Starting phenix.real_space_refine
on Fri Aug 22 15:18:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wrt_37789/08_2025/8wrt_37789.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wrt_37789/08_2025/8wrt_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wrt_37789/08_2025/8wrt_37789.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wrt_37789/08_2025/8wrt_37789.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wrt_37789/08_2025/8wrt_37789.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wrt_37789/08_2025/8wrt_37789.cif"
  }
  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-2.0-5787/lib/python3.9/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: 1.19, per 1000 atoms: 0.25
  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: 0.36
  Conformation dependent library (CDL) restraints added in 143.7 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.35
  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: 0.44

  Time building geometry restraints manager: 0.49 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:             4.000
  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:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.390
  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:0.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6010
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= 0.195
  Angle     :  0.744   9.487   6838  Z= 0.450
  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 aren 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
  covalent geometry    : bond        0.00318 ( 4969)
  covalent geometry    : angle       0.74406 ( 6838)
  hydrogen bonds       : bond        0.25320 (  180)
  hydrogen bonds       : angle       8.40816 (  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  : 0.157 
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: 0.6433 (mppt) cc_final: 0.6007 (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: 0.1084
  time to fit residues: 9.3951
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  : 0.167 
-------------------------------------------------------------------------------
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:    1.9990
   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:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 HIS ** 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 = 0.4334 r_free = 0.4334 target = 0.182599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.160378 restraints weight = 7720.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.4071 rms_B_bonded: 2.33
r_work: 0.3942 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6431
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   4969  Z= 0.215
  Angle     :  0.700   6.944   6838  Z= 0.364
  Chirality :  0.046   0.210    768
  Planarity :  0.007   0.088    785
  Dihedral  : 20.827 177.374   1006
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 10.75 %
    Favored  : 88.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.57 (0.37), residues: 514
  helix:  0.52 (0.33), residues: 217
  sheet: -2.33 (0.67), residues: 51
  loop : -0.66 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 262 
 TYR   0.031   0.003   TYR A 123 
 PHE   0.029   0.002   PHE A 335 
 TRP   0.018   0.002   TRP A 436 
 HIS   0.012   0.003   HIS A 641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 ( 4969)
  covalent geometry    : angle       0.70004 ( 6838)
  hydrogen bonds       : bond        0.04977 (  180)
  hydrogen bonds       : angle       4.81724 (  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: 5
    poor density    : 68
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 ARG cc_start: 0.7421 (tmt-80) cc_final: 0.6928 (tpt170)
REVERT: A  166 GLU cc_start: 0.6943 (tm-30) cc_final: 0.6463 (tm-30)
REVERT: A  444 LYS cc_start: 0.8311 (tmmt) cc_final: 0.8054 (tmmt)
REVERT: A  578 TYR cc_start: 0.6429 (t80) cc_final: 0.6071 (t80)
REVERT: A  633 LYS cc_start: 0.6401 (ptmm) cc_final: 0.5984 (tptp)
  outliers start: 5
  outliers final: 2
  residues processed: 71
  average time/residue: 0.1042
  time to fit residues: 8.7139
Evaluate side-chains
  69 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 67
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  490 SER
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:    0.0270
   chunk 12 optimal weight:    0.3980
   chunk 4 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0070
   overall best weight:    0.4256

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 253 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.184170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.161824 restraints weight = 7708.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.4082 rms_B_bonded: 2.39
r_work: 0.3962 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6390
moved from start:          0.2626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4969  Z= 0.140
  Angle     :  0.579   5.887   6838  Z= 0.300
  Chirality :  0.042   0.202    768
  Planarity :  0.006   0.063    785
  Dihedral  : 20.775 177.586   1004
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 14.25 %
    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 aren not related in a simple way.
  whole: -0.23 (0.38), residues: 514
  helix:  0.83 (0.34), residues: 225
  sheet: -2.15 (0.64), residues: 56
  loop : -0.50 (0.44), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 262 
 TYR   0.019   0.002   TYR A 432 
 PHE   0.019   0.001   PHE A 102 
 TRP   0.014   0.002   TRP A 112 
 HIS   0.009   0.001   HIS A 641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 4969)
  covalent geometry    : angle       0.57922 ( 6838)
  hydrogen bonds       : bond        0.04153 (  180)
  hydrogen bonds       : angle       4.30452 (  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
  71 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 ARG cc_start: 0.7313 (tmt-80) cc_final: 0.7020 (tpt90)
REVERT: A  578 TYR cc_start: 0.6458 (t80) cc_final: 0.6020 (t80)
REVERT: A  633 LYS cc_start: 0.6378 (ptmm) cc_final: 0.5904 (tptp)
  outliers start: 4
  outliers final: 3
  residues processed: 70
  average time/residue: 0.1091
  time to fit residues: 9.0169
Evaluate side-chains
  66 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
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  490 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 20 optimal weight:    0.2980
   chunk 21 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 52 optimal weight:    0.1980
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 214 HIS ** 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 = 0.4329 r_free = 0.4329 target = 0.182719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.160373 restraints weight = 7738.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.4063 rms_B_bonded: 2.37
r_work: 0.3933 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6439
moved from start:          0.3018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4969  Z= 0.167
  Angle     :  0.610   8.096   6838  Z= 0.312
  Chirality :  0.043   0.206    768
  Planarity :  0.006   0.058    785
  Dihedral  : 20.830 177.230   1004
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 16.45 %
    Favored  : 82.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.08 (0.38), residues: 514
  helix:  0.97 (0.33), residues: 227
  sheet: -1.93 (0.65), residues: 56
  loop : -0.49 (0.44), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 262 
 TYR   0.023   0.002   TYR A 123 
 PHE   0.018   0.001   PHE A 102 
 TRP   0.015   0.002   TRP A 112 
 HIS   0.011   0.002   HIS A 641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 4969)
  covalent geometry    : angle       0.61009 ( 6838)
  hydrogen bonds       : bond        0.04043 (  180)
  hydrogen bonds       : angle       4.20591 (  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
  73 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A   96 ARG cc_start: 0.7284 (tmt-80) cc_final: 0.7022 (tpt90)
REVERT: A  434 ARG cc_start: 0.7302 (ttt-90) cc_final: 0.7099 (ttt-90)
REVERT: A  578 TYR cc_start: 0.6513 (t80) cc_final: 0.6121 (t80)
REVERT: A  633 LYS cc_start: 0.6429 (ptmm) cc_final: 0.5987 (tptp)
  outliers start: 6
  outliers final: 3
  residues processed: 73
  average time/residue: 0.0921
  time to fit residues: 8.0599
Evaluate side-chains
  70 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
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  490 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 7 optimal weight:    0.3980
   chunk 22 optimal weight:    0.0870
   chunk 37 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0980
   chunk 6 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 214 HIS ** 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 = 0.4356 r_free = 0.4356 target = 0.184844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.162836 restraints weight = 7762.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.4101 rms_B_bonded: 2.33
r_work: 0.3966 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6409
moved from start:          0.3218

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= 0.138
  Angle     :  0.592   7.410   6838  Z= 0.306
  Chirality :  0.042   0.203    768
  Planarity :  0.006   0.059    785
  Dihedral  : 20.793 178.017   1004
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 17.76 %
    Favored  : 80.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.38), residues: 514
  helix:  1.20 (0.34), residues: 225
  sheet: -1.96 (0.64), residues: 56
  loop : -0.40 (0.44), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 262 
 TYR   0.018   0.002   TYR A 123 
 PHE   0.017   0.001   PHE A 102 
 TRP   0.014   0.002   TRP A 112 
 HIS   0.008   0.001   HIS A 641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 4969)
  covalent geometry    : angle       0.59178 ( 6838)
  hydrogen bonds       : bond        0.03665 (  180)
  hydrogen bonds       : angle       4.01092 (  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
  73 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.101 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.7260 (mp0) cc_final: 0.6789 (mm-30)
REVERT: A   96 ARG cc_start: 0.7257 (tmt-80) cc_final: 0.6999 (tpt90)
REVERT: A  444 LYS cc_start: 0.8417 (tmmt) cc_final: 0.8148 (tmmt)
REVERT: A  633 LYS cc_start: 0.6434 (ptmm) cc_final: 0.5995 (tptp)
  outliers start: 9
  outliers final: 7
  residues processed: 71
  average time/residue: 0.1057
  time to fit residues: 8.8380
Evaluate side-chains
  71 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  236 LEU
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  464 GLN
Chi-restraints excluded: chain A residue  490 SER
Chi-restraints excluded: chain A residue  601 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0050
   chunk 29 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0870
   chunk 48 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.4772

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 214 HIS ** 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 = 0.4351 r_free = 0.4351 target = 0.184259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.162318 restraints weight = 7852.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.4088 rms_B_bonded: 2.37
r_work: 0.3968 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6401
moved from start:          0.3408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4969  Z= 0.148
  Angle     :  0.599   7.203   6838  Z= 0.309
  Chirality :  0.042   0.205    768
  Planarity :  0.006   0.053    785
  Dihedral  : 20.795 177.589   1004
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 19.30 %
    Favored  : 78.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.38), residues: 514
  helix:  1.11 (0.34), residues: 229
  sheet: -1.97 (0.64), residues: 56
  loop : -0.55 (0.44), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 262 
 TYR   0.019   0.002   TYR A 123 
 PHE   0.017   0.001   PHE A 102 
 TRP   0.014   0.002   TRP A 112 
 HIS   0.009   0.002   HIS A 641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 4969)
  covalent geometry    : angle       0.59908 ( 6838)
  hydrogen bonds       : bond        0.03671 (  180)
  hydrogen bonds       : angle       3.97224 (  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
  73 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.7235 (mp0) cc_final: 0.6742 (mt-10)
REVERT: A  488 MET cc_start: 0.4019 (tpp) cc_final: 0.3640 (ptt)
REVERT: A  633 LYS cc_start: 0.6465 (ptmm) cc_final: 0.5987 (tptp)
  outliers start: 9
  outliers final: 6
  residues processed: 73
  average time/residue: 0.0887
  time to fit residues: 7.8095
Evaluate side-chains
  68 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  464 GLN
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:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0970
   chunk 13 optimal weight:    0.0770
   chunk 14 optimal weight:    0.2980
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 214 HIS ** 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 = 0.4347 r_free = 0.4347 target = 0.184211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.161988 restraints weight = 7739.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.4084 rms_B_bonded: 2.45
r_work: 0.3959 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6409
moved from start:          0.3551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4969  Z= 0.140
  Angle     :  0.589   7.769   6838  Z= 0.305
  Chirality :  0.042   0.204    768
  Planarity :  0.006   0.052    785
  Dihedral  : 20.752 177.490   1004
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 19.08 %
    Favored  : 78.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.38), residues: 514
  helix:  1.30 (0.35), residues: 225
  sheet: -1.94 (0.65), residues: 56
  loop : -0.49 (0.44), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 262 
 TYR   0.028   0.003   TYR A 578 
 PHE   0.016   0.001   PHE A 102 
 TRP   0.029   0.002   TRP A 614 
 HIS   0.009   0.001   HIS A 641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 4969)
  covalent geometry    : angle       0.58904 ( 6838)
  hydrogen bonds       : bond        0.03584 (  180)
  hydrogen bonds       : angle       3.93474 (  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
  75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.7240 (mp0) cc_final: 0.6789 (mp0)
REVERT: A  121 HIS cc_start: 0.7027 (OUTLIER) cc_final: 0.6474 (m170)
REVERT: A  633 LYS cc_start: 0.6478 (ptmm) cc_final: 0.5994 (tptp)
  outliers start: 10
  outliers final: 7
  residues processed: 74
  average time/residue: 0.1090
  time to fit residues: 9.6970
Evaluate side-chains
  72 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  121 HIS
Chi-restraints excluded: chain A residue  236 LEU
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  464 GLN
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:    0.9990
   chunk 49 optimal weight:    0.2980
   chunk 22 optimal weight:    0.3980
   chunk 23 optimal weight:    0.0980
   chunk 9 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0870
   chunk 44 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0870
   overall best weight:    0.1936

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 214 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.186907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.165398 restraints weight = 7801.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.4124 rms_B_bonded: 2.37
r_work: 0.4004 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.4004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6325
moved from start:          0.3690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   4969  Z= 0.108
  Angle     :  0.556   7.422   6838  Z= 0.286
  Chirality :  0.041   0.197    768
  Planarity :  0.006   0.051    785
  Dihedral  : 20.560 176.916   1004
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 19.96 %
    Favored  : 78.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.39), residues: 514
  helix:  1.49 (0.35), residues: 229
  sheet: -2.27 (0.63), residues: 60
  loop : -0.29 (0.45), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 262 
 TYR   0.025   0.002   TYR A 578 
 PHE   0.013   0.001   PHE A 102 
 TRP   0.031   0.002   TRP A 614 
 HIS   0.002   0.001   HIS A 472 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 4969)
  covalent geometry    : angle       0.55572 ( 6838)
  hydrogen bonds       : bond        0.03078 (  180)
  hydrogen bonds       : angle       3.73848 (  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
  70 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.7247 (mp0) cc_final: 0.6776 (mp0)
REVERT: A   96 ARG cc_start: 0.7195 (tmt-80) cc_final: 0.6937 (tpt90)
REVERT: A  112 TRP cc_start: 0.6689 (t60) cc_final: 0.6257 (t60)
REVERT: A  238 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7644 (mp)
REVERT: A  633 LYS cc_start: 0.6521 (ptmm) cc_final: 0.6013 (tptp)
  outliers start: 9
  outliers final: 7
  residues processed: 67
  average time/residue: 0.1002
  time to fit residues: 7.9620
Evaluate side-chains
  69 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  238 ILE
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  443 ILE
Chi-restraints excluded: chain A residue  464 GLN
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:    0.8980
   chunk 0 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 23 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 24 optimal weight:    0.4980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4327 r_free = 0.4327 target = 0.182498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.160243 restraints weight = 7729.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.4059 rms_B_bonded: 2.44
r_work: 0.3928 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6460
moved from start:          0.3880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   4969  Z= 0.209
  Angle     :  0.650   7.720   6838  Z= 0.338
  Chirality :  0.044   0.212    768
  Planarity :  0.007   0.094    785
  Dihedral  : 20.672 176.929   1004
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 19.52 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.00 (0.38), residues: 514
  helix:  1.20 (0.34), residues: 228
  sheet: -1.81 (0.69), residues: 56
  loop : -0.68 (0.43), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 262 
 TYR   0.024   0.003   TYR A 123 
 PHE   0.016   0.001   PHE A 102 
 TRP   0.020   0.003   TRP A 112 
 HIS   0.014   0.003   HIS A 641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 4969)
  covalent geometry    : angle       0.65014 ( 6838)
  hydrogen bonds       : bond        0.04031 (  180)
  hydrogen bonds       : angle       4.11075 (  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
  78 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.7251 (mp0) cc_final: 0.6963 (mp0)
REVERT: A   96 ARG cc_start: 0.7377 (tmt-80) cc_final: 0.7161 (tpt90)
REVERT: A  238 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7772 (mp)
REVERT: A  633 LYS cc_start: 0.6504 (ptmm) cc_final: 0.6051 (tptp)
  outliers start: 9
  outliers final: 8
  residues processed: 75
  average time/residue: 0.0948
  time to fit residues: 8.5503
Evaluate side-chains
  75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  249 TRP
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  464 GLN
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:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 49 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0270
   chunk 10 optimal weight:    3.9990
   chunk 13 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4335 r_free = 0.4335 target = 0.183146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.160801 restraints weight = 7695.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.4064 rms_B_bonded: 2.44
r_work: 0.3931 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6460
moved from start:          0.3978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4969  Z= 0.189
  Angle     :  0.646   7.947   6838  Z= 0.336
  Chirality :  0.044   0.212    768
  Planarity :  0.007   0.077    785
  Dihedral  : 20.781 177.187   1004
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.39 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 19.52 %
    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 aren not related in a simple way.
  whole: -0.10 (0.38), residues: 514
  helix:  1.11 (0.34), residues: 228
  sheet: -1.98 (0.67), residues: 56
  loop : -0.69 (0.43), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 262 
 TYR   0.023   0.003   TYR A 578 
 PHE   0.028   0.002   PHE A 102 
 TRP   0.020   0.002   TRP A 614 
 HIS   0.011   0.002   HIS A 641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 4969)
  covalent geometry    : angle       0.64564 ( 6838)
  hydrogen bonds       : bond        0.03876 (  180)
  hydrogen bonds       : angle       4.15676 (  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
  74 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 ARG cc_start: 0.7362 (tmt-80) cc_final: 0.7136 (tpt90)
REVERT: A  166 GLU cc_start: 0.6847 (tm-30) cc_final: 0.6337 (tm-30)
REVERT: A  238 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7747 (mp)
REVERT: A  564 LEU cc_start: 0.7412 (mt) cc_final: 0.7155 (mp)
REVERT: A  633 LYS cc_start: 0.6480 (ptmm) cc_final: 0.6031 (tptp)
  outliers start: 10
  outliers final: 8
  residues processed: 72
  average time/residue: 0.1006
  time to fit residues: 8.6448
Evaluate side-chains
  71 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  249 TRP
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  464 GLN
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:    0.8980
   chunk 12 optimal weight:    0.0570
   chunk 9 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 49 optimal weight:    8.9990
   chunk 11 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.7098

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 472 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.182728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.160782 restraints weight = 7639.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.4062 rms_B_bonded: 2.42
r_work: 0.3927 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6472
moved from start:          0.4130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4969  Z= 0.199
  Angle     :  0.681   7.740   6838  Z= 0.354
  Chirality :  0.044   0.213    768
  Planarity :  0.007   0.079    785
  Dihedral  : 20.871 176.196   1004
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.00 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 20.39 %
    Favored  : 77.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.24 (0.38), residues: 514
  helix:  1.01 (0.34), residues: 227
  sheet: -2.09 (0.67), residues: 56
  loop : -0.77 (0.42), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 262 
 TYR   0.023   0.003   TYR A 123 
 PHE   0.031   0.002   PHE A 102 
 TRP   0.023   0.002   TRP A 249 
 HIS   0.012   0.002   HIS A 641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 4969)
  covalent geometry    : angle       0.68058 ( 6838)
  hydrogen bonds       : bond        0.04028 (  180)
  hydrogen bonds       : angle       4.22067 (  506)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1135.16 seconds
wall clock time: 20 minutes 10.50 seconds (1210.50 seconds total)