Starting phenix.real_space_refine
on Thu Jul  2 00:42:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wrt_37789/07_2026/8wrt_37789.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wrt_37789/07_2026/8wrt_37789.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.31
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wrt_37789/07_2026/8wrt_37789.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wrt_37789/07_2026/8wrt_37789.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wrt_37789/07_2026/8wrt_37789.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wrt_37789/07_2026/8wrt_37789.map"
  }
  resolution = 3.31
  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=   0.017
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: 5
    Type Number    sf(0)   Gaussians
     P      26      5.49       5
     S       8      5.16       5
     C    2954      2.51       5
     N     884      2.21       5
     O     940      1.98       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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4812
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4267
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 530, 4267
          Classifications: {'peptide': 530}
          Link IDs: {'PTRANS': 35, 'TRANS': 494}
          Chain breaks: 7
    Chain: "B"
      Number of atoms: 545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 545
          Classifications: {'RNA': 26}
          Modifications used: {'rna2p_pyr': 5, 'rna3p_pur': 9, 'rna3p_pyr': 12}
          Link IDs: {'rna2p': 5, 'rna3p': 20}
  Time building chain proxies: 1.17, per 1000 atoms: 0.24
  Number of scatterers: 4812
  At special positions: 0
  Unit cell: (76.56, 85.14, 108.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       8     16.00
     P      26     15.00
     O     940      8.00
     N     884      7.00
     C    2954      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.42
  Conformation dependent library (CDL) restraints added in 152.3 milliseconds
  

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  990

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 2 sheets defined
      48.7% alpha, 7.7% beta
      3 base pairs and 13 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 71 through 74
    Processing helix  chain 'A' and resid 75 through 87
      removed outlier: 3.696A  pdb=" N   GLY A  83 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   GLN A  85 " --> pdb=" O   SER A  81 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   TYR A  87 " --> pdb=" O   GLY A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 99
      removed outlier: 3.838A  pdb=" N   GLU A  97 " --> pdb=" O   ALA A  93 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ALA A  98 " --> pdb=" O   ALA A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 117
      removed outlier: 3.567A  pdb=" N   LEU A 109 " --> pdb=" O   SER A 105 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ASP A 110 " --> pdb=" O   ARG A 106 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   PHE A 113 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA A 114 " --> pdb=" O   ASP A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 169
      removed outlier: 3.575A  pdb=" N   LEU A 133 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   HIS A 135 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   THR A 136 " --> pdb=" O   ILE A 132 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ILE A 144 " --> pdb=" O   TYR A 140 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ARG A 160 " --> pdb=" O   SER A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 205
    Processing helix  chain 'A' and resid 234 through 238
      removed outlier: 3.844A  pdb=" N   ILE A 238 " --> pdb=" O   ARG A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 254
      removed outlier: 3.524A  pdb=" N   HIS A 253 " --> pdb=" O   GLN A 250 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   LEU A 254 " --> pdb=" O   ARG A 251 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 250 through 254'
    Processing helix  chain 'A' and resid 272 through 278
      removed outlier: 3.925A  pdb=" N   ARG A 276 " --> pdb=" O   ARG A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 319
      removed outlier: 3.556A  pdb=" N   ALA A 315 " --> pdb=" O   GLY A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 335
      removed outlier: 3.804A  pdb=" N   PHE A 335 " --> pdb=" O   LEU A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 451
      removed outlier: 3.807A  pdb=" N   THR A 439 " --> pdb=" O   ALA A 435 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLU A 441 " --> pdb=" O   ASP A 437 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   GLN A 442 " --> pdb=" O   ALA A 438 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLU A 446 " --> pdb=" O   GLN A 442 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE A 448 " --> pdb=" O   LYS A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 464
      removed outlier: 4.184A  pdb=" N   GLU A 458 " --> pdb=" O   GLU A 454 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   VAL A 459 " --> pdb=" O   CYS A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 478
      removed outlier: 3.527A  pdb=" N   LEU A 475 " --> pdb=" O   LYS A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 503
      removed outlier: 3.881A  pdb=" N   SER A 496 " --> pdb=" O   THR A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 556
      removed outlier: 3.637A  pdb=" N   ALA A 546 " --> pdb=" O   GLU A 542 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ASP A 549 " --> pdb=" O   LYS A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 558 through 587
      removed outlier: 3.510A  pdb=" N   VAL A 562 " --> pdb=" O   SER A 558 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 613 through 619
      removed outlier: 3.931A  pdb=" N   PHE A 617 " --> pdb=" O   GLY A 613 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   PHE A 618 " --> pdb=" O   TRP A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 641
      removed outlier: 4.096A  pdb=" N   ALA A 639 " --> pdb=" O   PHE A 635 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   LEU A 640 " --> pdb=" O   SER A 636 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 199
      removed outlier: 4.476A  pdb=" N   ASN A  64 " --> pdb=" O   ASP A 308 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   VAL A 306 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
      removed outlier: 5.159A  pdb=" N   GLN A  68 " --> pdb=" O   TRP A 304 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   TRP A 304 " --> pdb=" O   GLN A  68 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 415 through 419
      removed outlier: 6.112A  pdb=" N   PHE A 401 " --> pdb=" O   LEU A 416 " (cutoff:3.500A)
      removed outlier: 4.838A  pdb=" N   GLN A 418 " --> pdb=" O   ALA A 399 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   ALA A 399 " --> pdb=" O   GLN A 418 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLU A 400 " --> pdb=" O   ALA A 388 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ALA A 388 " --> pdb=" O   GLU A 400 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   GLY A 385 " --> pdb=" O   ALA A 593 " (cutoff:3.500A)

    173 hydrogen bonds defined for protein.
    492 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      7 hydrogen bonds
      14 hydrogen bond angles
      0 basepair planarities
      3 basepair parallelities
      13 stacking parallelities
  Total time for adding SS restraints: 0.63

  Time building geometry restraints manager: 0.55 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1337
        1.33 -     1.45: 911
        1.45 -     1.57: 2659
        1.57 -     1.69: 51
        1.69 -     1.81: 11
  Bond restraints: 4969
  Sorted by residual:
  bond pdb=" C   ARG A 536 "
       pdb=" N   PRO A 537 "
    ideal  model  delta    sigma   weight residual
    1.330  1.359 -0.029 1.22e-02 6.72e+03 5.51e+00
  bond pdb=" CA  ARG A 536 "
       pdb=" C   ARG A 536 "
    ideal  model  delta    sigma   weight residual
    1.523  1.550 -0.027 1.19e-02 7.06e+03 4.96e+00
  bond pdb=" CA  HIS A 214 "
       pdb=" C   HIS A 214 "
    ideal  model  delta    sigma   weight residual
    1.524  1.549 -0.025 1.26e-02 6.30e+03 4.04e+00
  bond pdb=" C   LEU A 228 "
       pdb=" N   PRO A 229 "
    ideal  model  delta    sigma   weight residual
    1.329  1.354 -0.025 1.25e-02 6.40e+03 3.85e+00
  bond pdb=" C   SER A 466 "
       pdb=" O   SER A 466 "
    ideal  model  delta    sigma   weight residual
    1.235  1.217  0.019 1.26e-02 6.30e+03 2.18e+00
  ... (remaining 4964 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 6610
        1.90 -     3.79: 194
        3.79 -     5.69: 28
        5.69 -     7.59: 4
        7.59 -     9.49: 2
  Bond angle restraints: 6838
  Sorted by residual:
  angle pdb=" N   ARG A 406 "
        pdb=" CA  ARG A 406 "
        pdb=" C   ARG A 406 "
      ideal   model   delta    sigma   weight residual
     110.50  116.12   -5.62 1.41e+00 5.03e-01 1.59e+01
  angle pdb=" N   ARG A 251 "
        pdb=" CA  ARG A 251 "
        pdb=" C   ARG A 251 "
      ideal   model   delta    sigma   weight residual
     112.75  117.98   -5.23 1.36e+00 5.41e-01 1.48e+01
  angle pdb=" C   ASN A 195 "
        pdb=" N   PRO A 196 "
        pdb=" CA  PRO A 196 "
      ideal   model   delta    sigma   weight residual
     119.84  115.57    4.27 1.25e+00 6.40e-01 1.17e+01
  angle pdb=" CA  PRO A 239 "
        pdb=" N   PRO A 239 "
        pdb=" CD  PRO A 239 "
      ideal   model   delta    sigma   weight residual
     112.00  107.23    4.77 1.40e+00 5.10e-01 1.16e+01
  angle pdb=" N   PRO A 192 "
        pdb=" CA  PRO A 192 "
        pdb=" C   PRO A 192 "
      ideal   model   delta    sigma   weight residual
     111.21  116.23   -5.02 1.59e+00 3.96e-01 9.96e+00
  ... (remaining 6833 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.27: 2936
       35.27 -    70.53: 120
       70.53 -   105.80: 15
      105.80 -   141.06: 0
      141.06 -   176.33: 3
  Dihedral angle restraints: 3074
    sinusoidal: 1549
      harmonic: 1525
  Sorted by residual:
  dihedral pdb=" O4'   U B  -9 "
           pdb=" C1'   U B  -9 "
           pdb=" N1    U B  -9 "
           pdb=" C2    U B  -9 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   48.33 -176.33     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   C B  -8 "
           pdb=" C1'   C B  -8 "
           pdb=" N1    C B  -8 "
           pdb=" C2    C B  -8 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -47.56  -80.44     1      1.70e+01 3.46e-03 2.77e+01
  dihedral pdb=" C4'   C B  -8 "
           pdb=" C3'   C B  -8 "
           pdb=" O3'   C B  -8 "
           pdb=" P     G B  -7 "
      ideal   model   delta sinusoidal    sigma   weight residual
     250.00   74.08  175.92     1      3.50e+01 8.16e-04 1.57e+01
  ... (remaining 3071 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 650
       0.060 -    0.119: 102
       0.119 -    0.179: 12
       0.179 -    0.239: 3
       0.239 -    0.299: 1
  Chirality restraints: 768
  Sorted by residual:
  chirality pdb=" CA  ARG A 251 "
            pdb=" N   ARG A 251 "
            pdb=" C   ARG A 251 "
            pdb=" CB  ARG A 251 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.23e+00
  chirality pdb=" CA  ALA A 216 "
            pdb=" N   ALA A 216 "
            pdb=" C   ALA A 216 "
            pdb=" CB  ALA A 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.27    0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CA  PRO A 218 "
            pdb=" N   PRO A 218 "
            pdb=" C   PRO A 218 "
            pdb=" CB  PRO A 218 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.51    0.21 2.00e-01 2.50e+01 1.09e+00
  ... (remaining 765 not shown)

  Planarity restraints: 785
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 238 "   -0.091 5.00e-02 4.00e+02   1.36e-01 2.96e+01
        pdb=" N   PRO A 239 "    0.235 5.00e-02 4.00e+02
        pdb=" CA  PRO A 239 "   -0.075 5.00e-02 4.00e+02
        pdb=" CD  PRO A 239 "   -0.069 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 214 "    0.056 5.00e-02 4.00e+02   8.43e-02 1.14e+01
        pdb=" N   PRO A 215 "   -0.146 5.00e-02 4.00e+02
        pdb=" CA  PRO A 215 "    0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 215 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 273 "    0.031 5.00e-02 4.00e+02   4.65e-02 3.46e+00
        pdb=" N   PRO A 274 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 274 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 274 "    0.026 5.00e-02 4.00e+02
  ... (remaining 782 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1280
        2.81 -     3.33: 4515
        3.33 -     3.85: 7720
        3.85 -     4.38: 8885
        4.38 -     4.90: 14148
  Nonbonded interactions: 36548
  Sorted by model distance:
  nonbonded pdb=" O2'   C B   0 "
            pdb=" OP1   C B   2 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" NH2 ARG A 139 "
            pdb=" O3'   C B   4 "
     model   vdw
     2.333 3.120
  nonbonded pdb=" O   THR A 583 "
            pdb=" OG1 THR A 587 "
     model   vdw
     2.412 3.040
  nonbonded pdb=" O   LEU A 416 "
            pdb=" NE1 TRP A 586 "
     model   vdw
     2.426 3.120
  nonbonded pdb=" O   VAL A 547 "
            pdb=" OG1 THR A 551 "
     model   vdw
     2.449 3.040
  ... (remaining 36543 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             5.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     6.140
  Find NCS groups from input model:        0.020
  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:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6124
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   4969  Z= 0.200
  Angle     :  0.744   9.487   6838  Z= 0.462
  Chirality :  0.046   0.299    768
  Planarity :  0.008   0.136    785
  Dihedral  : 18.166 176.326   2084
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  1.75 %
    Favored  : 97.81 %
  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 are not related in a simple way.
  whole: -0.94 (0.36), residues: 514
  helix:  0.11 (0.33), residues: 211
  sheet: -2.37 (0.66), residues: 54
  loop : -0.74 (0.40), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 262 
 TYR   0.011   0.001   TYR A 578 
 PHE   0.015   0.002   PHE A 335 
 TRP   0.018   0.001   TRP A 626 
 HIS   0.004   0.001   HIS A 632 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.20 ( 4969)
  covalent geometry    : angle       0.74409 /  0.46 ( 6838)
  hydrogen bonds       : bond        0.25320 / 18.17 (  180)
  hydrogen bonds       : angle       8.40816 /  6.16 (  506)

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

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

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 73
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 ARG cc_start: 0.7323 (tmt-80) cc_final: 0.6837 (tpt170)
REVERT: A  308 ASP cc_start: 0.6394 (m-30) cc_final: 0.6101 (m-30)
REVERT: A  371 LYS cc_start: 0.6434 (mppt) cc_final: 0.6008 (tmtt)
REVERT: A  571 LEU cc_start: 0.7001 (mt) cc_final: 0.6799 (mt)
  outliers start: 2
  outliers final: 1
  residues processed: 74
  average time/residue: 0.1208
  time to fit residues: 10.4574
Evaluate side-chains
  68 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 67
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 214 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.183793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.161067 restraints weight = 7809.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.4071 rms_B_bonded: 2.45
r_work: 0.3945 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6489
moved from start:          0.1527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4969  Z= 0.208
  Angle     :  0.681   6.172   6838  Z= 0.362
  Chirality :  0.046   0.212    768
  Planarity :  0.007   0.089    785
  Dihedral  : 20.778 179.588   1006
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  9.43 %
    Favored  : 90.13 %
  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 are not related in a simple way.
  whole: -0.81 (0.36), residues: 514
  helix:  0.15 (0.32), residues: 217
  sheet: -2.33 (0.66), residues: 51
  loop : -0.64 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 251 
 TYR   0.026   0.003   TYR A 123 
 PHE   0.022   0.002   PHE A 335 
 TRP   0.013   0.002   TRP A 112 
 HIS   0.008   0.002   HIS A 641 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00444 /  0.21 ( 4969)
  covalent geometry    : angle       0.68113 /  0.36 ( 6838)
  hydrogen bonds       : bond        0.06592 /  4.48 (  180)
  hydrogen bonds       : angle       5.33462 /  3.79 (  506)

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

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

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
REVERT: A  308 ASP cc_start: 0.6952 (m-30) cc_final: 0.6616 (m-30)
REVERT: A  371 LYS cc_start: 0.6787 (mppt) cc_final: 0.6023 (tmtt)
REVERT: A  441 GLU cc_start: 0.7572 (mp0) cc_final: 0.7368 (mp0)
REVERT: A  578 TYR cc_start: 0.6381 (t80) cc_final: 0.6068 (t80)
  outliers start: 2
  outliers final: 2
  residues processed: 72
  average time/residue: 0.1041
  time to fit residues: 8.8431
Evaluate side-chains
  67 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  631 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 20 optimal weight:    0.1980
   chunk 48 optimal weight:    0.9980
   chunk 17 optimal weight:    0.1980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 250 GLN
A 253 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.183388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.161233 restraints weight = 7630.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.4079 rms_B_bonded: 2.38
r_work: 0.3954 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6487
moved from start:          0.2116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4969  Z= 0.159
  Angle     :  0.601   5.693   6838  Z= 0.318
  Chirality :  0.043   0.208    768
  Planarity :  0.006   0.065    785
  Dihedral  : 20.720 178.613   1004
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 12.94 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.37), residues: 514
  helix:  0.59 (0.33), residues: 218
  sheet: -2.25 (0.62), residues: 56
  loop : -0.56 (0.42), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 262 
 TYR   0.024   0.002   TYR A 432 
 PHE   0.021   0.002   PHE A 102 
 TRP   0.017   0.002   TRP A 436 
 HIS   0.009   0.002   HIS A 641 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.16 ( 4969)
  covalent geometry    : angle       0.60056 /  0.32 ( 6838)
  hydrogen bonds       : bond        0.05047 /  3.42 (  180)
  hydrogen bonds       : angle       4.66686 /  3.31 (  506)

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

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

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 ARG cc_start: 0.7349 (tmt-80) cc_final: 0.6978 (tpt170)
REVERT: A  166 GLU cc_start: 0.6878 (tm-30) cc_final: 0.6377 (tm-30)
REVERT: A  308 ASP cc_start: 0.6980 (m-30) cc_final: 0.6643 (m-30)
REVERT: A  371 LYS cc_start: 0.6816 (mppt) cc_final: 0.6031 (tmtt)
REVERT: A  444 LYS cc_start: 0.8278 (tmmt) cc_final: 0.8037 (tmmt)
REVERT: A  578 TYR cc_start: 0.6424 (t80) cc_final: 0.6133 (t80)
  outliers start: 10
  outliers final: 4
  residues processed: 71
  average time/residue: 0.1061
  time to fit residues: 8.7879
Evaluate side-chains
  68 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  405 LYS
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  631 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0980
   chunk 42 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0870
   chunk 25 optimal weight:    0.9990
   chunk 18 optimal weight:    0.1980
   chunk 52 optimal weight:    0.0870
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.2736

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 250 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.184764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.162550 restraints weight = 7686.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.4094 rms_B_bonded: 2.39
r_work: 0.3967 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6458
moved from start:          0.2290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4969  Z= 0.124
  Angle     :  0.563   5.752   6838  Z= 0.298
  Chirality :  0.042   0.199    768
  Planarity :  0.005   0.057    785
  Dihedral  : 20.662 177.907   1004
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 15.57 %
    Favored  : 82.89 %
  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 are not related in a simple way.
  whole: -0.31 (0.37), residues: 514
  helix:  0.79 (0.34), residues: 218
  sheet: -2.11 (0.62), residues: 56
  loop : -0.55 (0.42), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 262 
 TYR   0.023   0.002   TYR A 432 
 PHE   0.022   0.001   PHE A 102 
 TRP   0.020   0.002   TRP A 614 
 HIS   0.007   0.001   HIS A 641 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.12 ( 4969)
  covalent geometry    : angle       0.56252 /  0.30 ( 6838)
  hydrogen bonds       : bond        0.04307 /  2.84 (  180)
  hydrogen bonds       : angle       4.29021 /  3.04 (  506)

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

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

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 ARG cc_start: 0.7338 (tmt-80) cc_final: 0.6916 (tpt90)
REVERT: A  166 GLU cc_start: 0.6800 (tm-30) cc_final: 0.6299 (tm-30)
REVERT: A  277 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7416 (mttt)
REVERT: A  308 ASP cc_start: 0.6967 (m-30) cc_final: 0.6652 (m-30)
REVERT: A  371 LYS cc_start: 0.6807 (mppt) cc_final: 0.6055 (tmtt)
REVERT: A  578 TYR cc_start: 0.6437 (t80) cc_final: 0.6124 (t80)
  outliers start: 7
  outliers final: 4
  residues processed: 67
  average time/residue: 0.1151
  time to fit residues: 9.0303
Evaluate side-chains
  68 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 LYS
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  405 LYS
Chi-restraints excluded: chain A residue  631 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 22 optimal weight:    0.2980
   chunk 37 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 1 optimal weight:    0.4980
   chunk 6 optimal weight:    0.0470
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.4278

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 250 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.184126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.161856 restraints weight = 7735.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.4078 rms_B_bonded: 2.41
r_work: 0.3957 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6472
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4969  Z= 0.139
  Angle     :  0.567   5.708   6838  Z= 0.299
  Chirality :  0.042   0.204    768
  Planarity :  0.005   0.053    785
  Dihedral  : 20.622 177.517   1004
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 17.54 %
    Favored  : 80.92 %
  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 are not related in a simple way.
  whole: -0.23 (0.37), residues: 514
  helix:  0.89 (0.33), residues: 224
  sheet: -2.05 (0.63), residues: 56
  loop : -0.60 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 262 
 TYR   0.019   0.002   TYR A 432 
 PHE   0.019   0.001   PHE A 102 
 TRP   0.021   0.002   TRP A 485 
 HIS   0.009   0.001   HIS A 641 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.14 ( 4969)
  covalent geometry    : angle       0.56701 /  0.30 ( 6838)
  hydrogen bonds       : bond        0.04169 /  2.76 (  180)
  hydrogen bonds       : angle       4.18402 /  2.95 (  506)

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

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

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 ARG cc_start: 0.7364 (tmt-80) cc_final: 0.6963 (tpt170)
REVERT: A  277 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7442 (mttt)
REVERT: A  308 ASP cc_start: 0.6989 (m-30) cc_final: 0.6641 (m-30)
REVERT: A  371 LYS cc_start: 0.6819 (mppt) cc_final: 0.6037 (tmtt)
REVERT: A  441 GLU cc_start: 0.7816 (mp0) cc_final: 0.7592 (mp0)
REVERT: A  485 TRP cc_start: 0.5200 (OUTLIER) cc_final: 0.4888 (t-100)
REVERT: A  578 TYR cc_start: 0.6435 (t80) cc_final: 0.6096 (t80)
  outliers start: 7
  outliers final: 4
  residues processed: 72
  average time/residue: 0.1001
  time to fit residues: 8.4680
Evaluate side-chains
  71 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 LYS
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  405 LYS
Chi-restraints excluded: chain A residue  485 TRP
Chi-restraints excluded: chain A residue  631 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 4 optimal weight:    0.0870
   chunk 5 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 30 optimal weight:    0.4980
   chunk 33 optimal weight:    0.0980
   chunk 41 optimal weight:    0.3980
   chunk 48 optimal weight:    0.1980
   chunk 6 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.2558

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 250 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.184915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.162479 restraints weight = 7793.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.4089 rms_B_bonded: 2.43
r_work: 0.3964 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6459
moved from start:          0.2637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4969  Z= 0.116
  Angle     :  0.556   7.990   6838  Z= 0.289
  Chirality :  0.041   0.197    768
  Planarity :  0.005   0.051    785
  Dihedral  : 20.584 177.472   1004
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 17.32 %
    Favored  : 81.14 %
  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 are not related in a simple way.
  whole: -0.08 (0.38), residues: 514
  helix:  0.98 (0.34), residues: 223
  sheet: -1.89 (0.64), residues: 56
  loop : -0.50 (0.44), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 262 
 TYR   0.021   0.002   TYR A 432 
 PHE   0.017   0.001   PHE A 102 
 TRP   0.029   0.002   TRP A 485 
 HIS   0.008   0.001   HIS A 641 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.12 ( 4969)
  covalent geometry    : angle       0.55554 /  0.29 ( 6838)
  hydrogen bonds       : bond        0.03823 /  2.54 (  180)
  hydrogen bonds       : angle       4.01862 /  2.82 (  506)

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

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

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 ARG cc_start: 0.7285 (tmt-80) cc_final: 0.6914 (tpt170)
REVERT: A  277 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7413 (mttt)
REVERT: A  308 ASP cc_start: 0.6946 (m-30) cc_final: 0.6637 (m-30)
REVERT: A  371 LYS cc_start: 0.6844 (mppt) cc_final: 0.6024 (tmtt)
REVERT: A  441 GLU cc_start: 0.7880 (mp0) cc_final: 0.7637 (mp0)
REVERT: A  578 TYR cc_start: 0.6405 (t80) cc_final: 0.6093 (t80)
REVERT: A  633 LYS cc_start: 0.6389 (ptmm) cc_final: 0.5900 (tptp)
  outliers start: 7
  outliers final: 4
  residues processed: 64
  average time/residue: 0.1096
  time to fit residues: 8.2619
Evaluate side-chains
  66 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 LYS
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  601 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0070
   overall best weight:    0.6600

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 250 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.183104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.161440 restraints weight = 7635.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.4075 rms_B_bonded: 2.30
r_work: 0.3957 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6498
moved from start:          0.2850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4969  Z= 0.178
  Angle     :  0.611   7.921   6838  Z= 0.319
  Chirality :  0.043   0.211    768
  Planarity :  0.006   0.055    785
  Dihedral  : 20.616 177.870   1004
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 19.08 %
    Favored  : 79.39 %
  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 are not related in a simple way.
  whole: -0.13 (0.38), residues: 514
  helix:  1.07 (0.34), residues: 220
  sheet: -1.93 (0.63), residues: 56
  loop : -0.64 (0.43), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 262 
 TYR   0.019   0.003   TYR A 140 
 PHE   0.030   0.002   PHE A 102 
 TRP   0.038   0.003   TRP A 485 
 HIS   0.011   0.002   HIS A 641 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00391 /  0.18 ( 4969)
  covalent geometry    : angle       0.61067 /  0.32 ( 6838)
  hydrogen bonds       : bond        0.04254 /  2.83 (  180)
  hydrogen bonds       : angle       4.23822 /  2.95 (  506)

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

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

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 ARG cc_start: 0.7407 (tmt-80) cc_final: 0.6767 (tpt170)
REVERT: A  277 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7423 (mttt)
REVERT: A  578 TYR cc_start: 0.6469 (t80) cc_final: 0.6123 (t80)
REVERT: A  633 LYS cc_start: 0.6370 (ptmm) cc_final: 0.5937 (tptp)
  outliers start: 7
  outliers final: 3
  residues processed: 71
  average time/residue: 0.1187
  time to fit residues: 9.9113
Evaluate side-chains
  66 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 62
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 LYS
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  601 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 0 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 43 optimal weight:    6.9990
   chunk 49 optimal weight:    8.9990
   chunk 22 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 41 optimal weight:    0.1980
   chunk 44 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.7184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 250 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.183743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.161574 restraints weight = 7721.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.4086 rms_B_bonded: 2.36
r_work: 0.3966 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6507
moved from start:          0.2974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4969  Z= 0.190
  Angle     :  0.641   7.934   6838  Z= 0.340
  Chirality :  0.044   0.210    768
  Planarity :  0.006   0.072    785
  Dihedral  : 20.667 177.861   1004
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 19.74 %
    Favored  : 78.95 %
  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 are not related in a simple way.
  whole: -0.28 (0.38), residues: 514
  helix:  0.92 (0.33), residues: 222
  sheet: -2.01 (0.62), residues: 56
  loop : -0.72 (0.44), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 262 
 TYR   0.021   0.003   TYR A 123 
 PHE   0.026   0.002   PHE A 102 
 TRP   0.034   0.003   TRP A 614 
 HIS   0.011   0.002   HIS A 641 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00421 /  0.19 ( 4969)
  covalent geometry    : angle       0.64145 /  0.34 ( 6838)
  hydrogen bonds       : bond        0.04204 /  2.81 (  180)
  hydrogen bonds       : angle       4.24766 /  2.93 (  506)

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

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

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 ARG cc_start: 0.7345 (tmt-80) cc_final: 0.7049 (tpt90)
REVERT: A  277 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7432 (mttt)
REVERT: A  440 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7786 (mm-30)
REVERT: A  441 GLU cc_start: 0.7597 (mp0) cc_final: 0.7364 (mp0)
REVERT: A  578 TYR cc_start: 0.6507 (t80) cc_final: 0.6151 (t80)
REVERT: A  633 LYS cc_start: 0.6392 (ptmm) cc_final: 0.5952 (tptp)
  outliers start: 6
  outliers final: 4
  residues processed: 70
  average time/residue: 0.1173
  time to fit residues: 9.6593
Evaluate side-chains
  71 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 LYS
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  601 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 25 optimal weight:    0.2980
   chunk 16 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.7584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.183421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.160853 restraints weight = 7625.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.4078 rms_B_bonded: 2.42
r_work: 0.3939 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6549
moved from start:          0.3150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4969  Z= 0.200
  Angle     :  0.676  10.775   6838  Z= 0.358
  Chirality :  0.045   0.211    768
  Planarity :  0.006   0.064    785
  Dihedral  : 20.730 177.964   1004
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 19.96 %
    Favored  : 78.29 %
  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 are not related in a simple way.
  whole: -0.38 (0.37), residues: 514
  helix:  0.87 (0.33), residues: 222
  sheet: -2.06 (0.62), residues: 56
  loop : -0.80 (0.43), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 262 
 TYR   0.031   0.003   TYR A 432 
 PHE   0.022   0.001   PHE A 102 
 TRP   0.041   0.003   TRP A 614 
 HIS   0.012   0.002   HIS A 641 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00445 /  0.20 ( 4969)
  covalent geometry    : angle       0.67553 /  0.36 ( 6838)
  hydrogen bonds       : bond        0.04317 /  2.90 (  180)
  hydrogen bonds       : angle       4.31906 /  2.96 (  506)

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

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

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A  121 HIS cc_start: 0.7081 (OUTLIER) cc_final: 0.6542 (m170)
REVERT: A  277 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7449 (mttt)
REVERT: A  441 GLU cc_start: 0.7588 (mp0) cc_final: 0.7346 (mp0)
REVERT: A  578 TYR cc_start: 0.6544 (t80) cc_final: 0.6122 (t80)
REVERT: A  633 LYS cc_start: 0.6441 (ptmm) cc_final: 0.5999 (tptp)
  outliers start: 8
  outliers final: 3
  residues processed: 69
  average time/residue: 0.1267
  time to fit residues: 10.2433
Evaluate side-chains
  65 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 HIS
Chi-restraints excluded: chain A residue  277 LYS
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  601 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0980
   chunk 48 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0970
   chunk 27 optimal weight:    0.0970
   overall best weight:    0.3576

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.185411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.163273 restraints weight = 7646.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.4105 rms_B_bonded: 2.34
r_work: 0.3979 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6494
moved from start:          0.3207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4969  Z= 0.137
  Angle     :  0.633   9.630   6838  Z= 0.337
  Chirality :  0.043   0.200    768
  Planarity :  0.006   0.061    785
  Dihedral  : 20.732 177.728   1004
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 20.83 %
    Favored  : 78.29 %
  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 are not related in a simple way.
  whole: -0.21 (0.38), residues: 514
  helix:  1.00 (0.34), residues: 222
  sheet: -2.04 (0.61), residues: 56
  loop : -0.69 (0.44), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.000   ARG A 262 
 TYR   0.024   0.002   TYR A 432 
 PHE   0.020   0.001   PHE A 102 
 TRP   0.038   0.003   TRP A 614 
 HIS   0.008   0.001   HIS A 641 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.14 ( 4969)
  covalent geometry    : angle       0.63263 /  0.34 ( 6838)
  hydrogen bonds       : bond        0.03788 /  2.52 (  180)
  hydrogen bonds       : angle       4.14075 /  2.86 (  506)

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

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

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A  441 GLU cc_start: 0.7591 (mp0) cc_final: 0.7329 (mp0)
REVERT: A  578 TYR cc_start: 0.6520 (t80) cc_final: 0.6087 (t80)
REVERT: A  633 LYS cc_start: 0.6412 (ptmm) cc_final: 0.5981 (tptp)
  outliers start: 4
  outliers final: 3
  residues processed: 65
  average time/residue: 0.1281
  time to fit residues: 9.8158
Evaluate side-chains
  64 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 61
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  601 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 18 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.183584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.161177 restraints weight = 7680.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.4077 rms_B_bonded: 2.34
r_work: 0.3958 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6522
moved from start:          0.3347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   4969  Z= 0.212
  Angle     :  0.706   9.312   6838  Z= 0.375
  Chirality :  0.045   0.214    768
  Planarity :  0.006   0.059    785
  Dihedral  : 20.736 177.987   1004
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 20.83 %
    Favored  : 78.29 %
  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 are not related in a simple way.
  whole: -0.41 (0.37), residues: 514
  helix:  0.85 (0.34), residues: 222
  sheet: -2.03 (0.64), residues: 56
  loop : -0.85 (0.43), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  96 
 TYR   0.027   0.003   TYR A 432 
 PHE   0.018   0.002   PHE A 102 
 TRP   0.055   0.003   TRP A 614 
 HIS   0.012   0.002   HIS A 641 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00472 /  0.21 ( 4969)
  covalent geometry    : angle       0.70565 /  0.37 ( 6838)
  hydrogen bonds       : bond        0.04347 /  2.91 (  180)
  hydrogen bonds       : angle       4.36531 /  2.99 (  506)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1202.93 seconds
wall clock time: 21 minutes 20.92 seconds (1280.92 seconds total)