Starting phenix.real_space_refine
on Thu Jan 16 01:49:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9eo4_19845/01_2025/9eo4_19845_neut_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9eo4_19845/01_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_19845/01_2025/9eo4_19845.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9eo4_19845/01_2025/9eo4_19845.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9eo4_19845/01_2025/9eo4_19845_neut_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9eo4_19845/01_2025/9eo4_19845_neut_trim.cif"
  }
  resolution = 2.66
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.034
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 5.64, per 1000 atoms: 0.64
  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: 2.89
  Conformation dependent library (CDL) restraints added in 583.7 milliseconds
  

  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: 0.68
  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: 3.30

  Time building geometry restraints manager: 3.31 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:             5.000
  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:             0.140
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     24.340
  Find NCS groups from input model:        0.070
  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:12.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.140
-------------------------------------------------------------------------------
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   4600  Z= 0.347
  Angle     :  0.719  12.345   6300  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 (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:  1.45 (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
 TRP   0.008   0.001   TRP B 238 
 HIS   0.002   0.000   HIS B 616 
 PHE   0.013   0.001   PHE B 365 
 TYR   0.007   0.001   TYR B 575 
 ARG   0.012   0.001   ARG B 615 

*********************** 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  : 0.724 
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: 2.1879
  time to fit residues: 173.8532
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  : 0.679 
-------------------------------------------------------------------------------
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 45 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 16 optimal weight:    0.3980
   chunk 25 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0980
   overall best weight:    0.6986

-------------------------------------------------------------------------------
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 = 0.3300 r_free = 0.3300 target = 0.113888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.093780 restraints weight = 14945.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.2988 rms_B_bonded: 1.62
r_work: 0.2904 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.2803 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.0995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4600  Z= 0.207
  Angle     :  0.513   4.782   6300  Z= 0.263
  Chirality :  0.036   0.127    722
  Planarity :  0.008   0.183    750
  Dihedral  :  7.878  59.443    891
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 13.97 %
    Favored  : 84.93 %
  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:  1.44 (0.37), residues: 542
  helix:  1.12 (0.26), residues: 395
  sheet:  None (None), residues: 0
  loop :  0.81 (0.59), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 238 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.014   0.001   PHE B 365 
 TYR   0.010   0.001   TYR B 252 
 ARG   0.007   0.001   ARG B 443 

*********************** 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: 5
    poor density    : 64
  time to evaluate  : 0.633 
Fit side-chains
   revert: symmetry clash
REVERT: B  174 GLU cc_start: 0.7673 (tt0) cc_final: 0.7430 (pt0)
REVERT: B  295 ARG cc_start: 0.7609 (ttm-80) cc_final: 0.7117 (mtp180)
REVERT: B  353 ASN cc_start: 0.7781 (m110) cc_final: 0.7019 (t0)
REVERT: B  443 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6713 (mtm-85)
REVERT: B  483 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.8356 (p)
REVERT: B  544 ARG cc_start: 0.7147 (mtm-85) cc_final: 0.6885 (mtm-85)
  outliers start: 5
  outliers final: 2
  residues processed: 67
  average time/residue: 2.0959
  time to fit residues: 147.4629
Evaluate side-chains
  65 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  443 ARG
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 52 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 43 optimal weight:    0.3980
   chunk 1 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   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 = 0.3298 r_free = 0.3298 target = 0.113655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.093322 restraints weight = 15121.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 1.63
r_work: 0.2895 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2792 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.1257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4600  Z= 0.214
  Angle     :  0.485   4.464   6300  Z= 0.255
  Chirality :  0.036   0.129    722
  Planarity :  0.005   0.061    750
  Dihedral  :  7.376  59.745    890
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 14.63 %
    Favored  : 84.06 %
  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:  1.49 (0.37), residues: 542
  helix:  1.22 (0.26), residues: 394
  sheet:  None (None), residues: 0
  loop :  0.63 (0.58), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 238 
 HIS   0.007   0.001   HIS B 225 
 PHE   0.014   0.001   PHE B 365 
 TYR   0.009   0.001   TYR B 252 
 ARG   0.006   0.001   ARG B 615 

*********************** 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
  62 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.680 
Fit side-chains
   revert: symmetry clash
REVERT: B  174 GLU cc_start: 0.7781 (tt0) cc_final: 0.7516 (pt0)
REVERT: B  295 ARG cc_start: 0.7659 (ttm-80) cc_final: 0.7141 (mtp180)
REVERT: B  353 ASN cc_start: 0.7865 (m110) cc_final: 0.7087 (t0)
REVERT: B  443 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6894 (mtm-85)
REVERT: B  483 SER cc_start: 0.8561 (OUTLIER) cc_final: 0.8354 (p)
REVERT: B  544 ARG cc_start: 0.7207 (mtm-85) cc_final: 0.6931 (mtm-85)
  outliers start: 6
  outliers final: 2
  residues processed: 61
  average time/residue: 2.3254
  time to fit residues: 148.2471
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  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  443 ARG
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 39 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3336 r_free = 0.3336 target = 0.116053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.096215 restraints weight = 14924.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3032 rms_B_bonded: 1.56
r_work: 0.2948 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.1401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4600  Z= 0.235
  Angle     :  0.488   4.484   6300  Z= 0.255
  Chirality :  0.037   0.132    722
  Planarity :  0.005   0.058    750
  Dihedral  :  7.265  59.794    890
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 14.85 %
    Favored  : 84.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.37), residues: 542
  helix:  1.20 (0.26), residues: 394
  sheet:  None (None), residues: 0
  loop :  0.53 (0.57), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 132 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.014   0.001   PHE B 365 
 TYR   0.010   0.001   TYR B 252 
 ARG   0.007   0.001   ARG B 615 

*********************** 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
  63 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  174 GLU cc_start: 0.7746 (tt0) cc_final: 0.7491 (pt0)
REVERT: B  295 ARG cc_start: 0.7647 (ttm-80) cc_final: 0.7112 (mtp180)
REVERT: B  353 ASN cc_start: 0.7852 (m110) cc_final: 0.7076 (t0)
REVERT: B  443 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6872 (mtp-110)
REVERT: B  544 ARG cc_start: 0.7206 (mtm-85) cc_final: 0.6930 (mtm-85)
  outliers start: 5
  outliers final: 2
  residues processed: 62
  average time/residue: 2.4062
  time to fit residues: 155.6428
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  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  443 ARG
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 42 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 30 optimal weight:    0.1980
   chunk 32 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0980
   chunk 41 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   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 = 0.3353 r_free = 0.3353 target = 0.117471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.097637 restraints weight = 14865.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 1.59
r_work: 0.2972 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2869 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.1469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   4600  Z= 0.162
  Angle     :  0.454   4.415   6300  Z= 0.238
  Chirality :  0.035   0.124    722
  Planarity :  0.005   0.065    750
  Dihedral  :  6.786  59.355    889
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 15.28 %
    Favored  : 83.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.37), residues: 542
  helix:  1.36 (0.26), residues: 394
  sheet:  None (None), residues: 0
  loop :  0.61 (0.57), residues: 148

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

*********************** 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
  61 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  174 GLU cc_start: 0.7766 (tt0) cc_final: 0.7525 (pt0)
REVERT: B  295 ARG cc_start: 0.7679 (ttm-80) cc_final: 0.7158 (mtp180)
REVERT: B  353 ASN cc_start: 0.7833 (m110) cc_final: 0.7099 (t0)
REVERT: B  443 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.6838 (mtm-85)
REVERT: B  514 GLN cc_start: 0.7926 (pp30) cc_final: 0.7390 (pt0)
REVERT: B  544 ARG cc_start: 0.7203 (mtm-85) cc_final: 0.6936 (mtm-85)
  outliers start: 4
  outliers final: 2
  residues processed: 60
  average time/residue: 2.4732
  time to fit residues: 154.8446
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  : 0.694 
-------------------------------------------------------------------------------
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  443 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3338 r_free = 0.3338 target = 0.116387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.096494 restraints weight = 14879.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 1.58
r_work: 0.2954 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.2852 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.1525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4600  Z= 0.224
  Angle     :  0.474   4.496   6300  Z= 0.248
  Chirality :  0.036   0.130    722
  Planarity :  0.005   0.067    750
  Dihedral  :  6.938  59.643    888
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 15.28 %
    Favored  : 83.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.37), residues: 542
  helix:  1.33 (0.26), residues: 394
  sheet:  None (None), residues: 0
  loop :  0.54 (0.56), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 132 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.014   0.001   PHE B 365 
 TYR   0.009   0.001   TYR B 252 
 ARG   0.008   0.001   ARG B 615 

*********************** 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
  60 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.717 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  174 GLU cc_start: 0.7785 (tt0) cc_final: 0.7527 (pt0)
REVERT: B  295 ARG cc_start: 0.7698 (ttm-80) cc_final: 0.7423 (mtm-85)
REVERT: B  353 ASN cc_start: 0.7876 (m110) cc_final: 0.7133 (t0)
REVERT: B  443 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6829 (mtm-85)
REVERT: B  544 ARG cc_start: 0.7227 (mtm-85) cc_final: 0.6949 (mtm-85)
  outliers start: 4
  outliers final: 1
  residues processed: 59
  average time/residue: 2.5217
  time to fit residues: 154.9265
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  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  443 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 16 optimal weight:    0.1980
   chunk 43 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.117181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.097310 restraints weight = 15066.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.2991 rms_B_bonded: 1.58
r_work: 0.2904 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.2800 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4600  Z= 0.187
  Angle     :  0.459   4.452   6300  Z= 0.241
  Chirality :  0.036   0.126    722
  Planarity :  0.005   0.072    750
  Dihedral  :  6.757  58.963    888
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 15.50 %
    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 (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:  1.57 (0.37), residues: 542
  helix:  1.36 (0.26), residues: 396
  sheet:  None (None), residues: 0
  loop :  0.39 (0.55), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 238 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.013   0.001   PHE B 365 
 TYR   0.009   0.001   TYR B 252 
 ARG   0.010   0.001   ARG B 615 

*********************** 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
  62 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.634 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  174 GLU cc_start: 0.7765 (tt0) cc_final: 0.7391 (pt0)
REVERT: B  295 ARG cc_start: 0.7592 (ttm-80) cc_final: 0.7026 (mtp180)
REVERT: B  353 ASN cc_start: 0.7755 (m110) cc_final: 0.6982 (t0)
REVERT: B  443 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.6765 (mtm-85)
REVERT: B  514 GLN cc_start: 0.7878 (pp30) cc_final: 0.7334 (pt0)
REVERT: B  544 ARG cc_start: 0.7133 (mtm-85) cc_final: 0.6826 (mtm-85)
  outliers start: 4
  outliers final: 2
  residues processed: 61
  average time/residue: 2.4036
  time to fit residues: 153.1255
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  : 0.686 
-------------------------------------------------------------------------------
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  443 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.3980
   chunk 25 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 226 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.116921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.097019 restraints weight = 15177.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3017 rms_B_bonded: 1.59
r_work: 0.2932 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2828 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.1596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4600  Z= 0.201
  Angle     :  0.464   4.459   6300  Z= 0.243
  Chirality :  0.036   0.127    722
  Planarity :  0.005   0.076    750
  Dihedral  :  6.803  58.583    888
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 15.28 %
    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 (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:  1.54 (0.37), residues: 542
  helix:  1.34 (0.26), residues: 396
  sheet:  None (None), residues: 0
  loop :  0.36 (0.55), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 132 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.014   0.001   PHE B 365 
 TYR   0.009   0.001   TYR B 252 
 ARG   0.011   0.001   ARG B 615 

*********************** 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
  62 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  174 GLU cc_start: 0.7767 (tt0) cc_final: 0.7413 (pt0)
REVERT: B  295 ARG cc_start: 0.7624 (ttm-80) cc_final: 0.7340 (mtm-85)
REVERT: B  353 ASN cc_start: 0.7813 (m110) cc_final: 0.7050 (t0)
REVERT: B  443 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6787 (mtm-85)
REVERT: B  544 ARG cc_start: 0.7171 (mtm-85) cc_final: 0.6872 (mtm-85)
  outliers start: 5
  outliers final: 3
  residues processed: 61
  average time/residue: 2.3429
  time to fit residues: 149.2612
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  : 0.689 
-------------------------------------------------------------------------------
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  443 ARG
Chi-restraints excluded: chain B residue  453 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 4 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 24 optimal weight:    0.4980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3342 r_free = 0.3342 target = 0.116843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.097071 restraints weight = 15054.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3017 rms_B_bonded: 1.57
r_work: 0.2931 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.2828 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.1639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4600  Z= 0.199
  Angle     :  0.466   4.456   6300  Z= 0.244
  Chirality :  0.036   0.138    722
  Planarity :  0.005   0.078    750
  Dihedral  :  6.794  57.835    888
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 15.94 %
    Favored  : 83.41 %
  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:  1.55 (0.37), residues: 542
  helix:  1.35 (0.26), residues: 396
  sheet:  None (None), residues: 0
  loop :  0.37 (0.55), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 132 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.014   0.001   PHE B 365 
 TYR   0.009   0.001   TYR B 252 
 ARG   0.012   0.001   ARG B 615 

*********************** 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
  59 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  174 GLU cc_start: 0.7785 (tt0) cc_final: 0.7442 (pt0)
REVERT: B  295 ARG cc_start: 0.7589 (ttm-80) cc_final: 0.7134 (mtp180)
REVERT: B  353 ASN cc_start: 0.7771 (m110) cc_final: 0.6996 (t0)
REVERT: B  443 ARG cc_start: 0.7146 (ptt180) cc_final: 0.6758 (mtm-85)
REVERT: B  544 ARG cc_start: 0.7129 (mtm-85) cc_final: 0.6836 (mtm-85)
  outliers start: 3
  outliers final: 3
  residues processed: 59
  average time/residue: 2.1817
  time to fit residues: 135.0759
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  : 0.720 
-------------------------------------------------------------------------------
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  453 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 0 optimal weight:    0.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3343 r_free = 0.3343 target = 0.116905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.097152 restraints weight = 15076.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.3014 rms_B_bonded: 1.58
r_work: 0.2929 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.2825 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.1655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4600  Z= 0.192
  Angle     :  0.463   4.453   6300  Z= 0.242
  Chirality :  0.036   0.126    722
  Planarity :  0.005   0.079    750
  Dihedral  :  6.763  57.397    888
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 15.50 %
    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 (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:  1.56 (0.37), residues: 542
  helix:  1.36 (0.26), residues: 396
  sheet:  None (None), residues: 0
  loop :  0.38 (0.55), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 132 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.013   0.001   PHE B 365 
 TYR   0.009   0.001   TYR B 252 
 ARG   0.014   0.001   ARG B 615 

********************** 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
  60 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  174 GLU cc_start: 0.7794 (tt0) cc_final: 0.7425 (pt0)
REVERT: B  295 ARG cc_start: 0.7632 (ttm-80) cc_final: 0.7188 (mtp180)
REVERT: B  353 ASN cc_start: 0.7819 (m110) cc_final: 0.7061 (t0)
REVERT: B  443 ARG cc_start: 0.7169 (ptt180) cc_final: 0.6805 (mtm-85)
REVERT: B  544 ARG cc_start: 0.7160 (mtm-85) cc_final: 0.6821 (mtm-85)
  outliers start: 4
  outliers final: 3
  residues processed: 60
  average time/residue: 2.2396
  time to fit residues: 140.9168
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  : 0.716 
-------------------------------------------------------------------------------
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  453 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0570
   chunk 22 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.6298

-------------------------------------------------------------------------------
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 = 0.117178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.097388 restraints weight = 15068.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.2970 rms_B_bonded: 1.57
r_work: 0.2883 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.2777 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.1673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4600  Z= 0.185
  Angle     :  0.461   4.441   6300  Z= 0.242
  Chirality :  0.036   0.149    722
  Planarity :  0.005   0.078    750
  Dihedral  :  6.711  56.921    888
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  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 (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:  1.59 (0.37), residues: 542
  helix:  1.38 (0.26), residues: 396
  sheet:  None (None), residues: 0
  loop :  0.39 (0.55), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 238 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.013   0.001   PHE B 365 
 TYR   0.009   0.001   TYR B 252 
 ARG   0.013   0.001   ARG B 615 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6327.53 seconds
wall clock time: 112 minutes 21.80 seconds (6741.80 seconds total)