Starting phenix.real_space_refine
on Sat Aug 23 01:27:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9eo4_19845/08_2025/9eo4_19845_neut_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9eo4_19845/08_2025/9eo4_19845.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9eo4_19845/08_2025/9eo4_19845.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9eo4_19845/08_2025/9eo4_19845.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9eo4_19845/08_2025/9eo4_19845_neut_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9eo4_19845/08_2025/9eo4_19845_neut_trim.cif"
  }
  resolution = 2.66
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.034
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: 7
    Type Number    sf(0)   Gaussians
     S      23      5.16       5
     Cl      1      4.86       5
     Na      1      4.78       5
     C    3001      2.51       5
     N     685      2.21       5
     O     748      1.98       5
     H    4322      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8781
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 8634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 546, 8634
          Classifications: {'peptide': 546}
          Modifications used: {'ACID-ASP': 1, 'ACID-GLU': 1}
          Link IDs: {'PTRANS': 23, 'TRANS': 522}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 147
          Unusual residues: {' CL': 1, ' NA': 1, 'CLR': 3, 'COC': 1, 'Y01': 1}
          Classifications: {'undetermined': 7, 'water': 4}
          Link IDs: {None: 10}
  Time building chain proxies: 2.05, per 1000 atoms: 0.23
  Number of scatterers: 8781
  At special positions: 0
  Unit cell: (83.375, 66.7, 80.475, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Cl      1     17.00
     S      23     16.00
     Na      1     11.00
     O     748      8.00
     N     685      7.00
     C    3001      6.00
     H    4322      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 180 " - pdb=" SG  CYS B 189 " distance=2.03

  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: 1.49
  Conformation dependent library (CDL) restraints added in 291.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1004

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 1 sheets defined
      82.8% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'B' and resid 65 through 78
      removed outlier: 3.904A  pdb=" N   PHE B  69 " --> pdb=" O   LYS B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 85
    Processing helix  chain 'B' and resid 85 through 93
    Processing helix  chain 'B' and resid 94 through 97
    Processing helix  chain 'B' and resid 98 through 109
    Processing helix  chain 'B' and resid 109 through 125
      removed outlier: 3.543A  pdb=" N   LEU B 113 " --> pdb=" O   ALA B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 138
    Processing helix  chain 'B' and resid 139 through 153
      removed outlier: 3.800A  pdb=" N   PHE B 143 " --> pdb=" O   LYS B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 169
      removed outlier: 3.684A  pdb=" N   ILE B 159 " --> pdb=" O   PHE B 155 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ILE B 160 " --> pdb=" O   TYR B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 220
    Processing helix  chain 'B' and resid 223 through 227
      removed outlier: 3.538A  pdb=" N   GLN B 226 " --> pdb=" O   HIS B 223 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 256
    Processing helix  chain 'B' and resid 258 through 270
      removed outlier: 4.445A  pdb=" N   LYS B 264 " --> pdb=" O   LYS B 260 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   TRP B 267 " --> pdb=" O   GLY B 263 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   ILE B 268 " --> pdb=" O   LYS B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 286
      removed outlier: 4.033A  pdb=" N   THR B 286 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 299
    Processing helix  chain 'B' and resid 301 through 306
      removed outlier: 3.588A  pdb=" N   CYS B 306 " --> pdb=" O   TYR B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 322
      removed outlier: 3.834A  pdb=" N   TRP B 311 " --> pdb=" O   GLU B 307 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   LEU B 322 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 334
    Processing helix  chain 'B' and resid 341 through 376
      removed outlier: 3.693A  pdb=" N   GLY B 361 " --> pdb=" O   SER B 357 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   PHE B 362 " --> pdb=" O   PHE B 358 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   VAL B 363 " --> pdb=" O   SER B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 378 through 383
    Processing helix  chain 'B' and resid 388 through 400
      removed outlier: 3.708A  pdb=" N   ILE B 393 " --> pdb=" O   LEU B 389 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   TYR B 394 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
      Proline residue:  B 395  - end of helix
      removed outlier: 3.805A  pdb=" N   THR B 400 " --> pdb=" O   GLU B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 438
      removed outlier: 3.772A  pdb=" N   ASP B 421 " --> pdb=" O   THR B 417 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   SER B 422 " --> pdb=" O   LEU B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 442
    Processing helix  chain 'B' and resid 444 through 460
      removed outlier: 3.605A  pdb=" N   PHE B 448 " --> pdb=" O   HIS B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 461 through 463
      No H-bonds generated for 'chain 'B' and resid 461 through 463'
    Processing helix  chain 'B' and resid 467 through 479
      removed outlier: 3.801A  pdb=" N   VAL B 471 " --> pdb=" O   GLY B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 481 through 497
      removed outlier: 3.614A  pdb=" N   LEU B 485 " --> pdb=" O   GLY B 481 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 513
    Processing helix  chain 'B' and resid 517 through 526
    Processing helix  chain 'B' and resid 526 through 542
    Processing helix  chain 'B' and resid 554 through 570
      removed outlier: 3.835A  pdb=" N   SER B 568 " --> pdb=" O   ILE B 564 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   MET B 569 " --> pdb=" O   ALA B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 570 through 583
    Processing helix  chain 'B' and resid 586 through 596
      removed outlier: 3.561A  pdb=" N   LEU B 591 " --> pdb=" O   PHE B 587 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 597 through 599
      No H-bonds generated for 'chain 'B' and resid 597 through 599'
    Processing helix  chain 'B' and resid 600 through 607
    Processing helix  chain 'B' and resid 609 through 612
    Processing helix  chain 'B' and resid 613 through 619
      removed outlier: 3.648A  pdb=" N   TRP B 617 " --> pdb=" O   THR B 613 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 547 through 548
      removed outlier: 3.639A  pdb=" N   TYR B 548 " --> pdb=" O   TYR B 551 " (cutoff:3.500A)

    282 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: 1.66

  Time building geometry restraints manager: 1.21 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 4312
        1.03 -     1.23: 45
        1.23 -     1.43: 1925
        1.43 -     1.62: 2606
        1.62 -     1.82: 34
  Bond restraints: 8922
  Sorted by residual:
  bond pdb=" N   ALA B  57 "
       pdb=" H   ALA B  57 "
    ideal  model  delta    sigma   weight residual
    0.860  0.960 -0.100 2.00e-02 2.50e+03 2.50e+01
  bond pdb=" C   LYS B  66 "
       pdb=" O   LYS B  66 "
    ideal  model  delta    sigma   weight residual
    1.236  1.172  0.064 1.29e-02 6.01e+03 2.43e+01
  bond pdb=" C29 COC B 707 "
       pdb=" C8  COC B 707 "
    ideal  model  delta    sigma   weight residual
    1.528  1.615 -0.087 2.00e-02 2.50e+03 1.89e+01
  bond pdb=" C   SER B 586 "
       pdb=" O   SER B 586 "
    ideal  model  delta    sigma   weight residual
    1.234  1.189  0.045 1.07e-02 8.73e+03 1.80e+01
  bond pdb=" C   SER B 568 "
       pdb=" O   SER B 568 "
    ideal  model  delta    sigma   weight residual
    1.236  1.188  0.049 1.16e-02 7.43e+03 1.78e+01
  ... (remaining 8917 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.47: 15923
        2.47 -     4.94: 121
        4.94 -     7.41: 9
        7.41 -     9.88: 2
        9.88 -    12.34: 2
  Bond angle restraints: 16057
  Sorted by residual:
  angle pdb=" CA  SER B 568 "
        pdb=" C   SER B 568 "
        pdb=" O   SER B 568 "
      ideal   model   delta    sigma   weight residual
     120.90  115.19    5.71 1.03e+00 9.43e-01 3.07e+01
  angle pdb=" N   SER B 568 "
        pdb=" CA  SER B 568 "
        pdb=" C   SER B 568 "
      ideal   model   delta    sigma   weight residual
     111.03  105.21    5.82 1.11e+00 8.12e-01 2.75e+01
  angle pdb=" CA  SER B 586 "
        pdb=" C   SER B 586 "
        pdb=" O   SER B 586 "
      ideal   model   delta    sigma   weight residual
     121.67  116.04    5.63 1.26e+00 6.30e-01 2.00e+01
  angle pdb=" CA  MET B 569 "
        pdb=" C   MET B 569 "
        pdb=" O   MET B 569 "
      ideal   model   delta    sigma   weight residual
     120.10  115.18    4.92 1.13e+00 7.83e-01 1.90e+01
  angle pdb=" N   ARG B 588 "
        pdb=" CA  ARG B 588 "
        pdb=" C   ARG B 588 "
      ideal   model   delta    sigma   weight residual
     112.90  107.33    5.57 1.31e+00 5.83e-01 1.81e+01
  ... (remaining 16052 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.73: 4279
       35.73 -    71.46: 164
       71.46 -   107.19: 8
      107.19 -   142.92: 1
      142.92 -   178.64: 2
  Dihedral angle restraints: 4454
    sinusoidal: 2433
      harmonic: 2021
  Sorted by residual:
  dihedral pdb=" CD  ARG B 443 "
           pdb=" NE  ARG B 443 "
           pdb=" CZ  ARG B 443 "
           pdb=" NH1 ARG B 443 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -78.07   78.07     1      1.00e+01 1.00e-02 7.62e+01
  dihedral pdb=" CB  ASP B 421 "
           pdb=" CG  ASP B 421 "
           pdb=" OD2 ASP B 421 "
           pdb=" HD2 ASP B 421 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00   -1.36 -178.64     0      3.00e+01 1.11e-03 3.55e+01
  dihedral pdb=" CG  GLU B 491 "
           pdb=" CD  GLU B 491 "
           pdb=" OE2 GLU B 491 "
           pdb=" HE2 GLU B 491 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00    1.54  178.46     0      3.00e+01 1.11e-03 3.54e+01
  ... (remaining 4451 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 616
       0.057 -    0.113: 96
       0.113 -    0.170: 8
       0.170 -    0.226: 0
       0.226 -    0.283: 2
  Chirality restraints: 722
  Sorted by residual:
  chirality pdb=" C8  COC B 707 "
            pdb=" C10 COC B 707 "
            pdb=" C29 COC B 707 "
            pdb=" C6  COC B 707 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.81   -0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" C29 COC B 707 "
            pdb=" C26 COC B 707 "
            pdb=" C8  COC B 707 "
            pdb=" O1  COC B 707 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.38   -2.64    0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" CA  ILE B  67 "
            pdb=" N   ILE B  67 "
            pdb=" C   ILE B  67 "
            pdb=" CB  ILE B  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.05e-01
  ... (remaining 719 not shown)

  Planarity restraints: 1271
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 443 "    1.080 9.50e-02 1.11e+02   5.49e-01 3.98e+03
        pdb=" NE  ARG B 443 "   -0.081 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 443 "   -0.037 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 443 "    0.059 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 443 "   -0.056 2.00e-02 2.50e+03
        pdb="HH11 ARG B 443 "    0.729 2.00e-02 2.50e+03
        pdb="HH12 ARG B 443 "   -0.540 2.00e-02 2.50e+03
        pdb="HH21 ARG B 443 "    0.529 2.00e-02 2.50e+03
        pdb="HH22 ARG B 443 "   -0.651 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  85 "   -0.271 9.50e-02 1.11e+02   4.20e-01 3.79e+03
        pdb=" NE  ARG B  85 "    0.326 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  85 "    0.087 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  85 "   -0.058 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  85 "   -0.019 2.00e-02 2.50e+03
        pdb="HH11 ARG B  85 "    0.632 2.00e-02 2.50e+03
        pdb="HH12 ARG B  85 "   -0.842 2.00e-02 2.50e+03
        pdb="HH21 ARG B  85 "   -0.429 2.00e-02 2.50e+03
        pdb="HH22 ARG B  85 "    0.316 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B 317 "    0.125 2.00e-02 2.50e+03   1.31e-01 2.59e+02
        pdb=" CD  GLN B 317 "   -0.013 2.00e-02 2.50e+03
        pdb=" OE1 GLN B 317 "   -0.114 2.00e-02 2.50e+03
        pdb=" NE2 GLN B 317 "   -0.004 2.00e-02 2.50e+03
        pdb="HE21 GLN B 317 "    0.197 2.00e-02 2.50e+03
        pdb="HE22 GLN B 317 "   -0.190 2.00e-02 2.50e+03
  ... (remaining 1268 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.22: 727
        2.22 -     2.82: 18833
        2.82 -     3.41: 25416
        3.41 -     4.01: 34022
        4.01 -     4.60: 52869
  Nonbonded interactions: 131867
  Sorted by model distance:
  nonbonded pdb=" HH  TYR B 499 "
            pdb=" OD2 ASP B 507 "
     model   vdw
     1.628 2.450
  nonbonded pdb="HH22 ARG B 125 "
            pdb=" O   ASN B 336 "
     model   vdw
     1.642 2.450
  nonbonded pdb=" O   GLN B 611 "
            pdb=" HE1 TRP B 617 "
     model   vdw
     1.647 2.450
  nonbonded pdb=" OE2 GLU B 428 "
            pdb="HH22 ARG B 445 "
     model   vdw
     1.667 2.450
  nonbonded pdb=" O   VAL B 107 "
            pdb=" HH  TYR B 519 "
     model   vdw
     1.695 2.450
  ... (remaining 131862 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:             3.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.070
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     10.380
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
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      :  0.006   0.087   4601  Z= 0.325
  Angle     :  0.720  12.345   6302  Z= 0.419
  Chirality :  0.041   0.283    722
  Planarity :  0.022   0.488    750
  Dihedral  : 15.975 123.651   1808
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 14.63 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.38), residues: 542
  helix:  1.09 (0.27), residues: 377
  sheet:  None (None), residues: 0
  loop :  0.99 (0.55), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 615 
 TYR   0.007   0.001   TYR B 575 
 PHE   0.013   0.001   PHE B 365 
 TRP   0.008   0.001   TRP B 238 
 HIS   0.002   0.000   HIS B 616 

Details of bonding type rmsd
  covalent geometry    : bond        0.00556 ( 4600)
  covalent geometry    : angle       0.71909 ( 6300)
  SS BOND              : bond        0.00075 (    1)
  SS BOND              : angle       1.59848 (    2)
  hydrogen bonds       : bond        0.12818 (  282)
  hydrogen bonds       : angle       6.07813 (  822)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
REVERT: B  174 GLU cc_start: 0.7159 (tt0) cc_final: 0.6793 (pt0)
REVERT: B  239 GLN cc_start: 0.7865 (mp10) cc_final: 0.7628 (mt0)
REVERT: B  295 ARG cc_start: 0.7225 (ttm-80) cc_final: 0.6746 (mtm-85)
REVERT: B  360 SER cc_start: 0.8702 (m) cc_final: 0.8474 (p)
REVERT: B  483 SER cc_start: 0.8544 (OUTLIER) cc_final: 0.8292 (p)
REVERT: B  544 ARG cc_start: 0.6954 (mtm-85) cc_final: 0.6689 (mtm-85)
  outliers start: 4
  outliers final: 3
  residues processed: 76
  average time/residue: 1.0615
  time to fit residues: 84.2968
Evaluate side-chains
  67 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  483 SER
Chi-restraints excluded: chain B residue  568 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.3980
   chunk 32 optimal weight:    0.0170
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.4618

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

Flipped N/Q/H residues before XYZ refinement:
B 226 GLN
B 353 ASN
B 444 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.113502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.093528 restraints weight = 15094.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 1.61
r_work: 0.2921 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.2821 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.0967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4601  Z= 0.123
  Angle     :  0.494   4.433   6302  Z= 0.255
  Chirality :  0.036   0.123    722
  Planarity :  0.009   0.193    750
  Dihedral  :  7.724  57.021    891
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 13.97 %
    Favored  : 84.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.52 (0.38), residues: 542
  helix:  1.18 (0.26), residues: 395
  sheet:  None (None), residues: 0
  loop :  0.84 (0.59), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 443 
 TYR   0.009   0.001   TYR B 252 
 PHE   0.013   0.001   PHE B 365 
 TRP   0.008   0.001   TRP B 238 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 4600)
  covalent geometry    : angle       0.49371 ( 6300)
  SS BOND              : bond        0.00083 (    1)
  SS BOND              : angle       1.56584 (    2)
  hydrogen bonds       : bond        0.04393 (  282)
  hydrogen bonds       : angle       4.65222 (  822)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: B  174 GLU cc_start: 0.7693 (tt0) cc_final: 0.7468 (pt0)
REVERT: B  295 ARG cc_start: 0.7599 (ttm-80) cc_final: 0.7114 (mtp180)
REVERT: B  353 ASN cc_start: 0.7759 (m110) cc_final: 0.7003 (t0)
REVERT: B  483 SER cc_start: 0.8549 (OUTLIER) cc_final: 0.8343 (p)
REVERT: B  544 ARG cc_start: 0.7131 (mtm-85) cc_final: 0.6872 (mtm-85)
  outliers start: 6
  outliers final: 3
  residues processed: 67
  average time/residue: 1.0476
  time to fit residues: 73.3571
Evaluate side-chains
  64 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  429 SER
Chi-restraints excluded: chain B residue  483 SER
Chi-restraints excluded: chain B residue  568 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3301 r_free = 0.3301 target = 0.113903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.093678 restraints weight = 15113.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.2987 rms_B_bonded: 1.60
r_work: 0.2901 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2799 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.1189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4601  Z= 0.142
  Angle     :  0.485   4.472   6302  Z= 0.253
  Chirality :  0.036   0.129    722
  Planarity :  0.005   0.063    750
  Dihedral  :  7.432  59.929    890
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 14.85 %
    Favored  : 84.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.37), residues: 542
  helix:  1.24 (0.26), residues: 394
  sheet:  None (None), residues: 0
  loop :  0.62 (0.58), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 443 
 TYR   0.009   0.001   TYR B 252 
 PHE   0.014   0.001   PHE B 365 
 TRP   0.008   0.001   TRP B 238 
 HIS   0.007   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 4600)
  covalent geometry    : angle       0.48329 ( 6300)
  SS BOND              : bond        0.00059 (    1)
  SS BOND              : angle       1.98315 (    2)
  hydrogen bonds       : bond        0.04175 (  282)
  hydrogen bonds       : angle       4.45501 (  822)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
REVERT: B  174 GLU cc_start: 0.7775 (tt0) cc_final: 0.7526 (pt0)
REVERT: B  295 ARG cc_start: 0.7654 (ttm-80) cc_final: 0.7148 (mtp180)
REVERT: B  353 ASN cc_start: 0.7858 (m110) cc_final: 0.7094 (t0)
REVERT: B  483 SER cc_start: 0.8555 (OUTLIER) cc_final: 0.8353 (p)
REVERT: B  544 ARG cc_start: 0.7218 (mtm-85) cc_final: 0.6946 (mtm-85)
  outliers start: 4
  outliers final: 3
  residues processed: 61
  average time/residue: 0.7981
  time to fit residues: 51.1408
Evaluate side-chains
  60 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  429 SER
Chi-restraints excluded: chain B residue  483 SER
Chi-restraints excluded: chain B residue  568 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 44 optimal weight:    0.4980
   chunk 0 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.2980
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3359 r_free = 0.3359 target = 0.117797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.097785 restraints weight = 15165.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 1.61
r_work: 0.2945 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2843 rms_B_bonded: 3.04 restraints_weight: 0.2500
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.1322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4601  Z= 0.121
  Angle     :  0.460   4.422   6302  Z= 0.241
  Chirality :  0.035   0.126    722
  Planarity :  0.004   0.034    750
  Dihedral  :  6.988  57.655    890
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  : 15.07 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.37), residues: 542
  helix:  1.32 (0.26), residues: 395
  sheet:  None (None), residues: 0
  loop :  0.58 (0.57), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 615 
 TYR   0.009   0.001   TYR B 252 
 PHE   0.013   0.001   PHE B 365 
 TRP   0.008   0.001   TRP B 238 
 HIS   0.002   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 4600)
  covalent geometry    : angle       0.45931 ( 6300)
  SS BOND              : bond        0.00087 (    1)
  SS BOND              : angle       1.72123 (    2)
  hydrogen bonds       : bond        0.03891 (  282)
  hydrogen bonds       : angle       4.30997 (  822)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  174 GLU cc_start: 0.7766 (tt0) cc_final: 0.7549 (pt0)
REVERT: B  295 ARG cc_start: 0.7680 (ttm-80) cc_final: 0.7167 (mtp180)
REVERT: B  353 ASN cc_start: 0.7842 (m110) cc_final: 0.7099 (t0)
REVERT: B  544 ARG cc_start: 0.7188 (mtm-85) cc_final: 0.6926 (mtm-85)
  outliers start: 2
  outliers final: 2
  residues processed: 58
  average time/residue: 0.9744
  time to fit residues: 59.1332
Evaluate side-chains
  58 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  568 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 19 optimal weight:    0.2980
   chunk 33 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.3351 r_free = 0.3351 target = 0.117252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.097352 restraints weight = 14997.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 1.59
r_work: 0.2968 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4601  Z= 0.132
  Angle     :  0.466   4.454   6302  Z= 0.244
  Chirality :  0.036   0.128    722
  Planarity :  0.005   0.071    750
  Dihedral  :  6.934  58.344    889
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 14.85 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.37), residues: 542
  helix:  1.32 (0.26), residues: 395
  sheet:  None (None), residues: 0
  loop :  0.51 (0.57), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 615 
 TYR   0.009   0.001   TYR B 252 
 PHE   0.014   0.001   PHE B 365 
 TRP   0.008   0.001   TRP B 132 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 4600)
  covalent geometry    : angle       0.46461 ( 6300)
  SS BOND              : bond        0.00050 (    1)
  SS BOND              : angle       1.88977 (    2)
  hydrogen bonds       : bond        0.03927 (  282)
  hydrogen bonds       : angle       4.27715 (  822)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 57
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  174 GLU cc_start: 0.7774 (tt0) cc_final: 0.7549 (pt0)
REVERT: B  295 ARG cc_start: 0.7712 (ttm-80) cc_final: 0.7198 (mtp180)
REVERT: B  353 ASN cc_start: 0.7870 (m110) cc_final: 0.7132 (t0)
REVERT: B  544 ARG cc_start: 0.7221 (mtm-85) cc_final: 0.6956 (mtm-85)
  outliers start: 3
  outliers final: 2
  residues processed: 60
  average time/residue: 1.0324
  time to fit residues: 64.3594
Evaluate side-chains
  59 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 57
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  429 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3340 r_free = 0.3340 target = 0.116487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.096563 restraints weight = 14932.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 1.58
r_work: 0.2922 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 3.04 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.1435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4601  Z= 0.158
  Angle     :  0.482   4.480   6302  Z= 0.252
  Chirality :  0.037   0.131    722
  Planarity :  0.005   0.066    750
  Dihedral  :  7.049  59.091    888
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 15.72 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.49 (0.37), residues: 542
  helix:  1.27 (0.26), residues: 394
  sheet:  None (None), residues: 0
  loop :  0.47 (0.56), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 615 
 TYR   0.010   0.001   TYR B 252 
 PHE   0.014   0.001   PHE B 365 
 TRP   0.008   0.001   TRP B 132 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 4600)
  covalent geometry    : angle       0.48065 ( 6300)
  SS BOND              : bond        0.00088 (    1)
  SS BOND              : angle       2.11421 (    2)
  hydrogen bonds       : bond        0.04035 (  282)
  hydrogen bonds       : angle       4.31308 (  822)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  174 GLU cc_start: 0.7758 (tt0) cc_final: 0.7455 (pt0)
REVERT: B  226 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8171 (mt0)
REVERT: B  295 ARG cc_start: 0.7676 (ttm-80) cc_final: 0.7395 (mtm-85)
REVERT: B  353 ASN cc_start: 0.7872 (m110) cc_final: 0.7120 (t0)
REVERT: B  544 ARG cc_start: 0.7224 (mtm-85) cc_final: 0.6945 (mtm-85)
  outliers start: 3
  outliers final: 1
  residues processed: 59
  average time/residue: 1.0098
  time to fit residues: 62.0936
Evaluate side-chains
  58 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  226 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 15 optimal weight:    0.4980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.116916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.096917 restraints weight = 15057.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 1.59
r_work: 0.2958 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2854 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.1481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4601  Z= 0.140
  Angle     :  0.472   4.454   6302  Z= 0.247
  Chirality :  0.036   0.128    722
  Planarity :  0.005   0.073    750
  Dihedral  :  6.937  59.807    888
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  : 16.38 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.37), residues: 542
  helix:  1.29 (0.26), residues: 394
  sheet:  None (None), residues: 0
  loop :  0.48 (0.56), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 615 
 TYR   0.009   0.001   TYR B 252 
 PHE   0.014   0.001   PHE B 365 
 TRP   0.008   0.001   TRP B 132 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 4600)
  covalent geometry    : angle       0.47062 ( 6300)
  SS BOND              : bond        0.00118 (    1)
  SS BOND              : angle       1.97638 (    2)
  hydrogen bonds       : bond        0.03946 (  282)
  hydrogen bonds       : angle       4.28266 (  822)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  174 GLU cc_start: 0.7759 (tt0) cc_final: 0.7462 (pt0)
REVERT: B  295 ARG cc_start: 0.7690 (ttm-80) cc_final: 0.7410 (mtm-85)
REVERT: B  353 ASN cc_start: 0.7879 (m110) cc_final: 0.7133 (t0)
REVERT: B  443 ARG cc_start: 0.7487 (mtm-85) cc_final: 0.7285 (mtp180)
REVERT: B  544 ARG cc_start: 0.7235 (mtm-85) cc_final: 0.6954 (mtm-85)
  outliers start: 2
  outliers final: 1
  residues processed: 58
  average time/residue: 1.1434
  time to fit residues: 69.2108
Evaluate side-chains
  57 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  131 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 16 optimal weight:    0.3980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.117136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.097322 restraints weight = 14979.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 1.57
r_work: 0.2963 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.2861 rms_B_bonded: 3.04 restraints_weight: 0.2500
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.1517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4601  Z= 0.131
  Angle     :  0.466   4.444   6302  Z= 0.244
  Chirality :  0.036   0.128    722
  Planarity :  0.005   0.076    750
  Dihedral  :  6.840  58.996    888
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  : 16.59 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.37), residues: 542
  helix:  1.28 (0.26), residues: 396
  sheet:  None (None), residues: 0
  loop :  0.29 (0.55), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 615 
 TYR   0.009   0.001   TYR B 252 
 PHE   0.014   0.001   PHE B 365 
 TRP   0.008   0.001   TRP B 132 
 HIS   0.002   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 4600)
  covalent geometry    : angle       0.46437 ( 6300)
  SS BOND              : bond        0.00089 (    1)
  SS BOND              : angle       1.90168 (    2)
  hydrogen bonds       : bond        0.03873 (  282)
  hydrogen bonds       : angle       4.25071 (  822)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 55
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  174 GLU cc_start: 0.7794 (tt0) cc_final: 0.7491 (pt0)
REVERT: B  295 ARG cc_start: 0.7696 (ttm-80) cc_final: 0.7417 (mtm-85)
REVERT: B  353 ASN cc_start: 0.7883 (m110) cc_final: 0.7143 (t0)
REVERT: B  514 GLN cc_start: 0.7942 (pp30) cc_final: 0.7395 (pt0)
REVERT: B  544 ARG cc_start: 0.7227 (mtm-85) cc_final: 0.6943 (mtm-85)
  outliers start: 1
  outliers final: 1
  residues processed: 56
  average time/residue: 0.9197
  time to fit residues: 53.6864
Evaluate side-chains
  56 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 55
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  131 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 12 optimal weight:    0.4980
   chunk 51 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.117034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.097112 restraints weight = 15035.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 1.58
r_work: 0.2963 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2860 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.1559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4601  Z= 0.138
  Angle     :  0.470   4.459   6302  Z= 0.246
  Chirality :  0.036   0.129    722
  Planarity :  0.005   0.079    750
  Dihedral  :  6.861  58.402    888
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  : 16.59 %
    Favored  : 82.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.37), residues: 542
  helix:  1.28 (0.26), residues: 396
  sheet:  None (None), residues: 0
  loop :  0.29 (0.55), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 615 
 TYR   0.009   0.001   TYR B 252 
 PHE   0.014   0.001   PHE B 365 
 TRP   0.008   0.001   TRP B 132 
 HIS   0.002   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 4600)
  covalent geometry    : angle       0.46902 ( 6300)
  SS BOND              : bond        0.00085 (    1)
  SS BOND              : angle       1.95332 (    2)
  hydrogen bonds       : bond        0.03901 (  282)
  hydrogen bonds       : angle       4.25434 (  822)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  174 GLU cc_start: 0.7793 (tt0) cc_final: 0.7468 (pt0)
REVERT: B  295 ARG cc_start: 0.7682 (ttm-80) cc_final: 0.7406 (mtm-85)
REVERT: B  353 ASN cc_start: 0.7884 (m110) cc_final: 0.7140 (t0)
REVERT: B  544 ARG cc_start: 0.7205 (mtm-85) cc_final: 0.6927 (mtm-85)
  outliers start: 2
  outliers final: 1
  residues processed: 58
  average time/residue: 1.0990
  time to fit residues: 66.5845
Evaluate side-chains
  57 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  131 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 44 optimal weight:    0.2980
   chunk 34 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 4 optimal weight:    0.2980
   chunk 46 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0570
   chunk 36 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.4498

-------------------------------------------------------------------------------
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 = 0.3359 r_free = 0.3359 target = 0.118074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.098187 restraints weight = 14952.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 1.59
r_work: 0.2982 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.2880 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   4601  Z= 0.107
  Angle     :  0.451   4.400   6302  Z= 0.236
  Chirality :  0.035   0.127    722
  Planarity :  0.005   0.080    750
  Dihedral  :  6.601  57.424    888
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  : 16.59 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.37), residues: 542
  helix:  1.35 (0.26), residues: 397
  sheet:  None (None), residues: 0
  loop :  0.30 (0.55), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 615 
 TYR   0.008   0.001   TYR B 252 
 PHE   0.013   0.001   PHE B 365 
 TRP   0.008   0.001   TRP B 238 
 HIS   0.002   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 4600)
  covalent geometry    : angle       0.44974 ( 6300)
  SS BOND              : bond        0.00080 (    1)
  SS BOND              : angle       1.60648 (    2)
  hydrogen bonds       : bond        0.03721 (  282)
  hydrogen bonds       : angle       4.19413 (  822)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  174 GLU cc_start: 0.7780 (tt0) cc_final: 0.7540 (pt0)
REVERT: B  295 ARG cc_start: 0.7683 (ttm-80) cc_final: 0.7151 (mtp180)
REVERT: B  353 ASN cc_start: 0.7854 (m110) cc_final: 0.7135 (t0)
REVERT: B  514 GLN cc_start: 0.7941 (pp30) cc_final: 0.7395 (pt0)
REVERT: B  544 ARG cc_start: 0.7173 (mtm-85) cc_final: 0.6848 (mtm-85)
  outliers start: 1
  outliers final: 1
  residues processed: 57
  average time/residue: 1.1719
  time to fit residues: 69.4901
Evaluate side-chains
  56 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 55
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  131 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 47 optimal weight:    0.0040
   chunk 15 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.5192

-------------------------------------------------------------------------------
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 = 0.3360 r_free = 0.3360 target = 0.118174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.098372 restraints weight = 14875.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.3066 rms_B_bonded: 1.58
r_work: 0.2982 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4601  Z= 0.113
  Angle     :  0.455   4.426   6302  Z= 0.238
  Chirality :  0.036   0.187    722
  Planarity :  0.005   0.077    750
  Dihedral  :  6.572  57.058    888
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 16.16 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.58 (0.37), residues: 542
  helix:  1.38 (0.26), residues: 397
  sheet:  None (None), residues: 0
  loop :  0.33 (0.55), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 615 
 TYR   0.008   0.001   TYR B 252 
 PHE   0.013   0.001   PHE B 365 
 TRP   0.008   0.001   TRP B 238 
 HIS   0.002   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 4600)
  covalent geometry    : angle       0.45449 ( 6300)
  SS BOND              : bond        0.00045 (    1)
  SS BOND              : angle       1.63355 (    2)
  hydrogen bonds       : bond        0.03715 (  282)
  hydrogen bonds       : angle       4.17386 (  822)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2928.93 seconds
wall clock time: 50 minutes 16.83 seconds (3016.83 seconds total)