Starting phenix.real_space_refine
on Sat May 10 03:14:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wrt_37789/05_2025/8wrt_37789.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wrt_37789/05_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_37789/05_2025/8wrt_37789.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wrt_37789/05_2025/8wrt_37789.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wrt_37789/05_2025/8wrt_37789.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wrt_37789/05_2025/8wrt_37789.cif"
  }
  resolution = 3.31
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.017
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.03, per 1000 atoms: 0.84
  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: 1.26
  Conformation dependent library (CDL) restraints added in 513.9 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: 1.33
  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: 1.41

  Time building geometry restraints manager: 1.47 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.220
  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:             0.020
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.880
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.030
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (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
 TRP   0.018   0.001   TRP A 626 
 HIS   0.004   0.001   HIS A 632 
 PHE   0.015   0.002   PHE A 335 
 TYR   0.011   0.001   TYR A 578 
 ARG   0.006   0.000   ARG A 262 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25320 (  180)
  hydrogen bonds       : angle       8.40816 (  506)
  covalent geometry    : bond        0.00318 ( 4969)
  covalent geometry    : angle       0.74406 ( 6838)

*********************** 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  : 0.440 
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: 0.6108 (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: 0.2891
  time to fit residues: 24.8985
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  : 0.440 
-------------------------------------------------------------------------------
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 46 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0670
   chunk 26 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 49 optimal weight:    0.0670
   overall best weight:    0.5658

-------------------------------------------------------------------------------
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 = 0.4338 r_free = 0.4338 target = 0.183380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.161123 restraints weight = 7622.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.4073 rms_B_bonded: 2.41
r_work: 0.3950 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6380
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4969  Z= 0.172
  Angle     :  0.652   6.379   6838  Z= 0.338
  Chirality :  0.044   0.206    768
  Planarity :  0.007   0.089    785
  Dihedral  : 20.699 177.265   1006
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  9.87 %
    Favored  : 89.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.37), residues: 514
  helix:  0.64 (0.34), residues: 212
  sheet: -2.32 (0.66), residues: 51
  loop : -0.58 (0.40), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 436 
 HIS   0.009   0.002   HIS A 641 
 PHE   0.023   0.002   PHE A 335 
 TYR   0.027   0.003   TYR A 123 
 ARG   0.004   0.000   ARG A 262 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04782 (  180)
  hydrogen bonds       : angle       4.68623 (  506)
  covalent geometry    : bond        0.00370 ( 4969)
  covalent geometry    : angle       0.65238 ( 6838)

*********************** 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
  70 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 ARG cc_start: 0.7344 (tmt-80) cc_final: 0.6980 (tpt170)
REVERT: A  166 GLU cc_start: 0.6857 (tm-30) cc_final: 0.6326 (tm-30)
REVERT: A  308 ASP cc_start: 0.6985 (m-30) cc_final: 0.6618 (m-30)
REVERT: A  444 LYS cc_start: 0.8315 (tmmt) cc_final: 0.8016 (tmmt)
REVERT: A  573 ARG cc_start: 0.6671 (mpp80) cc_final: 0.6446 (mpp80)
REVERT: A  578 TYR cc_start: 0.6367 (t80) cc_final: 0.6005 (t80)
REVERT: A  633 LYS cc_start: 0.6379 (ptmm) cc_final: 0.5934 (tptp)
  outliers start: 5
  outliers final: 2
  residues processed: 68
  average time/residue: 0.2761
  time to fit residues: 22.2251
Evaluate side-chains
  65 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
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 10 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0670
   chunk 2 optimal weight:    0.7980
   chunk 48 optimal weight:    0.3980
   chunk 21 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0470
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.3816

-------------------------------------------------------------------------------
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 = 0.4353 r_free = 0.4353 target = 0.184459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.162686 restraints weight = 7644.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.4095 rms_B_bonded: 2.35
r_work: 0.3971 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6376
moved from start:          0.2522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4969  Z= 0.130
  Angle     :  0.561   5.833   6838  Z= 0.291
  Chirality :  0.042   0.201    768
  Planarity :  0.006   0.067    785
  Dihedral  : 20.656 177.268   1004
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 14.91 %
    Favored  : 84.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.38), residues: 514
  helix:  0.89 (0.33), residues: 228
  sheet: -2.12 (0.65), residues: 56
  loop : -0.50 (0.44), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 112 
 HIS   0.008   0.001   HIS A 641 
 PHE   0.018   0.001   PHE A 102 
 TYR   0.016   0.002   TYR A 432 
 ARG   0.004   0.000   ARG A 262 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04066 (  180)
  hydrogen bonds       : angle       4.23852 (  506)
  covalent geometry    : bond        0.00284 ( 4969)
  covalent geometry    : angle       0.56145 ( 6838)

*********************** 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
  67 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 ARG cc_start: 0.7321 (tmt-80) cc_final: 0.6757 (tpt170)
REVERT: A  633 LYS cc_start: 0.6377 (ptmm) cc_final: 0.5930 (tptp)
  outliers start: 3
  outliers final: 2
  residues processed: 67
  average time/residue: 0.2531
  time to fit residues: 20.3624
Evaluate side-chains
  64 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  490 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 6 optimal weight:    0.4980
   chunk 35 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.4304 r_free = 0.4304 target = 0.180609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.158705 restraints weight = 7663.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.4049 rms_B_bonded: 2.27
r_work: 0.3920 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6480
moved from start:          0.3080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   4969  Z= 0.230
  Angle     :  0.682   8.337   6838  Z= 0.352
  Chirality :  0.045   0.215    768
  Planarity :  0.006   0.059    785
  Dihedral  : 20.868 177.403   1004
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.00 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 16.01 %
    Favored  : 82.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.37), residues: 514
  helix:  0.74 (0.33), residues: 226
  sheet: -1.83 (0.69), residues: 51
  loop : -0.69 (0.43), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP A 112 
 HIS   0.015   0.003   HIS A 641 
 PHE   0.022   0.002   PHE A 102 
 TYR   0.022   0.003   TYR A 123 
 ARG   0.009   0.000   ARG A 262 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04621 (  180)
  hydrogen bonds       : angle       4.44155 (  506)
  covalent geometry    : bond        0.00502 ( 4969)
  covalent geometry    : angle       0.68167 ( 6838)

*********************** 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
  74 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
REVERT: A  434 ARG cc_start: 0.7295 (ttt-90) cc_final: 0.7086 (ttt-90)
REVERT: A  578 TYR cc_start: 0.6555 (t80) cc_final: 0.6013 (t80)
REVERT: A  633 LYS cc_start: 0.6420 (ptmm) cc_final: 0.5997 (tptp)
  outliers start: 7
  outliers final: 4
  residues processed: 74
  average time/residue: 0.2754
  time to fit residues: 23.9380
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  : 0.427 
-------------------------------------------------------------------------------
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  464 GLN
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 25 optimal weight:    0.6980
   chunk 50 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 20 optimal weight:    0.4980
   chunk 40 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 49 optimal weight:    6.9990
   chunk 39 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 29 optimal weight:    0.3980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.4322 r_free = 0.4322 target = 0.182201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.160182 restraints weight = 7755.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.4061 rms_B_bonded: 2.29
r_work: 0.3947 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6417
moved from start:          0.3300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4969  Z= 0.163
  Angle     :  0.618   7.552   6838  Z= 0.320
  Chirality :  0.043   0.208    768
  Planarity :  0.006   0.055    785
  Dihedral  : 20.844 178.117   1004
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 18.86 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.38), residues: 514
  helix:  0.86 (0.33), residues: 227
  sheet: -2.03 (0.65), residues: 56
  loop : -0.56 (0.44), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 112 
 HIS   0.010   0.002   HIS A 641 
 PHE   0.019   0.001   PHE A 102 
 TYR   0.020   0.002   TYR A 432 
 ARG   0.002   0.000   ARG A 642 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03947 (  180)
  hydrogen bonds       : angle       4.18573 (  506)
  covalent geometry    : bond        0.00359 ( 4969)
  covalent geometry    : angle       0.61776 ( 6838)

*********************** 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
  75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.487 
Fit side-chains
REVERT: A   74 GLU cc_start: 0.7232 (mp0) cc_final: 0.6797 (mm-30)
REVERT: A   96 ARG cc_start: 0.7294 (tmt-80) cc_final: 0.7069 (tpt90)
REVERT: A  121 HIS cc_start: 0.7042 (OUTLIER) cc_final: 0.6385 (m170)
REVERT: A  578 TYR cc_start: 0.6530 (t80) cc_final: 0.6053 (t80)
REVERT: A  633 LYS cc_start: 0.6436 (ptmm) cc_final: 0.5990 (tptp)
  outliers start: 9
  outliers final: 6
  residues processed: 74
  average time/residue: 0.2476
  time to fit residues: 21.9706
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  : 0.473 
-------------------------------------------------------------------------------
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  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 1 optimal weight:    0.3980
   chunk 36 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0670
   overall best weight:    0.5518

-------------------------------------------------------------------------------
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 = 0.4343 r_free = 0.4343 target = 0.183600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.161496 restraints weight = 7723.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.4082 rms_B_bonded: 2.33
r_work: 0.3958 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6421
moved from start:          0.3506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4969  Z= 0.163
  Angle     :  0.622   7.464   6838  Z= 0.321
  Chirality :  0.042   0.207    768
  Planarity :  0.006   0.061    785
  Dihedral  : 20.838 177.336   1004
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.39 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 19.08 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.38), residues: 514
  helix:  0.88 (0.34), residues: 229
  sheet: -2.06 (0.65), residues: 56
  loop : -0.66 (0.44), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 436 
 HIS   0.010   0.002   HIS A 641 
 PHE   0.030   0.002   PHE A 102 
 TYR   0.016   0.002   TYR A 432 
 ARG   0.010   0.000   ARG A 262 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03909 (  180)
  hydrogen bonds       : angle       4.15292 (  506)
  covalent geometry    : bond        0.00363 ( 4969)
  covalent geometry    : angle       0.62156 ( 6838)

*********************** 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
  74 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 ARG cc_start: 0.7308 (tmt-80) cc_final: 0.7092 (tpt90)
REVERT: A  488 MET cc_start: 0.4104 (tpp) cc_final: 0.3747 (ptt)
REVERT: A  633 LYS cc_start: 0.6435 (ptmm) cc_final: 0.5997 (tptp)
  outliers start: 12
  outliers final: 9
  residues processed: 72
  average time/residue: 0.2462
  time to fit residues: 21.2374
Evaluate side-chains
  72 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 48 optimal weight:    0.3980
   chunk 29 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.4299 r_free = 0.4299 target = 0.179806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.157887 restraints weight = 7652.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.4039 rms_B_bonded: 2.30
r_work: 0.3918 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6487
moved from start:          0.3841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   4969  Z= 0.251
  Angle     :  0.713   8.587   6838  Z= 0.371
  Chirality :  0.046   0.221    768
  Planarity :  0.006   0.056    785
  Dihedral  : 21.004 176.232   1004
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 13.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.39 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 18.20 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.37), residues: 514
  helix:  0.66 (0.34), residues: 227
  sheet: -2.11 (0.67), residues: 56
  loop : -0.83 (0.43), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP A 436 
 HIS   0.016   0.003   HIS A 641 
 PHE   0.024   0.002   PHE A 102 
 TYR   0.018   0.003   TYR A 140 
 ARG   0.004   0.000   ARG A 260 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04702 (  180)
  hydrogen bonds       : angle       4.48399 (  506)
  covalent geometry    : bond        0.00553 ( 4969)
  covalent geometry    : angle       0.71270 ( 6838)

*********************** 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
  78 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.7252 (mp0) cc_final: 0.6762 (mm-30)
REVERT: A  121 HIS cc_start: 0.7125 (OUTLIER) cc_final: 0.6347 (m170)
REVERT: A  263 LYS cc_start: 0.7241 (mtmm) cc_final: 0.6770 (mtmt)
REVERT: A  633 LYS cc_start: 0.6447 (ptmm) cc_final: 0.6052 (tptp)
  outliers start: 11
  outliers final: 9
  residues processed: 75
  average time/residue: 0.2651
  time to fit residues: 23.9184
Evaluate side-chains
  77 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
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  121 HIS
Chi-restraints excluded: chain A residue  236 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 3 optimal weight:    0.1980
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.4314 r_free = 0.4314 target = 0.181359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.159467 restraints weight = 7742.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.4057 rms_B_bonded: 2.32
r_work: 0.3929 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6475
moved from start:          0.3921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4969  Z= 0.195
  Angle     :  0.655   7.833   6838  Z= 0.339
  Chirality :  0.044   0.215    768
  Planarity :  0.006   0.058    785
  Dihedral  : 20.976 176.441   1004
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 19.96 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.38), residues: 514
  helix:  0.78 (0.34), residues: 227
  sheet: -2.14 (0.67), residues: 56
  loop : -0.75 (0.44), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP A 614 
 HIS   0.012   0.002   HIS A 641 
 PHE   0.019   0.002   PHE A 102 
 TYR   0.017   0.003   TYR A 432 
 ARG   0.007   0.000   ARG A 262 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04177 (  180)
  hydrogen bonds       : angle       4.34785 (  506)
  covalent geometry    : bond        0.00432 ( 4969)
  covalent geometry    : angle       0.65511 ( 6838)

*********************** 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
  76 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.7219 (mp0) cc_final: 0.6841 (mp0)
REVERT: A  468 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7461 (tm-30)
REVERT: A  633 LYS cc_start: 0.6436 (ptmm) cc_final: 0.5990 (tptp)
  outliers start: 10
  outliers final: 9
  residues processed: 73
  average time/residue: 0.2541
  time to fit residues: 22.1070
Evaluate side-chains
  72 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
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  121 HIS
Chi-restraints excluded: chain A residue  236 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 39 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0670
   chunk 47 optimal weight:    0.0470
   chunk 21 optimal weight:    0.1980
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.3216

-------------------------------------------------------------------------------
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 = 0.4354 r_free = 0.4354 target = 0.184822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.162837 restraints weight = 7655.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.4091 rms_B_bonded: 2.36
r_work: 0.3971 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6400
moved from start:          0.3953

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= 0.126
  Angle     :  0.591   6.753   6838  Z= 0.304
  Chirality :  0.041   0.203    768
  Planarity :  0.006   0.056    785
  Dihedral  : 20.899 176.773   1004
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 20.83 %
    Favored  : 77.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.39), residues: 514
  helix:  1.02 (0.35), residues: 231
  sheet: -2.07 (0.65), residues: 56
  loop : -0.67 (0.45), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 614 
 HIS   0.007   0.001   HIS A 641 
 PHE   0.018   0.001   PHE A 102 
 TYR   0.017   0.002   TYR A 432 
 ARG   0.003   0.000   ARG A 434 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03396 (  180)
  hydrogen bonds       : angle       4.05654 (  506)
  covalent geometry    : bond        0.00286 ( 4969)
  covalent geometry    : angle       0.59114 ( 6838)

*********************** 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
  67 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.554 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 ARG cc_start: 0.7258 (tmt-80) cc_final: 0.7035 (tpt90)
REVERT: A  468 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7305 (tm-30)
REVERT: A  564 LEU cc_start: 0.7379 (mt) cc_final: 0.7112 (mp)
REVERT: A  633 LYS cc_start: 0.6479 (ptmm) cc_final: 0.5979 (tptp)
  outliers start: 7
  outliers final: 7
  residues processed: 67
  average time/residue: 0.2782
  time to fit residues: 22.2847
Evaluate side-chains
  65 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
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  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 42 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 34 optimal weight:    0.3980
   chunk 15 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0870
   chunk 1 optimal weight:    0.0970
   overall best weight:    0.4956

-------------------------------------------------------------------------------
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 = 0.4335 r_free = 0.4335 target = 0.183117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.161383 restraints weight = 7763.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.4077 rms_B_bonded: 2.36
r_work: 0.3956 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6428
moved from start:          0.4072

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= 0.154
  Angle     :  0.630   7.380   6838  Z= 0.324
  Chirality :  0.042   0.209    768
  Planarity :  0.006   0.056    785
  Dihedral  : 20.845 176.407   1004
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 21.05 %
    Favored  : 77.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.38), residues: 514
  helix:  1.03 (0.34), residues: 229
  sheet: -2.07 (0.66), residues: 56
  loop : -0.67 (0.44), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 614 
 HIS   0.010   0.002   HIS A 641 
 PHE   0.015   0.001   PHE A 102 
 TYR   0.018   0.002   TYR A 578 
 ARG   0.012   0.000   ARG A 262 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03647 (  180)
  hydrogen bonds       : angle       4.12699 (  506)
  covalent geometry    : bond        0.00347 ( 4969)
  covalent geometry    : angle       0.62986 ( 6838)

********************** 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
  68 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
REVERT: A  564 LEU cc_start: 0.7385 (mt) cc_final: 0.7130 (mp)
REVERT: A  633 LYS cc_start: 0.6482 (ptmm) cc_final: 0.5997 (tptp)
  outliers start: 7
  outliers final: 7
  residues processed: 68
  average time/residue: 0.2520
  time to fit residues: 20.6761
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  : 0.478 
-------------------------------------------------------------------------------
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  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:    0.9990
   chunk 19 optimal weight:    0.2980
   chunk 12 optimal weight:    0.2980
   chunk 9 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0970
   chunk 15 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.3978

-------------------------------------------------------------------------------
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**
A 472 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.184183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.162285 restraints weight = 7687.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.4087 rms_B_bonded: 2.43
r_work: 0.3966 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6408
moved from start:          0.4198

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= 0.138
  Angle     :  0.616   6.823   6838  Z= 0.318
  Chirality :  0.042   0.205    768
  Planarity :  0.006   0.056    785
  Dihedral  : 20.798 176.376   1004
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 21.05 %
    Favored  : 76.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.38), residues: 514
  helix:  1.11 (0.34), residues: 226
  sheet: -2.08 (0.65), residues: 56
  loop : -0.64 (0.44), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 614 
 HIS   0.008   0.001   HIS A 641 
 PHE   0.016   0.001   PHE A 102 
 TYR   0.027   0.002   TYR A 578 
 ARG   0.003   0.000   ARG A 262 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03421 (  180)
  hydrogen bonds       : angle       4.04198 (  506)
  covalent geometry    : bond        0.00312 ( 4969)
  covalent geometry    : angle       0.61604 ( 6838)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2571.33 seconds
wall clock time: 45 minutes 31.81 seconds (2731.81 seconds total)