Starting phenix.real_space_refine
on Tue Mar  3 16:50:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vjy_21220/03_2026/6vjy_21220.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vjy_21220/03_2026/6vjy_21220.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vjy_21220/03_2026/6vjy_21220.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vjy_21220/03_2026/6vjy_21220.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vjy_21220/03_2026/6vjy_21220.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vjy_21220/03_2026/6vjy_21220.map"
  }
  resolution = 4.3
  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=   0.000 sd=   0.003
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: 4
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     C    4716      2.51       5
     N    1204      2.21       5
     O    1312      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7266
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 2343
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2343
          Classifications: {'peptide': 280}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 275}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 4923
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 603, 4923
          Classifications: {'peptide': 603}
          Link IDs: {'PTRANS': 20, 'TRANS': 582}
          Chain breaks: 4
  Time building chain proxies: 1.42, per 1000 atoms: 0.20
  Number of scatterers: 7266
  At special positions: 0
  Unit cell: (93.79, 124.3, 123.17, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      34     16.00
     O    1312      8.00
     N    1204      7.00
     C    4716      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: 0.79
  Conformation dependent library (CDL) restraints added in 331.6 milliseconds
  

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1702

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 0 sheets defined
      80.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'B' and resid 3 through 31
    Processing helix  chain 'B' and resid 34 through 43
    Processing helix  chain 'B' and resid 44 through 72
    Processing helix  chain 'B' and resid 75 through 99
      Proline residue:  B  87  - end of helix
    Processing helix  chain 'B' and resid 105 through 135
      removed outlier: 3.537A  pdb=" N   ALA B 109 " --> pdb=" O   PHE B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 175
    Processing helix  chain 'B' and resid 179 through 220
      removed outlier: 3.516A  pdb=" N   THR B 183 " --> pdb=" O   ASP B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 294
      removed outlier: 4.071A  pdb=" N   TYR B 270 " --> pdb=" O   GLY B 266 " (cutoff:3.500A)
      Proline residue:  B 292  - end of helix
    Processing helix  chain 'B' and resid 296 through 324
      removed outlier: 4.214A  pdb=" N   LEU B 300 " --> pdb=" O   PRO B 296 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   TRP B 305 " --> pdb=" O   LYS B 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 27 through 35
    Processing helix  chain 'A' and resid 42 through 47
      removed outlier: 3.829A  pdb=" N   GLU A  46 " --> pdb=" O   ASP A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 81
    Processing helix  chain 'A' and resid 83 through 100
      removed outlier: 3.637A  pdb=" N   PHE A 100 " --> pdb=" O   SER A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 116
      removed outlier: 3.645A  pdb=" N   THR A 108 " --> pdb=" O   GLU A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 139
      removed outlier: 3.751A  pdb=" N   HIS A 128 " --> pdb=" O   MET A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 156
      removed outlier: 3.518A  pdb=" N   ILE A 146 " --> pdb=" O   ASN A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 184
      removed outlier: 3.630A  pdb=" N   ALA A 174 " --> pdb=" O   ASP A 170 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU A 184 " --> pdb=" O   ARG A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 200
    Processing helix  chain 'A' and resid 207 through 225
      removed outlier: 3.604A  pdb=" N   TYR A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 232
    Processing helix  chain 'A' and resid 315 through 331
      removed outlier: 3.668A  pdb=" N   ILE A 319 " --> pdb=" O   SER A 315 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ILE A 320 " --> pdb=" O   GLU A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 355
    Processing helix  chain 'A' and resid 357 through 361
      removed outlier: 3.751A  pdb=" N   ASN A 360 " --> pdb=" O   HIS A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 383
      removed outlier: 3.852A  pdb=" N   TYR A 368 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 407
      removed outlier: 3.827A  pdb=" N   ARG A 407 " --> pdb=" O   GLU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 426
      removed outlier: 3.549A  pdb=" N   TYR A 425 " --> pdb=" O   LEU A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 441
    Processing helix  chain 'A' and resid 448 through 461
    Processing helix  chain 'A' and resid 462 through 465
    Processing helix  chain 'A' and resid 468 through 480
    Processing helix  chain 'A' and resid 481 through 495
      removed outlier: 3.670A  pdb=" N   TYR A 486 " --> pdb=" O   ILE A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 517
      removed outlier: 4.202A  pdb=" N   GLU A 517 " --> pdb=" O   VAL A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 532
      removed outlier: 4.226A  pdb=" N   THR A 526 " --> pdb=" O   PRO A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 549
      removed outlier: 3.951A  pdb=" N   ALA A 539 " --> pdb=" O   ARG A 535 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLU A 548 " --> pdb=" O   SER A 544 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   GLN A 549 " --> pdb=" O   GLN A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 563
    Processing helix  chain 'A' and resid 576 through 594
      removed outlier: 3.649A  pdb=" N   LYS A 580 " --> pdb=" O   THR A 576 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   SER A 585 " --> pdb=" O   THR A 581 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLY A 594 " --> pdb=" O   ALA A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 609
      removed outlier: 3.651A  pdb=" N   VAL A 600 " --> pdb=" O   ILE A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 624
    Processing helix  chain 'A' and resid 627 through 640
    Processing helix  chain 'A' and resid 647 through 662
      removed outlier: 3.797A  pdb=" N   ASP A 662 " --> pdb=" O   VAL A 658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 686
      removed outlier: 3.862A  pdb=" N   THR A 686 " --> pdb=" O   LEU A 682 " (cutoff:3.500A)

    508 hydrogen bonds defined for protein.
    1518 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.22

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2272
        1.34 -     1.46: 1757
        1.46 -     1.58: 3355
        1.58 -     1.69: 0
        1.69 -     1.81: 61
  Bond restraints: 7445
  Sorted by residual:
  bond pdb=" N   ARG B 294 "
       pdb=" CA  ARG B 294 "
    ideal  model  delta    sigma   weight residual
    1.457  1.475 -0.018 1.29e-02 6.01e+03 1.94e+00
  bond pdb=" C   ALA A 521 "
       pdb=" N   PRO A 522 "
    ideal  model  delta    sigma   weight residual
    1.337  1.320  0.017 1.24e-02 6.50e+03 1.84e+00
  bond pdb=" C   VAL B   2 "
       pdb=" O   VAL B   2 "
    ideal  model  delta    sigma   weight residual
    1.232  1.242 -0.011 1.01e-02 9.80e+03 1.12e+00
  bond pdb=" C   ASN B 153 "
       pdb=" O   ASN B 153 "
    ideal  model  delta    sigma   weight residual
    1.236  1.247 -0.010 1.15e-02 7.56e+03 8.08e-01
  bond pdb=" CA  ILE A 596 "
       pdb=" CB  ILE A 596 "
    ideal  model  delta    sigma   weight residual
    1.545  1.537  0.008 9.10e-03 1.21e+04 8.03e-01
  ... (remaining 7440 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 9894
        1.97 -     3.94: 161
        3.94 -     5.92: 19
        5.92 -     7.89: 3
        7.89 -     9.86: 1
  Bond angle restraints: 10078
  Sorted by residual:
  angle pdb=" CA  ILE B 291 "
        pdb=" C   ILE B 291 "
        pdb=" N   PRO B 292 "
      ideal   model   delta    sigma   weight residual
     120.83  117.79    3.04 6.10e-01 2.69e+00 2.49e+01
  angle pdb=" O   ILE B 291 "
        pdb=" C   ILE B 291 "
        pdb=" N   PRO B 292 "
      ideal   model   delta    sigma   weight residual
     120.42  123.40   -2.98 6.40e-01 2.44e+00 2.17e+01
  angle pdb=" C   ASN A 533 "
        pdb=" N   ASP A 534 "
        pdb=" CA  ASP A 534 "
      ideal   model   delta    sigma   weight residual
     121.54  127.83   -6.29 1.91e+00 2.74e-01 1.09e+01
  angle pdb=" C   PHE B 214 "
        pdb=" N   TYR B 215 "
        pdb=" CA  TYR B 215 "
      ideal   model   delta    sigma   weight residual
     120.44  124.14   -3.70 1.30e+00 5.92e-01 8.10e+00
  angle pdb=" C   PHE A 201 "
        pdb=" N   ASN A 202 "
        pdb=" CA  ASN A 202 "
      ideal   model   delta    sigma   weight residual
     121.54  126.96   -5.42 1.91e+00 2.74e-01 8.05e+00
  ... (remaining 10073 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 3925
       17.78 -    35.55: 406
       35.55 -    53.33: 59
       53.33 -    71.11: 15
       71.11 -    88.89: 3
  Dihedral angle restraints: 4408
    sinusoidal: 1773
      harmonic: 2635
  Sorted by residual:
  dihedral pdb=" CA  ASN A 516 "
           pdb=" C   ASN A 516 "
           pdb=" N   GLU A 517 "
           pdb=" CA  GLU A 517 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.20   22.80     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  ASN A 645 "
           pdb=" C   ASN A 645 "
           pdb=" N   ARG A 646 "
           pdb=" CA  ARG A 646 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.37   20.63     0      5.00e+00 4.00e-02 1.70e+01
  dihedral pdb=" CA  ALA A  38 "
           pdb=" C   ALA A  38 "
           pdb=" N   LYS A  39 "
           pdb=" CA  LYS A  39 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.59  -18.41     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 4405 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 758
       0.036 -    0.072: 280
       0.072 -    0.109: 59
       0.109 -    0.145: 10
       0.145 -    0.181: 1
  Chirality restraints: 1108
  Sorted by residual:
  chirality pdb=" CA  ASP A 362 "
            pdb=" N   ASP A 362 "
            pdb=" C   ASP A 362 "
            pdb=" CB  ASP A 362 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.19e-01
  chirality pdb=" CA  VAL A 203 "
            pdb=" N   VAL A 203 "
            pdb=" C   VAL A 203 "
            pdb=" CB  VAL A 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.82e-01
  chirality pdb=" CB  VAL B 303 "
            pdb=" CA  VAL B 303 "
            pdb=" CG1 VAL B 303 "
            pdb=" CG2 VAL B 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 4.61e-01
  ... (remaining 1105 not shown)

  Planarity restraints: 1259
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 295 "   -0.027 5.00e-02 4.00e+02   4.16e-02 2.77e+00
        pdb=" N   PRO B 296 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B 296 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 296 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 282 "   -0.008 2.00e-02 2.50e+03   1.65e-02 2.72e+00
        pdb=" C   LYS B 282 "    0.029 2.00e-02 2.50e+03
        pdb=" O   LYS B 282 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   THR B 283 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A  27 "   -0.023 5.00e-02 4.00e+02   3.48e-02 1.94e+00
        pdb=" N   PRO A  28 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A  28 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  28 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1256 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1297
        2.76 -     3.29: 7787
        3.29 -     3.83: 11944
        3.83 -     4.36: 12907
        4.36 -     4.90: 21608
  Nonbonded interactions: 55543
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 118 "
            pdb=" ND1 HIS B 122 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" O   VAL B  25 "
            pdb=" OG1 THR B  29 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OE2 GLU A 639 "
            pdb=" ND1 HIS A 640 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" OE1 GLN A 424 "
            pdb=" OH  TYR A 437 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   PHE B 147 "
            pdb=" OG  SER B 151 "
     model   vdw
     2.298 3.040
  ... (remaining 55538 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 group one per residue
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:             0.740
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.460
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
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   0.025   7445  Z= 0.178
  Angle     :  0.641   9.861  10078  Z= 0.388
  Chirality :  0.039   0.181   1108
  Planarity :  0.003   0.042   1259
  Dihedral  : 14.400  88.885   2706
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  5.83 %
    Favored  : 94.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.62 (0.25), residues: 869
  helix: -0.34 (0.18), residues: 660
  sheet:  None (None), residues: 0
  loop : -3.25 (0.35), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 589 
 TYR   0.017   0.001   TYR A 107 
 PHE   0.018   0.001   PHE A 528 
 TRP   0.019   0.002   TRP A 632 
 HIS   0.005   0.001   HIS A 661 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 7445)
  covalent geometry    : angle       0.64069 (10078)
  hydrogen bonds       : bond        0.10285 (  508)
  hydrogen bonds       : angle       5.17183 ( 1518)

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 212
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   69 LEU cc_start: 0.9330 (tt) cc_final: 0.8902 (mt)
REVERT: B   81 HIS cc_start: 0.8819 (m170) cc_final: 0.8302 (m170)
REVERT: B  125 LEU cc_start: 0.9264 (tp) cc_final: 0.9034 (mt)
REVERT: B  130 GLU cc_start: 0.8918 (tp30) cc_final: 0.8543 (tm-30)
REVERT: B  152 PHE cc_start: 0.7690 (t80) cc_final: 0.7375 (t80)
REVERT: B  203 LEU cc_start: 0.9441 (mm) cc_final: 0.9146 (mm)
REVERT: B  307 ILE cc_start: 0.6196 (mm) cc_final: 0.5665 (mm)
REVERT: A  215 ARG cc_start: 0.9131 (ttm110) cc_final: 0.8898 (ttp80)
REVERT: A  238 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7915 (mt-10)
REVERT: A  317 ARG cc_start: 0.7755 (tpt170) cc_final: 0.7222 (mmp80)
REVERT: A  499 LYS cc_start: 0.8357 (mmmt) cc_final: 0.8052 (tmtt)
REVERT: A  510 LYS cc_start: 0.9133 (tttt) cc_final: 0.8693 (tttp)
REVERT: A  552 GLU cc_start: 0.8745 (pp20) cc_final: 0.8475 (pp20)
REVERT: A  593 GLN cc_start: 0.8803 (tt0) cc_final: 0.8397 (tm-30)
REVERT: A  609 MET cc_start: 0.8575 (ttt) cc_final: 0.8138 (tmm)
REVERT: A  666 TYR cc_start: 0.8388 (t80) cc_final: 0.7445 (t80)
REVERT: A  670 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8553 (mptt)
  outliers start: 1
  outliers final: 0
  residues processed: 213
  average time/residue: 0.0892
  time to fit residues: 25.1940
Evaluate side-chains
  139 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.1980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
B 101 HIS
B 218 GLN
A  86 GLN
A 123 ASN
A 179 GLN
A 186 ASN
A 191 GLN
A 257 ASN
** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 374 GLN
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.107735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.081678 restraints weight = 22766.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.082354 restraints weight = 12219.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.082578 restraints weight = 8608.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.082847 restraints weight = 8290.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.083081 restraints weight = 7332.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.2472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7445  Z= 0.127
  Angle     :  0.587   9.988  10078  Z= 0.307
  Chirality :  0.039   0.212   1108
  Planarity :  0.004   0.044   1259
  Dihedral  :  4.454  20.450    975
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  4.06 %
    Favored  : 95.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.28), residues: 869
  helix:  1.24 (0.19), residues: 661
  sheet:  None (None), residues: 0
  loop : -2.79 (0.38), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  75 
 TYR   0.022   0.001   TYR B 117 
 PHE   0.030   0.001   PHE B 214 
 TRP   0.054   0.002   TRP B 321 
 HIS   0.013   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 7445)
  covalent geometry    : angle       0.58691 (10078)
  hydrogen bonds       : bond        0.04227 (  508)
  hydrogen bonds       : angle       3.96536 ( 1518)

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 192
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   49 MET cc_start: 0.8608 (ptt) cc_final: 0.8372 (tmm)
REVERT: B   69 LEU cc_start: 0.9357 (tt) cc_final: 0.8986 (mt)
REVERT: B   81 HIS cc_start: 0.8880 (m170) cc_final: 0.8670 (m170)
REVERT: B  117 TYR cc_start: 0.8795 (m-80) cc_final: 0.8509 (m-80)
REVERT: B  127 ASP cc_start: 0.8310 (t0) cc_final: 0.7744 (t0)
REVERT: B  130 GLU cc_start: 0.8931 (tp30) cc_final: 0.8687 (tm-30)
REVERT: B  152 PHE cc_start: 0.7731 (t80) cc_final: 0.7377 (t80)
REVERT: B  307 ILE cc_start: 0.5611 (mm) cc_final: 0.5356 (mm)
REVERT: A   34 LEU cc_start: 0.9180 (mt) cc_final: 0.8974 (mt)
REVERT: A   72 LYS cc_start: 0.9281 (mttt) cc_final: 0.8690 (mptt)
REVERT: A  169 GLN cc_start: 0.9038 (pm20) cc_final: 0.8510 (pp30)
REVERT: A  215 ARG cc_start: 0.9175 (ttm110) cc_final: 0.8892 (ttp80)
REVERT: A  217 ILE cc_start: 0.9578 (mt) cc_final: 0.9192 (tp)
REVERT: A  321 ARG cc_start: 0.8524 (ptt90) cc_final: 0.8247 (ptt-90)
REVERT: A  371 ARG cc_start: 0.8892 (ttm170) cc_final: 0.8652 (ttm110)
REVERT: A  466 ILE cc_start: 0.7967 (pt) cc_final: 0.7748 (tp)
REVERT: A  499 LYS cc_start: 0.8275 (mmmt) cc_final: 0.7789 (tptt)
REVERT: A  510 LYS cc_start: 0.9041 (tttt) cc_final: 0.8766 (tttp)
REVERT: A  609 MET cc_start: 0.8661 (ttt) cc_final: 0.8166 (tmm)
REVERT: A  666 TYR cc_start: 0.8594 (t80) cc_final: 0.8062 (t80)
  outliers start: 3
  outliers final: 0
  residues processed: 194
  average time/residue: 0.0869
  time to fit residues: 22.5271
Evaluate side-chains
  147 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 68 optimal weight:    0.6980
   chunk 62 optimal weight:    7.9990
   chunk 13 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
B  79 HIS
B 218 GLN
A 123 ASN
** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 633 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.107302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.081094 restraints weight = 22818.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.081704 restraints weight = 12071.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.082610 restraints weight = 9429.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.082853 restraints weight = 8214.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.083226 restraints weight = 7117.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.2921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7445  Z= 0.127
  Angle     :  0.563   9.435  10078  Z= 0.294
  Chirality :  0.038   0.222   1108
  Planarity :  0.003   0.037   1259
  Dihedral  :  4.270  19.922    975
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.68 %
    Favored  : 96.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.28), residues: 869
  helix:  1.65 (0.20), residues: 663
  sheet:  None (None), residues: 0
  loop : -2.55 (0.39), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  85 
 TYR   0.025   0.001   TYR A 153 
 PHE   0.021   0.001   PHE B 214 
 TRP   0.050   0.002   TRP B 321 
 HIS   0.004   0.001   HIS A 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 7445)
  covalent geometry    : angle       0.56339 (10078)
  hydrogen bonds       : bond        0.04042 (  508)
  hydrogen bonds       : angle       3.77870 ( 1518)

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 187
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   69 LEU cc_start: 0.9348 (tt) cc_final: 0.8983 (mt)
REVERT: B  127 ASP cc_start: 0.8270 (t0) cc_final: 0.7440 (t70)
REVERT: B  134 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8459 (tm-30)
REVERT: B  152 PHE cc_start: 0.7635 (t80) cc_final: 0.7237 (t80)
REVERT: B  215 TYR cc_start: 0.4409 (t80) cc_final: 0.4196 (t80)
REVERT: A   34 LEU cc_start: 0.9194 (mt) cc_final: 0.8951 (mt)
REVERT: A   41 ARG cc_start: 0.8312 (ppt170) cc_final: 0.8020 (ptm-80)
REVERT: A   72 LYS cc_start: 0.9267 (mttt) cc_final: 0.8705 (mptt)
REVERT: A  152 MET cc_start: 0.8941 (tpp) cc_final: 0.8613 (tpt)
REVERT: A  169 GLN cc_start: 0.9014 (pm20) cc_final: 0.8573 (pp30)
REVERT: A  215 ARG cc_start: 0.9149 (ttm110) cc_final: 0.8734 (ttp-110)
REVERT: A  217 ILE cc_start: 0.9545 (mt) cc_final: 0.9207 (tp)
REVERT: A  321 ARG cc_start: 0.8475 (ptt90) cc_final: 0.7807 (tmm-80)
REVERT: A  344 LYS cc_start: 0.9554 (tmtt) cc_final: 0.9309 (tmtt)
REVERT: A  349 LEU cc_start: 0.9668 (tp) cc_final: 0.9433 (tp)
REVERT: A  371 ARG cc_start: 0.8854 (ttm170) cc_final: 0.8640 (ttm110)
REVERT: A  466 ILE cc_start: 0.8077 (pt) cc_final: 0.7797 (tp)
REVERT: A  510 LYS cc_start: 0.9014 (tttt) cc_final: 0.8493 (tmtt)
REVERT: A  609 MET cc_start: 0.8602 (ttt) cc_final: 0.8120 (tmm)
REVERT: A  652 LYS cc_start: 0.8475 (pttp) cc_final: 0.8061 (pttp)
REVERT: A  656 ASP cc_start: 0.8682 (m-30) cc_final: 0.8444 (m-30)
REVERT: A  666 TYR cc_start: 0.8519 (t80) cc_final: 0.7999 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 187
  average time/residue: 0.0806
  time to fit residues: 20.5140
Evaluate side-chains
  138 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 82 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 86 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
B  79 HIS
B  81 HIS
B 218 GLN
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.107420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.079949 restraints weight = 23736.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.081243 restraints weight = 13554.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.082334 restraints weight = 9073.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.082392 restraints weight = 8455.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.082580 restraints weight = 7498.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.3241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7445  Z= 0.127
  Angle     :  0.574   8.813  10078  Z= 0.297
  Chirality :  0.038   0.212   1108
  Planarity :  0.003   0.033   1259
  Dihedral  :  4.166  20.463    975
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.92 %
    Favored  : 96.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.28), residues: 869
  helix:  1.88 (0.20), residues: 663
  sheet:  None (None), residues: 0
  loop : -2.40 (0.40), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  85 
 TYR   0.033   0.001   TYR B 117 
 PHE   0.020   0.001   PHE B 214 
 TRP   0.056   0.002   TRP B 321 
 HIS   0.003   0.001   HIS A 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 7445)
  covalent geometry    : angle       0.57376 (10078)
  hydrogen bonds       : bond        0.03973 (  508)
  hydrogen bonds       : angle       3.72506 ( 1518)

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 177
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 ASN cc_start: 0.8792 (m-40) cc_final: 0.8548 (m-40)
REVERT: B   49 MET cc_start: 0.8504 (ptt) cc_final: 0.8263 (tmm)
REVERT: B   69 LEU cc_start: 0.9379 (tt) cc_final: 0.9169 (pp)
REVERT: B  117 TYR cc_start: 0.8852 (m-80) cc_final: 0.8580 (m-80)
REVERT: B  127 ASP cc_start: 0.8224 (t0) cc_final: 0.7244 (t70)
REVERT: B  134 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8471 (tm-30)
REVERT: B  152 PHE cc_start: 0.7658 (t80) cc_final: 0.7261 (t80)
REVERT: B  215 TYR cc_start: 0.4278 (t80) cc_final: 0.4019 (t80)
REVERT: A   41 ARG cc_start: 0.8312 (ppt170) cc_final: 0.7982 (ptm-80)
REVERT: A   72 LYS cc_start: 0.9300 (mttt) cc_final: 0.8756 (mptt)
REVERT: A  169 GLN cc_start: 0.9034 (pm20) cc_final: 0.8576 (pp30)
REVERT: A  215 ARG cc_start: 0.9139 (ttm110) cc_final: 0.8719 (ttp-110)
REVERT: A  217 ILE cc_start: 0.9534 (mt) cc_final: 0.9248 (tp)
REVERT: A  321 ARG cc_start: 0.8496 (ptt90) cc_final: 0.7963 (tmm-80)
REVERT: A  353 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8794 (tm-30)
REVERT: A  393 MET cc_start: 0.8955 (ppp) cc_final: 0.8735 (ppp)
REVERT: A  510 LYS cc_start: 0.8977 (tttt) cc_final: 0.8269 (tmtt)
REVERT: A  514 ASP cc_start: 0.8313 (m-30) cc_final: 0.8063 (m-30)
REVERT: A  609 MET cc_start: 0.8485 (ttt) cc_final: 0.8061 (tmm)
REVERT: A  666 TYR cc_start: 0.8498 (t80) cc_final: 0.7911 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 177
  average time/residue: 0.0797
  time to fit residues: 19.1889
Evaluate side-chains
  135 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 26 optimal weight:   20.0000
   chunk 1 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   chunk 85 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
B  79 HIS
B  81 HIS
B 189 GLN
B 218 GLN
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.107275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.081524 restraints weight = 23038.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.080560 restraints weight = 14318.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.081438 restraints weight = 11439.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.081999 restraints weight = 9019.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.082398 restraints weight = 7906.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.3345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7445  Z= 0.119
  Angle     :  0.567   8.613  10078  Z= 0.290
  Chirality :  0.037   0.159   1108
  Planarity :  0.003   0.031   1259
  Dihedral  :  4.093  19.805    975
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  1.90 %
    Favored  : 97.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.53 (0.28), residues: 869
  helix:  1.94 (0.19), residues: 663
  sheet:  None (None), residues: 0
  loop : -2.20 (0.41), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 653 
 TYR   0.028   0.001   TYR B 117 
 PHE   0.020   0.001   PHE B 214 
 TRP   0.059   0.002   TRP B 321 
 HIS   0.004   0.001   HIS A 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 7445)
  covalent geometry    : angle       0.56718 (10078)
  hydrogen bonds       : bond        0.03873 (  508)
  hydrogen bonds       : angle       3.67970 ( 1518)

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 179
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 ASN cc_start: 0.8829 (m-40) cc_final: 0.8547 (m-40)
REVERT: B   49 MET cc_start: 0.8514 (ptt) cc_final: 0.8257 (tmm)
REVERT: B   69 LEU cc_start: 0.9391 (tt) cc_final: 0.9163 (pp)
REVERT: B  117 TYR cc_start: 0.8882 (m-80) cc_final: 0.8572 (m-80)
REVERT: B  127 ASP cc_start: 0.8262 (t0) cc_final: 0.7243 (t70)
REVERT: B  134 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8470 (tm-30)
REVERT: B  152 PHE cc_start: 0.7567 (t80) cc_final: 0.7152 (t80)
REVERT: B  215 TYR cc_start: 0.4281 (t80) cc_final: 0.3933 (t80)
REVERT: A   41 ARG cc_start: 0.8178 (ppt170) cc_final: 0.7957 (ptm-80)
REVERT: A   72 LYS cc_start: 0.9277 (mttt) cc_final: 0.8778 (mptt)
REVERT: A  124 MET cc_start: 0.7969 (tpp) cc_final: 0.7762 (tpp)
REVERT: A  152 MET cc_start: 0.8524 (tpt) cc_final: 0.7475 (tpt)
REVERT: A  153 TYR cc_start: 0.8410 (m-80) cc_final: 0.8171 (m-10)
REVERT: A  215 ARG cc_start: 0.9169 (ttm110) cc_final: 0.8768 (ttp-110)
REVERT: A  217 ILE cc_start: 0.9526 (mt) cc_final: 0.9260 (tp)
REVERT: A  321 ARG cc_start: 0.8537 (ptt90) cc_final: 0.7981 (tmm-80)
REVERT: A  353 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8780 (tm-30)
REVERT: A  371 ARG cc_start: 0.8823 (ttm170) cc_final: 0.8568 (ttm110)
REVERT: A  393 MET cc_start: 0.8968 (ppp) cc_final: 0.8760 (ppp)
REVERT: A  441 MET cc_start: 0.8986 (tmm) cc_final: 0.8603 (tmm)
REVERT: A  510 LYS cc_start: 0.9000 (tttt) cc_final: 0.8225 (tmtt)
REVERT: A  514 ASP cc_start: 0.8390 (m-30) cc_final: 0.8091 (m-30)
REVERT: A  520 MET cc_start: 0.8773 (mmp) cc_final: 0.8446 (mmm)
REVERT: A  609 MET cc_start: 0.8495 (ttt) cc_final: 0.8093 (tmm)
REVERT: A  666 TYR cc_start: 0.8489 (t80) cc_final: 0.7947 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 179
  average time/residue: 0.0837
  time to fit residues: 20.2355
Evaluate side-chains
  131 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 68 optimal weight:    0.0470
   chunk 27 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    1.2084

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

Flipped N/Q/H residues before XYZ refinement:
B  47 ASN
B  81 HIS
B 189 GLN
B 218 GLN
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 611 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.107142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.081081 restraints weight = 23643.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.079538 restraints weight = 14522.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.080494 restraints weight = 12100.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.080963 restraints weight = 9422.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.081113 restraints weight = 8400.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.3562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7445  Z= 0.127
  Angle     :  0.578   8.972  10078  Z= 0.297
  Chirality :  0.038   0.225   1108
  Planarity :  0.003   0.031   1259
  Dihedral  :  4.094  20.571    975
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  1.65 %
    Favored  : 98.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.63 (0.28), residues: 869
  helix:  1.97 (0.19), residues: 665
  sheet:  None (None), residues: 0
  loop : -2.05 (0.42), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 317 
 TYR   0.023   0.001   TYR B 117 
 PHE   0.018   0.001   PHE B 214 
 TRP   0.064   0.002   TRP B 321 
 HIS   0.004   0.001   HIS A 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 7445)
  covalent geometry    : angle       0.57755 (10078)
  hydrogen bonds       : bond        0.03890 (  508)
  hydrogen bonds       : angle       3.69504 ( 1518)

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 173
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   49 MET cc_start: 0.8592 (ptt) cc_final: 0.8307 (tmm)
REVERT: B   69 LEU cc_start: 0.9426 (tt) cc_final: 0.9194 (pp)
REVERT: B  117 TYR cc_start: 0.8918 (m-80) cc_final: 0.8652 (m-80)
REVERT: B  118 LEU cc_start: 0.9466 (mt) cc_final: 0.9254 (mt)
REVERT: B  122 HIS cc_start: 0.9385 (m90) cc_final: 0.9143 (m90)
REVERT: B  127 ASP cc_start: 0.8194 (t0) cc_final: 0.7202 (t70)
REVERT: B  134 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8461 (tm-30)
REVERT: B  215 TYR cc_start: 0.4199 (t80) cc_final: 0.3845 (t80)
REVERT: A   41 ARG cc_start: 0.8306 (ppt170) cc_final: 0.7821 (ptm-80)
REVERT: A   72 LYS cc_start: 0.9279 (mttt) cc_final: 0.8870 (mmtm)
REVERT: A  152 MET cc_start: 0.8538 (tpt) cc_final: 0.7364 (tpt)
REVERT: A  153 TYR cc_start: 0.8507 (m-80) cc_final: 0.8250 (m-80)
REVERT: A  215 ARG cc_start: 0.9161 (ttm110) cc_final: 0.8742 (ttp-110)
REVERT: A  217 ILE cc_start: 0.9537 (mt) cc_final: 0.9257 (tp)
REVERT: A  321 ARG cc_start: 0.8536 (ptt90) cc_final: 0.7990 (tmm-80)
REVERT: A  353 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8756 (tm-30)
REVERT: A  371 ARG cc_start: 0.8834 (ttm170) cc_final: 0.8597 (ttm110)
REVERT: A  393 MET cc_start: 0.9019 (ppp) cc_final: 0.8811 (ppp)
REVERT: A  418 ASP cc_start: 0.9256 (m-30) cc_final: 0.9026 (m-30)
REVERT: A  441 MET cc_start: 0.9046 (tmm) cc_final: 0.8668 (tmm)
REVERT: A  510 LYS cc_start: 0.8996 (tttt) cc_final: 0.8251 (tmtt)
REVERT: A  514 ASP cc_start: 0.8419 (m-30) cc_final: 0.8158 (m-30)
REVERT: A  555 GLN cc_start: 0.8999 (mt0) cc_final: 0.8612 (mt0)
REVERT: A  609 MET cc_start: 0.8549 (ttt) cc_final: 0.8161 (tmm)
REVERT: A  666 TYR cc_start: 0.8498 (t80) cc_final: 0.7914 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 175
  average time/residue: 0.0831
  time to fit residues: 19.5264
Evaluate side-chains
  138 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 85 optimal weight:    4.9990
   chunk 19 optimal weight:    9.9990
   chunk 38 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 32 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
B  79 HIS
B 218 GLN
** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 113 HIS
A 117 GLN
A 186 ASN
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 429 ASN
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 611 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.103319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.077329 restraints weight = 23386.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.077055 restraints weight = 14402.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.077723 restraints weight = 10888.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.078070 restraints weight = 9144.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.078291 restraints weight = 8336.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.3596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7445  Z= 0.211
  Angle     :  0.687   9.709  10078  Z= 0.351
  Chirality :  0.041   0.179   1108
  Planarity :  0.004   0.033   1259
  Dihedral  :  4.450  29.008    975
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  2.66 %
    Favored  : 97.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.51 (0.28), residues: 869
  helix:  1.85 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -1.97 (0.42), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 589 
 TYR   0.020   0.002   TYR A  74 
 PHE   0.017   0.002   PHE B 214 
 TRP   0.068   0.002   TRP B 321 
 HIS   0.003   0.001   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 7445)
  covalent geometry    : angle       0.68669 (10078)
  hydrogen bonds       : bond        0.04462 (  508)
  hydrogen bonds       : angle       4.06347 ( 1518)

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 156
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   69 LEU cc_start: 0.9434 (tt) cc_final: 0.9202 (pp)
REVERT: B  117 TYR cc_start: 0.8973 (m-80) cc_final: 0.8612 (m-80)
REVERT: B  127 ASP cc_start: 0.8184 (t0) cc_final: 0.7655 (t70)
REVERT: B  134 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8492 (tm-30)
REVERT: B  195 MET cc_start: 0.8023 (mtm) cc_final: 0.7751 (mtp)
REVERT: B  215 TYR cc_start: 0.4334 (t80) cc_final: 0.4074 (t80)
REVERT: A  152 MET cc_start: 0.8531 (tpt) cc_final: 0.7352 (tpt)
REVERT: A  153 TYR cc_start: 0.8643 (m-80) cc_final: 0.8245 (m-80)
REVERT: A  215 ARG cc_start: 0.9225 (ttm110) cc_final: 0.8758 (ttp-110)
REVERT: A  321 ARG cc_start: 0.8508 (ptt90) cc_final: 0.7992 (tmm-80)
REVERT: A  353 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8734 (tm-30)
REVERT: A  371 ARG cc_start: 0.8820 (ttm170) cc_final: 0.8573 (ttm110)
REVERT: A  418 ASP cc_start: 0.9268 (m-30) cc_final: 0.9058 (m-30)
REVERT: A  473 MET cc_start: 0.9110 (mmp) cc_final: 0.8826 (mmp)
REVERT: A  510 LYS cc_start: 0.9032 (tttt) cc_final: 0.8713 (tttp)
REVERT: A  555 GLN cc_start: 0.9029 (mt0) cc_final: 0.8685 (mt0)
REVERT: A  609 MET cc_start: 0.8647 (ttt) cc_final: 0.8148 (tmm)
  outliers start: 2
  outliers final: 2
  residues processed: 158
  average time/residue: 0.0784
  time to fit residues: 16.8824
Evaluate side-chains
  124 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 122
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 72 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 42 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 55 optimal weight:    6.9990
   chunk 85 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 37 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B  81 HIS
B 189 GLN
B 218 GLN
** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 611 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.106348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.080571 restraints weight = 23618.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.079152 restraints weight = 15087.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.080152 restraints weight = 12041.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.080618 restraints weight = 9304.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.080801 restraints weight = 8302.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.3788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7445  Z= 0.126
  Angle     :  0.625   9.396  10078  Z= 0.321
  Chirality :  0.040   0.246   1108
  Planarity :  0.003   0.032   1259
  Dihedral  :  4.232  23.667    975
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.52 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.70 (0.28), residues: 869
  helix:  2.00 (0.19), residues: 665
  sheet:  None (None), residues: 0
  loop : -1.92 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 317 
 TYR   0.020   0.001   TYR B 117 
 PHE   0.017   0.001   PHE B 214 
 TRP   0.071   0.002   TRP B 321 
 HIS   0.007   0.001   HIS A 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7445)
  covalent geometry    : angle       0.62452 (10078)
  hydrogen bonds       : bond        0.04135 (  508)
  hydrogen bonds       : angle       3.84120 ( 1518)

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 161
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   49 MET cc_start: 0.8497 (ptt) cc_final: 0.8186 (tmm)
REVERT: B   69 LEU cc_start: 0.9439 (tt) cc_final: 0.9187 (pp)
REVERT: B  117 TYR cc_start: 0.8906 (m-80) cc_final: 0.8631 (m-80)
REVERT: B  118 LEU cc_start: 0.9527 (mt) cc_final: 0.9314 (mt)
REVERT: B  122 HIS cc_start: 0.9404 (m90) cc_final: 0.9096 (m90)
REVERT: B  127 ASP cc_start: 0.8141 (t0) cc_final: 0.7383 (t0)
REVERT: B  134 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8484 (tm-30)
REVERT: B  215 TYR cc_start: 0.4283 (t80) cc_final: 0.3951 (t80)
REVERT: A   72 LYS cc_start: 0.9239 (mttt) cc_final: 0.8656 (mmtm)
REVERT: A  124 MET cc_start: 0.8495 (mmp) cc_final: 0.8210 (tpp)
REVERT: A  152 MET cc_start: 0.8103 (tpt) cc_final: 0.7255 (tpt)
REVERT: A  153 TYR cc_start: 0.8562 (m-80) cc_final: 0.8246 (m-80)
REVERT: A  215 ARG cc_start: 0.9202 (ttm110) cc_final: 0.8725 (ttp-110)
REVERT: A  217 ILE cc_start: 0.9511 (mt) cc_final: 0.9256 (tp)
REVERT: A  321 ARG cc_start: 0.8491 (ptt90) cc_final: 0.7934 (tmm-80)
REVERT: A  353 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8737 (tm-30)
REVERT: A  361 LEU cc_start: 0.9435 (mp) cc_final: 0.9218 (mm)
REVERT: A  371 ARG cc_start: 0.8847 (ttm170) cc_final: 0.8618 (ttm110)
REVERT: A  418 ASP cc_start: 0.9235 (m-30) cc_final: 0.9008 (m-30)
REVERT: A  510 LYS cc_start: 0.8963 (tttt) cc_final: 0.8288 (tmtt)
REVERT: A  514 ASP cc_start: 0.8409 (m-30) cc_final: 0.8134 (m-30)
REVERT: A  609 MET cc_start: 0.8602 (ttt) cc_final: 0.8093 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 161
  average time/residue: 0.0784
  time to fit residues: 17.2797
Evaluate side-chains
  127 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 54 optimal weight:    7.9990
   chunk 85 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 78 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 16 optimal weight:    7.9990
   chunk 84 optimal weight:    0.9990
   overall best weight:    1.1588

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

Flipped N/Q/H residues before XYZ refinement:
B  81 HIS
B 189 GLN
B 218 GLN
** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 453 GLN
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 611 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.105734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.080989 restraints weight = 22640.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.079521 restraints weight = 14485.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.080469 restraints weight = 11451.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.080996 restraints weight = 8712.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.081175 restraints weight = 7716.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.3926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7445  Z= 0.131
  Angle     :  0.646   9.434  10078  Z= 0.328
  Chirality :  0.040   0.234   1108
  Planarity :  0.003   0.031   1259
  Dihedral  :  4.208  24.483    975
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.38 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.73 (0.28), residues: 869
  helix:  2.06 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.95 (0.43), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 317 
 TYR   0.018   0.001   TYR B 117 
 PHE   0.014   0.001   PHE B 214 
 TRP   0.074   0.002   TRP B 321 
 HIS   0.005   0.001   HIS A 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 7445)
  covalent geometry    : angle       0.64582 (10078)
  hydrogen bonds       : bond        0.04041 (  508)
  hydrogen bonds       : angle       3.91403 ( 1518)

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 167
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   69 LEU cc_start: 0.9413 (tt) cc_final: 0.9162 (pp)
REVERT: B  117 TYR cc_start: 0.8829 (m-80) cc_final: 0.8553 (m-80)
REVERT: B  122 HIS cc_start: 0.9362 (m90) cc_final: 0.9148 (m90)
REVERT: B  134 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8526 (tm-30)
REVERT: B  189 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8675 (mm-40)
REVERT: B  215 TYR cc_start: 0.4287 (t80) cc_final: 0.3934 (t80)
REVERT: A   34 LEU cc_start: 0.9045 (mt) cc_final: 0.8840 (pp)
REVERT: A   72 LYS cc_start: 0.9255 (mttt) cc_final: 0.8655 (mmtm)
REVERT: A  153 TYR cc_start: 0.8540 (m-80) cc_final: 0.8247 (m-80)
REVERT: A  215 ARG cc_start: 0.9203 (ttm110) cc_final: 0.8784 (ttp-110)
REVERT: A  217 ILE cc_start: 0.9497 (mt) cc_final: 0.8927 (tp)
REVERT: A  220 GLN cc_start: 0.8626 (mp10) cc_final: 0.8320 (mp10)
REVERT: A  321 ARG cc_start: 0.8442 (ptt90) cc_final: 0.7850 (tmm-80)
REVERT: A  353 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8717 (tm-30)
REVERT: A  361 LEU cc_start: 0.9407 (mp) cc_final: 0.9199 (mm)
REVERT: A  371 ARG cc_start: 0.8747 (ttm170) cc_final: 0.8527 (ttm110)
REVERT: A  418 ASP cc_start: 0.9231 (m-30) cc_final: 0.8993 (m-30)
REVERT: A  510 LYS cc_start: 0.8950 (tttt) cc_final: 0.8284 (tmtt)
REVERT: A  514 ASP cc_start: 0.8385 (m-30) cc_final: 0.8145 (m-30)
REVERT: A  609 MET cc_start: 0.8530 (ttt) cc_final: 0.8018 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 167
  average time/residue: 0.0843
  time to fit residues: 19.1309
Evaluate side-chains
  131 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 130
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 29 optimal weight:    0.2980
   chunk 0 optimal weight:   10.0000
   chunk 80 optimal weight:    0.2980
   chunk 59 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 64 optimal weight:    8.9990
   chunk 6 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9980
   chunk 67 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
B  47 ASN
B 189 GLN
B 218 GLN
** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 453 GLN
A 611 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.106355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.080766 restraints weight = 23103.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.080351 restraints weight = 13260.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.081025 restraints weight = 10696.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.081510 restraints weight = 8485.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.081728 restraints weight = 7781.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.4057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7445  Z= 0.126
  Angle     :  0.646   9.620  10078  Z= 0.327
  Chirality :  0.039   0.215   1108
  Planarity :  0.003   0.041   1259
  Dihedral  :  4.185  22.641    975
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.72 (0.29), residues: 869
  helix:  2.03 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.87 (0.43), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 317 
 TYR   0.020   0.001   TYR B 117 
 PHE   0.027   0.001   PHE B 193 
 TRP   0.072   0.002   TRP B 321 
 HIS   0.007   0.001   HIS A 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 7445)
  covalent geometry    : angle       0.64636 (10078)
  hydrogen bonds       : bond        0.04042 (  508)
  hydrogen bonds       : angle       3.88411 ( 1518)

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 ASN cc_start: 0.8839 (m-40) cc_final: 0.8602 (m-40)
REVERT: B   69 LEU cc_start: 0.9422 (tt) cc_final: 0.9173 (pp)
REVERT: B  130 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8320 (mm-30)
REVERT: B  189 GLN cc_start: 0.9251 (mm-40) cc_final: 0.8855 (mm-40)
REVERT: B  215 TYR cc_start: 0.4284 (t80) cc_final: 0.3934 (t80)
REVERT: A   72 LYS cc_start: 0.9247 (mttt) cc_final: 0.8663 (mmtm)
REVERT: A  124 MET cc_start: 0.7816 (tpp) cc_final: 0.7483 (tpp)
REVERT: A  131 LEU cc_start: 0.8859 (mm) cc_final: 0.8644 (tp)
REVERT: A  152 MET cc_start: 0.8303 (tpt) cc_final: 0.7558 (tpt)
REVERT: A  215 ARG cc_start: 0.9196 (ttm110) cc_final: 0.8771 (ttp-110)
REVERT: A  217 ILE cc_start: 0.9472 (mt) cc_final: 0.9176 (tp)
REVERT: A  321 ARG cc_start: 0.8417 (ptt90) cc_final: 0.7826 (tmm-80)
REVERT: A  353 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8756 (tm-30)
REVERT: A  361 LEU cc_start: 0.9431 (mp) cc_final: 0.9213 (mm)
REVERT: A  371 ARG cc_start: 0.8739 (ttm170) cc_final: 0.8538 (ttm110)
REVERT: A  418 ASP cc_start: 0.9201 (m-30) cc_final: 0.8991 (m-30)
REVERT: A  510 LYS cc_start: 0.8934 (tttt) cc_final: 0.8256 (tmtt)
REVERT: A  514 ASP cc_start: 0.8390 (m-30) cc_final: 0.8156 (m-30)
REVERT: A  520 MET cc_start: 0.8600 (mmp) cc_final: 0.8267 (mmm)
REVERT: A  609 MET cc_start: 0.8516 (ttt) cc_final: 0.8006 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.0732
  time to fit residues: 16.8054
Evaluate side-chains
  129 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 11 optimal weight:    8.9990
   chunk 27 optimal weight:    7.9990
   chunk 80 optimal weight:    0.9980
   chunk 20 optimal weight:    6.9990
   chunk 21 optimal weight:    7.9990
   chunk 70 optimal weight:    4.9990
   chunk 77 optimal weight:    0.7980
   chunk 83 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
B 137 ASN
B 218 GLN
** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 611 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.106560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.079748 restraints weight = 23675.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.079614 restraints weight = 14388.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.080397 restraints weight = 11930.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.080650 restraints weight = 9159.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.080747 restraints weight = 8386.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.4148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7445  Z= 0.133
  Angle     :  0.662   9.424  10078  Z= 0.338
  Chirality :  0.040   0.208   1108
  Planarity :  0.003   0.041   1259
  Dihedral  :  4.142  23.131    975
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.25 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.68 (0.29), residues: 869
  helix:  2.00 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -1.98 (0.43), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  75 
 TYR   0.043   0.001   TYR B 117 
 PHE   0.025   0.001   PHE B 193 
 TRP   0.078   0.002   TRP B 321 
 HIS   0.006   0.001   HIS A 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7445)
  covalent geometry    : angle       0.66248 (10078)
  hydrogen bonds       : bond        0.04045 (  508)
  hydrogen bonds       : angle       3.93005 ( 1518)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1202.22 seconds
wall clock time: 21 minutes 26.78 seconds (1286.78 seconds total)