -2.93 (0.21), residues: 310
  sheet:  None (None), residues: 0
  loop : -2.34 (0.58), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 289 
 PHE   0.009   0.001   PHE A 447 
 TYR   0.010   0.001   TYR A  35 
 ARG   0.007   0.000   ARG A 263 

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A   22 LEU cc_start: 0.6165 (tp) cc_final: 0.5717 (pp)
REVERT: A   26 ARG cc_start: 0.6931 (tpt-90) cc_final: 0.6110 (ttm170)
REVERT: A   38 MET cc_start: 0.8568 (mmt) cc_final: 0.8288 (tpp)
REVERT: A  122 MET cc_start: 0.9014 (tmm) cc_final: 0.8760 (tmm)
REVERT: A  277 ASN cc_start: 0.8999 (t0) cc_final: 0.8596 (t0)
REVERT: A  434 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7884 (tt)
  outliers start: 7
  outliers final: 3
  residues processed: 50
  average time/residue: 0.1830
  time to fit residues: 11.0685
Evaluate side-chains
  46 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  40 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.110662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.094176 restraints weight = 4409.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 2.01
r_work: 0.2969 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.2170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3316  Z= 0.277
  Angle     :  0.577   5.940   4520  Z= 0.296
  Chirality :  0.040   0.122    528
  Planarity :  0.004   0.033    546
  Dihedral  :  4.903  19.315    449
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 15.27 %
    Favored  : 82.42 %
  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: -3.14 (0.37), residues: 398
  helix: -1.91 (0.25), residues: 310
  sheet:  None (None), residues: 0
  loop : -1.87 (0.63), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 358 
 PHE   0.009   0.001   PHE A 276 
 TYR   0.012   0.001   TYR A  35 
 ARG   0.004   0.000   ARG A 263 

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6957 (tpt-90) cc_final: 0.6081 (ttm170)
REVERT: A   38 MET cc_start: 0.8600 (mmt) cc_final: 0.8358 (tpp)
REVERT: A   40 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7644 (mm-40)
REVERT: A  277 ASN cc_start: 0.8977 (t0) cc_final: 0.8579 (t0)
REVERT: A  357 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7853 (mpt-90)
REVERT: A  434 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7768 (tt)
  outliers start: 8
  outliers final: 4
  residues processed: 49
  average time/residue: 0.1403
  time to fit residues: 8.8353
Evaluate side-chains
  48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  357 ARG
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 27 optimal weight:    0.0670
   chunk 2 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0770
   chunk 5 optimal weight:    0.1980
   chunk 4 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.3076

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

Flipped N/Q/H residues before XYZ refinement:
A  66 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.115374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.098641 restraints weight = 4361.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 2.06
r_work: 0.3031 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2905 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   3316  Z= 0.143
  Angle     :  0.500   6.184   4520  Z= 0.256
  Chirality :  0.037   0.116    528
  Planarity :  0.003   0.028    546
  Dihedral  :  4.634  17.297    449
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 17.00 %
    Favored  : 81.84 %
  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: -2.30 (0.40), residues: 398
  helix: -1.27 (0.28), residues: 314
  sheet:  None (None), residues: 0
  loop : -1.76 (0.66), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 107 
 HIS   0.000   0.000   HIS A 358 
 PHE   0.023   0.001   PHE A  84 
 TYR   0.008   0.001   TYR A  35 
 ARG   0.003   0.000   ARG A 263 

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.412 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6871 (tpt-90) cc_final: 0.6005 (ttm170)
REVERT: A  211 PHE cc_start: 0.8498 (m-80) cc_final: 0.8066 (m-80)
REVERT: A  277 ASN cc_start: 0.8965 (t0) cc_final: 0.8587 (t0)
REVERT: A  434 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7613 (tt)
  outliers start: 4
  outliers final: 3
  residues processed: 49
  average time/residue: 0.1550
  time to fit residues: 9.7567
Evaluate side-chains
  49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  334 TRP
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0000
   chunk 12 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.5584

-------------------------------------------------------------------------------
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 = 0.3322 r_free = 0.3322 target = 0.113320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.096571 restraints weight = 4418.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 2.02
r_work: 0.3002 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.2601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3316  Z= 0.197
  Angle     :  0.524   6.056   4520  Z= 0.264
  Chirality :  0.038   0.120    528
  Planarity :  0.003   0.027    546
  Dihedral  :  4.590  20.079    449
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 16.14 %
    Favored  : 81.27 %
  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: -1.90 (0.41), residues: 398
  helix: -0.95 (0.28), residues: 318
  sheet:  None (None), residues: 0
  loop : -1.81 (0.69), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 273 
 HIS   0.001   0.000   HIS A 289 
 PHE   0.007   0.001   PHE A 276 
 TYR   0.010   0.001   TYR A  35 
 ARG   0.002   0.000   ARG A 263 

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.343 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6946 (tpt-90) cc_final: 0.6063 (ttm170)
REVERT: A  277 ASN cc_start: 0.8997 (t0) cc_final: 0.8578 (t0)
REVERT: A  434 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7549 (tt)
  outliers start: 9
  outliers final: 5
  residues processed: 52
  average time/residue: 0.1381
  time to fit residues: 9.1375
Evaluate side-chains
  50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 12 optimal weight:    0.2980
   chunk 27 optimal weight:    0.0060
   chunk 13 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 22 optimal weight:    0.4980
   chunk 8 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.3996

-------------------------------------------------------------------------------
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 = 0.3344 r_free = 0.3344 target = 0.115015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.099220 restraints weight = 4362.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 1.94
r_work: 0.3037 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2915 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.2796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3316  Z= 0.162
  Angle     :  0.509   6.055   4520  Z= 0.256
  Chirality :  0.038   0.117    528
  Planarity :  0.003   0.025    546
  Dihedral  :  4.467  19.280    449
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.43 %
    Favored  : 81.27 %
  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: -1.53 (0.42), residues: 398
  helix: -0.69 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop : -1.68 (0.69), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 273 
 HIS   0.000   0.000   HIS A 358 
 PHE   0.019   0.001   PHE A  84 
 TYR   0.009   0.001   TYR A  92 
 ARG   0.002   0.000   ARG A 263 

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6940 (tpt-90) cc_final: 0.6068 (ttm170)
REVERT: A  434 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7521 (tt)
  outliers start: 8
  outliers final: 7
  residues processed: 48
  average time/residue: 0.1390
  time to fit residues: 8.5246
Evaluate side-chains
  50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  334 TRP
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   chunk 28 optimal weight:    0.3980
   chunk 22 optimal weight:    0.1980
   chunk 17 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.3339 r_free = 0.3339 target = 0.114555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.098181 restraints weight = 4411.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 2.05
r_work: 0.3019 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2894 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7340
moved from start:          0.2855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3316  Z= 0.179
  Angle     :  0.515   6.068   4520  Z= 0.259
  Chirality :  0.038   0.133    528
  Planarity :  0.003   0.025    546
  Dihedral  :  4.406  19.340    449
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 17.29 %
    Favored  : 80.40 %
  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: -1.29 (0.42), residues: 398
  helix: -0.53 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop : -1.60 (0.70), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 273 
 HIS   0.001   0.000   HIS A 289 
 PHE   0.013   0.001   PHE A 447 
 TYR   0.009   0.001   TYR A  92 
 ARG   0.001   0.000   ARG A 263 

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.360 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6930 (tpt-90) cc_final: 0.6047 (ttm170)
REVERT: A  434 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7475 (tt)
  outliers start: 8
  outliers final: 7
  residues processed: 50
  average time/residue: 0.1554
  time to fit residues: 9.7358
Evaluate side-chains
  51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  334 TRP
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 28 optimal weight:    0.3980
   chunk 18 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0870
   chunk 33 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.4758

-------------------------------------------------------------------------------
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 = 0.3347 r_free = 0.3347 target = 0.115118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.098534 restraints weight = 4380.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 2.05
r_work: 0.3115 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2982 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.2928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3316  Z= 0.175
  Angle     :  0.513   6.043   4520  Z= 0.256
  Chirality :  0.038   0.140    528
  Planarity :  0.003   0.025    546
  Dihedral  :  4.349  19.030    449
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.71 %
    Favored  : 80.98 %
  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: -1.05 (0.43), residues: 398
  helix: -0.36 (0.30), residues: 319
  sheet:  None (None), residues: 0
  loop : -1.52 (0.71), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 273 
 HIS   0.000   0.000   HIS A 358 
 PHE   0.021   0.001   PHE A  84 
 TYR   0.009   0.001   TYR A  92 
 ARG   0.001   0.000   ARG A 263 

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6994 (tpt-90) cc_final: 0.6108 (ttm170)
REVERT: A  211 PHE cc_start: 0.8405 (m-80) cc_final: 0.8101 (m-80)
  outliers start: 8
  outliers final: 8
  residues processed: 49
  average time/residue: 0.1485
  time to fit residues: 9.0408
Evaluate side-chains
  51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  334 TRP
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0470
   chunk 31 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 15 optimal weight:    0.8980
   chunk 5 optimal weight:    0.4980
   chunk 32 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.5478

-------------------------------------------------------------------------------
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 = 0.3344 r_free = 0.3344 target = 0.114873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.097792 restraints weight = 4389.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 2.09
r_work: 0.3017 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2892 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.2967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3316  Z= 0.196
  Angle     :  0.551   6.926   4520  Z= 0.274
  Chirality :  0.039   0.150    528
  Planarity :  0.003   0.025    546
  Dihedral  :  4.382  19.104    449
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.71 %
    Favored  : 80.98 %
  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: -0.97 (0.43), residues: 398
  helix: -0.32 (0.30), residues: 318
  sheet:  None (None), residues: 0
  loop : -1.39 (0.71), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 273 
 HIS   0.000   0.000   HIS A 289 
 PHE   0.017   0.001   PHE A 447 
 TYR   0.010   0.001   TYR A  92 
 ARG   0.002   0.000   ARG A 253 

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6937 (tpt-90) cc_final: 0.6045 (ttm170)
  outliers start: 8
  outliers final: 8
  residues processed: 50
  average time/residue: 0.1675
  time to fit residues: 10.3123
Evaluate side-chains
  52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  334 TRP
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 6 optimal weight:    0.2980
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 16 optimal weight:    0.4980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3344 r_free = 0.3344 target = 0.114974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.098755 restraints weight = 4266.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 1.91
r_work: 0.3026 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.3015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3316  Z= 0.199
  Angle     :  0.551   6.516   4520  Z= 0.275
  Chirality :  0.039   0.155    528
  Planarity :  0.003   0.025    546
  Dihedral  :  4.387  18.935    449
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.71 %
    Favored  : 80.98 %
  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: -0.95 (0.42), residues: 398
  helix: -0.29 (0.29), residues: 317
  sheet:  None (None), residues: 0
  loop : -1.45 (0.70), residues: 81

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 273 
 HIS   0.001   0.000   HIS A 289 
 PHE   0.024   0.001   PHE A  84 
 TYR   0.011   0.001   TYR A  92 
 ARG   0.001   0.000   ARG A 263 

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6982 (tpt-90) cc_final: 0.6096 (ttm170)
REVERT: A  255 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6917 (pp)
  outliers start: 8
  outliers final: 6
  residues processed: 47
  average time/residue: 0.1518
  time to fit residues: 9.0107
Evaluate side-chains
  48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  334 TRP
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  424 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 34 optimal weight:    0.0980
   chunk 25 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 36 optimal weight:    0.4980
   chunk 16 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3348 r_free = 0.3348 target = 0.115263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.098971 restraints weight = 4324.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 1.93
r_work: 0.3028 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2904 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.3046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3316  Z= 0.190
  Angle     :  0.566   8.221   4520  Z= 0.280
  Chirality :  0.039   0.158    528
  Planarity :  0.003   0.025    546
  Dihedral  :  4.361  18.664    449
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 17.87 %
    Favored  : 80.12 %
  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: -0.83 (0.42), residues: 398
  helix: -0.21 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop : -1.39 (0.70), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 273 
 HIS   0.000   0.000   HIS A 358 
 PHE   0.019   0.001   PHE A 447 
 TYR   0.010   0.001   TYR A  92 
 ARG   0.001   0.000   ARG A 263 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1836.54 seconds
wall clock time: 33 minutes 31.99 seconds (2011.99 seconds total)