Starting phenix.real_space_refine
on Wed Feb  4 00:54:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9l8t_62890/02_2026/9l8t_62890.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9l8t_62890/02_2026/9l8t_62890.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9l8t_62890/02_2026/9l8t_62890.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9l8t_62890/02_2026/9l8t_62890.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9l8t_62890/02_2026/9l8t_62890.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9l8t_62890/02_2026/9l8t_62890.map"
  }
  resolution = 2.92
  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=   0.082
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      51      5.16       5
     C    5137      2.51       5
     N    1349      2.21       5
     O    1471      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8008
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 8008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 982, 8008
          Classifications: {'peptide': 982}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 45, 'TRANS': 936}
          Chain breaks: 1
  Time building chain proxies: 1.54, per 1000 atoms: 0.19
  Number of scatterers: 8008
  At special positions: 0
  Unit cell: (75.257, 114.953, 103.375, 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      51     16.00
     O    1471      8.00
     N    1349      7.00
     C    5137      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: 0.59
  Conformation dependent library (CDL) restraints added in 286.2 milliseconds
  

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1876

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 7 sheets defined
      50.3% alpha, 14.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 15
    Processing helix  chain 'A' and resid 15 through 29
    Processing helix  chain 'A' and resid 79 through 92
    Processing helix  chain 'A' and resid 128 through 143
    Processing helix  chain 'A' and resid 153 through 162
      removed outlier: 4.353A  pdb=" N   MET A 157 " --> pdb=" O   CYS A 153 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU A 162 " --> pdb=" O   VAL A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 191
      No H-bonds generated for 'chain 'A' and resid 189 through 191'
    Processing helix  chain 'A' and resid 271 through 287
    Processing helix  chain 'A' and resid 299 through 312
    Processing helix  chain 'A' and resid 313 through 323
    Processing helix  chain 'A' and resid 328 through 335
    Processing helix  chain 'A' and resid 366 through 374
    Processing helix  chain 'A' and resid 381 through 389
    Processing helix  chain 'A' and resid 398 through 409
    Processing helix  chain 'A' and resid 410 through 435
    Processing helix  chain 'A' and resid 436 through 449
    Processing helix  chain 'A' and resid 451 through 458
    Processing helix  chain 'A' and resid 460 through 473
    Processing helix  chain 'A' and resid 520 through 530
    Processing helix  chain 'A' and resid 532 through 534
      No H-bonds generated for 'chain 'A' and resid 532 through 534'
    Processing helix  chain 'A' and resid 539 through 549
    Processing helix  chain 'A' and resid 580 through 609
    Processing helix  chain 'A' and resid 616 through 647
      removed outlier: 4.839A  pdb=" N   TYR A 642 " --> pdb=" O   MET A 638 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   GLY A 643 " --> pdb=" O   ASN A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 679
    Processing helix  chain 'A' and resid 696 through 699
    Processing helix  chain 'A' and resid 700 through 709
    Processing helix  chain 'A' and resid 713 through 748
    Processing helix  chain 'A' and resid 800 through 815
    Processing helix  chain 'A' and resid 826 through 841
    Processing helix  chain 'A' and resid 842 through 845
    Processing helix  chain 'A' and resid 846 through 851
      removed outlier: 3.580A  pdb=" N   ILE A 851 " --> pdb=" O   GLU A 848 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 862 through 880
    Processing helix  chain 'A' and resid 920 through 925
      removed outlier: 3.600A  pdb=" N   MET A 925 " --> pdb=" O   GLY A 922 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 927 through 935
    Processing helix  chain 'A' and resid 939 through 948
      removed outlier: 3.586A  pdb=" N   TYR A 943 " --> pdb=" O   ASP A 939 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 948 through 953
    Processing helix  chain 'A' and resid 954 through 956
      No H-bonds generated for 'chain 'A' and resid 954 through 956'
    Processing helix  chain 'A' and resid 959 through 963
    Processing helix  chain 'A' and resid 970 through 990
    Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 180
      removed outlier: 6.356A  pdb=" N   SER A  54 " --> pdb=" O   PRO A  36 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LEU A  32 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 147
      removed outlier: 4.185A  pdb=" N   VAL A  70 " --> pdb=" O   PHE A 126 " (cutoff:3.500A)
      removed outlier: 7.426A  pdb=" N   ALA A 481 " --> pdb=" O   THR A 104 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   ARG A 106 " --> pdb=" O   ALA A 481 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 268
      removed outlier: 6.945A  pdb=" N   ILE A 239 " --> pdb=" O   LEU A 248 " (cutoff:3.500A)
      removed outlier: 4.849A  pdb=" N   SER A 250 " --> pdb=" O   MET A 237 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   MET A 237 " --> pdb=" O   SER A 250 " (cutoff:3.500A)
      removed outlier: 4.996A  pdb=" N   CYS A 252 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   ILE A 235 " --> pdb=" O   CYS A 252 " (cutoff:3.500A)
      removed outlier: 4.967A  pdb=" N   THR A 254 " --> pdb=" O   PHE A 233 " (cutoff:3.500A)
      removed outlier: 7.650A  pdb=" N   PHE A 233 " --> pdb=" O   THR A 254 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   GLU A 213 " --> pdb=" O   PHE A 233 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   ILE A 235 " --> pdb=" O   ASP A 211 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   ASP A 211 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   MET A 237 " --> pdb=" O   ALA A 209 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   ALA A 209 " --> pdb=" O   MET A 237 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   ILE A 239 " --> pdb=" O   VAL A 207 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   VAL A 207 " --> pdb=" O   ILE A 239 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   CYS A 291 " --> pdb=" O   ILE A 364 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 344
      removed outlier: 5.002A  pdb=" N   LYS A 339 " --> pdb=" O   PHE A 355 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   PHE A 355 " --> pdb=" O   LYS A 339 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 500 through 501
      removed outlier: 4.452A  pdb=" N   GLY A 686 " --> pdb=" O   ILE A 501 " (cutoff:3.500A)
      removed outlier: 5.413A  pdb=" N   ILE A 683 " --> pdb=" O   THR A 694 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   THR A 694 " --> pdb=" O   ILE A 683 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 506 through 508
      removed outlier: 3.512A  pdb=" N   VAL A 763 " --> pdb=" O   GLU A 508 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   LYS A 770 " --> pdb=" O   THR A 766 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   TYR A 771 " --> pdb=" O   ARG A 790 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 536 through 537

    426 hydrogen bonds defined for protein.
    1221 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: 1.14

  Time building geometry restraints manager: 0.80 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2550
        1.34 -     1.46: 1299
        1.46 -     1.57: 4273
        1.57 -     1.69: 0
        1.69 -     1.81: 81
  Bond restraints: 8203
  Sorted by residual:
  bond pdb=" CA  ILE A 792 "
       pdb=" CB  ILE A 792 "
    ideal  model  delta    sigma   weight residual
    1.553  1.539  0.014 7.40e-03 1.83e+04 3.75e+00
  bond pdb=" SD  MET A 872 "
       pdb=" CE  MET A 872 "
    ideal  model  delta    sigma   weight residual
    1.791  1.756  0.035 2.50e-02 1.60e+03 1.98e+00
  bond pdb=" SD  MET A  35 "
       pdb=" CE  MET A  35 "
    ideal  model  delta    sigma   weight residual
    1.791  1.762  0.029 2.50e-02 1.60e+03 1.39e+00
  bond pdb=" CB  ILE A 940 "
       pdb=" CG2 ILE A 940 "
    ideal  model  delta    sigma   weight residual
    1.521  1.486  0.035 3.30e-02 9.18e+02 1.11e+00
  bond pdb=" CB  MET A 234 "
       pdb=" CG  MET A 234 "
    ideal  model  delta    sigma   weight residual
    1.520  1.489  0.031 3.00e-02 1.11e+03 1.09e+00
  ... (remaining 8198 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 10915
        2.09 -     4.17: 154
        4.17 -     6.26: 16
        6.26 -     8.34: 6
        8.34 -    10.43: 1
  Bond angle restraints: 11092
  Sorted by residual:
  angle pdb=" N   ILE A 794 "
        pdb=" CA  ILE A 794 "
        pdb=" C   ILE A 794 "
      ideal   model   delta    sigma   weight residual
     111.62  107.92    3.70 7.90e-01 1.60e+00 2.20e+01
  angle pdb=" N   GLN A 888 "
        pdb=" CA  GLN A 888 "
        pdb=" C   GLN A 888 "
      ideal   model   delta    sigma   weight residual
     112.88  108.91    3.97 1.29e+00 6.01e-01 9.45e+00
  angle pdb=" CA  LEU A  89 "
        pdb=" CB  LEU A  89 "
        pdb=" CG  LEU A  89 "
      ideal   model   delta    sigma   weight residual
     116.30  126.73  -10.43 3.50e+00 8.16e-02 8.87e+00
  angle pdb=" C   LEU A  26 "
        pdb=" N   GLN A  27 "
        pdb=" CA  GLN A  27 "
      ideal   model   delta    sigma   weight residual
     120.72  115.82    4.90 1.67e+00 3.59e-01 8.62e+00
  angle pdb=" N   ILE A 944 "
        pdb=" CA  ILE A 944 "
        pdb=" CB  ILE A 944 "
      ideal   model   delta    sigma   weight residual
     110.62  113.82   -3.20 1.09e+00 8.42e-01 8.62e+00
  ... (remaining 11087 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 4534
       17.82 -    35.63: 362
       35.63 -    53.45: 45
       53.45 -    71.26: 10
       71.26 -    89.08: 11
  Dihedral angle restraints: 4962
    sinusoidal: 2049
      harmonic: 2913
  Sorted by residual:
  dihedral pdb=" CA  HIS A 474 "
           pdb=" C   HIS A 474 "
           pdb=" N   ASP A 475 "
           pdb=" CA  ASP A 475 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.74  -19.26     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  PHE A 240 "
           pdb=" C   PHE A 240 "
           pdb=" N   TRP A 241 "
           pdb=" CA  TRP A 241 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.11   16.89     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" CB  GLU A 926 "
           pdb=" CG  GLU A 926 "
           pdb=" CD  GLU A 926 "
           pdb=" OE1 GLU A 926 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.08  -89.08     1      3.00e+01 1.11e-03 1.05e+01
  ... (remaining 4959 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 723
       0.028 -    0.057: 277
       0.057 -    0.085: 113
       0.085 -    0.113: 62
       0.113 -    0.142: 22
  Chirality restraints: 1197
  Sorted by residual:
  chirality pdb=" CA  ASP A 861 "
            pdb=" N   ASP A 861 "
            pdb=" C   ASP A 861 "
            pdb=" CB  ASP A 861 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.03e-01
  chirality pdb=" CB  ILE A 938 "
            pdb=" CA  ILE A 938 "
            pdb=" CG1 ILE A 938 "
            pdb=" CG2 ILE A 938 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.14 2.00e-01 2.50e+01 4.84e-01
  chirality pdb=" CA  PRO A 439 "
            pdb=" N   PRO A 439 "
            pdb=" C   PRO A 439 "
            pdb=" CB  PRO A 439 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.42e-01
  ... (remaining 1194 not shown)

  Planarity restraints: 1418
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 891 "   -0.053 5.00e-02 4.00e+02   8.03e-02 1.03e+01
        pdb=" N   PRO A 892 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO A 892 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A 892 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 403 "   -0.022 2.00e-02 2.50e+03   1.93e-02 9.30e+00
        pdb=" CG  TRP A 403 "    0.052 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 403 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 403 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 403 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 403 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 403 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 403 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 403 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 403 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 216 "    0.010 2.00e-02 2.50e+03   1.93e-02 3.72e+00
        pdb=" C   SER A 216 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   SER A 216 "    0.012 2.00e-02 2.50e+03
        pdb=" N   PRO A 217 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1415 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1224
        2.76 -     3.29: 8379
        3.29 -     3.83: 14468
        3.83 -     4.36: 16465
        4.36 -     4.90: 27717
  Nonbonded interactions: 68253
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 514 "
            pdb=" O   GLU A 758 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" OH  TYR A 471 "
            pdb=" OD2 ASP A 588 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" O   ASN A  15 "
            pdb=" OG1 THR A  19 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OE1 GLN A 799 "
            pdb=" OH  TYR A 947 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" NH1 ARG A 106 "
            pdb=" O   TYR A 477 "
     model   vdw
     2.272 3.120
  ... (remaining 68248 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.990
  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:         0.010
  Set scattering table:                    0.030
  Process input model:                     7.490
  Find NCS groups from input model:        0.030
  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:6.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5712
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      :  0.004   0.039   8203  Z= 0.160
  Angle     :  0.622  10.426  11092  Z= 0.337
  Chirality :  0.042   0.142   1197
  Planarity :  0.004   0.080   1418
  Dihedral  : 13.450  89.076   3086
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.27), residues: 978
  helix:  1.63 (0.25), residues: 446
  sheet: -0.32 (0.45), residues: 126
  loop : -0.34 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 978 
 TYR   0.011   0.001   TYR A 374 
 PHE   0.017   0.001   PHE A 868 
 TRP   0.052   0.002   TRP A 403 
 HIS   0.004   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 8203)
  covalent geometry    : angle       0.62171 (11092)
  hydrogen bonds       : bond        0.16752 (  426)
  hydrogen bonds       : angle       6.99845 ( 1221)

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A    5 MET cc_start: 0.5660 (mmp) cc_final: 0.5248 (mmt)
REVERT: A   44 TYR cc_start: 0.7350 (m-80) cc_final: 0.6827 (m-80)
REVERT: A   66 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6641 (mm-30)
REVERT: A   97 TYR cc_start: 0.7556 (p90) cc_final: 0.6428 (p90)
REVERT: A  127 LYS cc_start: 0.6888 (tppp) cc_final: 0.6483 (tptt)
REVERT: A  134 LYS cc_start: 0.6679 (mtpp) cc_final: 0.6334 (mtmt)
REVERT: A  141 ASN cc_start: 0.7237 (m-40) cc_final: 0.7026 (m110)
REVERT: A  144 TYR cc_start: 0.7063 (m-80) cc_final: 0.6542 (m-80)
REVERT: A  185 ARG cc_start: 0.6540 (mtp-110) cc_final: 0.6225 (mtp-110)
REVERT: A  334 LYS cc_start: 0.7020 (ttpp) cc_final: 0.6780 (tmmt)
REVERT: A  344 LYS cc_start: 0.7363 (tppt) cc_final: 0.6409 (ttpt)
REVERT: A  378 GLU cc_start: 0.5400 (pm20) cc_final: 0.5077 (pm20)
REVERT: A  492 HIS cc_start: 0.7532 (t70) cc_final: 0.7292 (m90)
REVERT: A  511 LYS cc_start: 0.7571 (mttt) cc_final: 0.7025 (mmmm)
REVERT: A  517 ASP cc_start: 0.6634 (m-30) cc_final: 0.6348 (m-30)
REVERT: A  573 ASN cc_start: 0.6508 (m-40) cc_final: 0.6265 (m110)
REVERT: A  601 LYS cc_start: 0.7154 (tppt) cc_final: 0.6934 (tppt)
REVERT: A  730 LYS cc_start: 0.7300 (tmmt) cc_final: 0.6946 (tptp)
REVERT: A  744 ARG cc_start: 0.6107 (ttp80) cc_final: 0.5265 (ttp-110)
REVERT: A  745 GLN cc_start: 0.6998 (tp-100) cc_final: 0.6417 (mt0)
REVERT: A  787 LEU cc_start: 0.7039 (mt) cc_final: 0.6595 (mp)
REVERT: A  813 GLU cc_start: 0.7863 (tp30) cc_final: 0.7571 (tm-30)
REVERT: A  818 ARG cc_start: 0.6520 (mtt180) cc_final: 0.6194 (mtt90)
REVERT: A  830 ILE cc_start: 0.7005 (tt) cc_final: 0.6505 (tt)
REVERT: A  872 MET cc_start: 0.2341 (tmm) cc_final: 0.1782 (tmm)
  outliers start: 0
  outliers final: 1
  residues processed: 190
  average time/residue: 0.5231
  time to fit residues: 105.2479
Evaluate side-chains
  123 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 122
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  957 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A  24 ASN
A 598 GLN
A 781 ASN
A 984 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.211588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.149225 restraints weight = 8901.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3712 rms_B_bonded: 2.33
r_work: 0.3541 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.1982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8203  Z= 0.168
  Angle     :  0.636   8.335  11092  Z= 0.331
  Chirality :  0.045   0.165   1197
  Planarity :  0.005   0.067   1418
  Dihedral  :  4.452  18.807   1088
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 12.02 %
    Favored  : 84.69 %
  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:  0.63 (0.26), residues: 978
  helix:  1.47 (0.24), residues: 455
  sheet: -0.36 (0.44), residues: 132
  loop : -0.48 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 809 
 TYR   0.016   0.001   TYR A 772 
 PHE   0.017   0.002   PHE A 637 
 TRP   0.013   0.001   TRP A 856 
 HIS   0.005   0.001   HIS A 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 8203)
  covalent geometry    : angle       0.63631 (11092)
  hydrogen bonds       : bond        0.04349 (  426)
  hydrogen bonds       : angle       5.31670 ( 1221)

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 134
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A   44 TYR cc_start: 0.7878 (m-80) cc_final: 0.7445 (m-80)
REVERT: A   75 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7709 (mt0)
REVERT: A   89 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7546 (pt)
REVERT: A   97 TYR cc_start: 0.7783 (p90) cc_final: 0.7042 (p90)
REVERT: A  127 LYS cc_start: 0.8331 (tppp) cc_final: 0.8006 (tptt)
REVERT: A  144 TYR cc_start: 0.7585 (m-80) cc_final: 0.7324 (m-80)
REVERT: A  285 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7733 (ptp90)
REVERT: A  342 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6885 (mmm-85)
REVERT: A  344 LYS cc_start: 0.8379 (tppt) cc_final: 0.7515 (ttpt)
REVERT: A  378 GLU cc_start: 0.6082 (pm20) cc_final: 0.5751 (pm20)
REVERT: A  511 LYS cc_start: 0.8355 (mttt) cc_final: 0.7844 (mmmm)
REVERT: A  547 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7364 (mtt)
REVERT: A  601 LYS cc_start: 0.7718 (tppt) cc_final: 0.7501 (tppt)
REVERT: A  626 MET cc_start: 0.7401 (ptm) cc_final: 0.7124 (ppp)
REVERT: A  730 LYS cc_start: 0.7945 (tmmt) cc_final: 0.7698 (tptp)
REVERT: A  744 ARG cc_start: 0.7921 (ttp80) cc_final: 0.7246 (ttp-110)
REVERT: A  758 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7854 (pm20)
REVERT: A  818 ARG cc_start: 0.7339 (mtt180) cc_final: 0.6972 (mtt90)
REVERT: A  819 ARG cc_start: 0.8148 (mtm110) cc_final: 0.7929 (mtm-85)
REVERT: A  830 ILE cc_start: 0.8031 (tt) cc_final: 0.7446 (tt)
  outliers start: 29
  outliers final: 4
  residues processed: 149
  average time/residue: 0.5828
  time to fit residues: 91.4420
Evaluate side-chains
  122 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 112
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   75 GLN
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  285 ARG
Chi-restraints excluded: chain A residue  322 SER
Chi-restraints excluded: chain A residue  342 ARG
Chi-restraints excluded: chain A residue  547 MET
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  758 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 95 optimal weight:    6.9990
   chunk 57 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9980
   chunk 93 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 83 optimal weight:    3.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A 141 ASN
A 492 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.205373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.141437 restraints weight = 8760.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 2.24
r_work: 0.3436 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3285 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.2662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8203  Z= 0.169
  Angle     :  0.608   8.123  11092  Z= 0.313
  Chirality :  0.044   0.150   1197
  Planarity :  0.004   0.061   1418
  Dihedral  :  4.371  19.148   1086
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.86 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 15.31 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.62 (0.26), residues: 978
  helix:  1.45 (0.24), residues: 455
  sheet: -0.54 (0.43), residues: 129
  loop : -0.40 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 160 
 TYR   0.012   0.001   TYR A 927 
 PHE   0.015   0.002   PHE A 637 
 TRP   0.017   0.001   TRP A 856 
 HIS   0.003   0.001   HIS A 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 8203)
  covalent geometry    : angle       0.60822 (11092)
  hydrogen bonds       : bond        0.04217 (  426)
  hydrogen bonds       : angle       5.06544 ( 1221)

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 0.307 
Fit side-chains
REVERT: A   44 TYR cc_start: 0.8001 (m-80) cc_final: 0.7525 (m-80)
REVERT: A   89 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7571 (pt)
REVERT: A   97 TYR cc_start: 0.7888 (p90) cc_final: 0.7000 (p90)
REVERT: A  127 LYS cc_start: 0.8353 (tppp) cc_final: 0.8029 (tptt)
REVERT: A  144 TYR cc_start: 0.7746 (m-80) cc_final: 0.7452 (m-80)
REVERT: A  285 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7517 (ptp90)
REVERT: A  306 GLU cc_start: 0.7587 (tp30) cc_final: 0.7353 (tp30)
REVERT: A  342 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6849 (tpm-80)
REVERT: A  344 LYS cc_start: 0.8349 (tppt) cc_final: 0.7505 (ttpt)
REVERT: A  371 MET cc_start: 0.7648 (mmm) cc_final: 0.6932 (mtm)
REVERT: A  378 GLU cc_start: 0.6267 (pm20) cc_final: 0.5821 (pm20)
REVERT: A  407 GLU cc_start: 0.6715 (mt-10) cc_final: 0.6004 (mm-30)
REVERT: A  601 LYS cc_start: 0.7721 (tppt) cc_final: 0.7476 (tppt)
REVERT: A  730 LYS cc_start: 0.7982 (tmmt) cc_final: 0.7681 (tptp)
REVERT: A  744 ARG cc_start: 0.7876 (ttp80) cc_final: 0.6989 (ttp-110)
REVERT: A  809 ARG cc_start: 0.7747 (ttp-170) cc_final: 0.7428 (ttm110)
REVERT: A  959 ASN cc_start: 0.6842 (OUTLIER) cc_final: 0.6594 (m-40)
  outliers start: 29
  outliers final: 5
  residues processed: 136
  average time/residue: 0.5859
  time to fit residues: 84.0576
Evaluate side-chains
  116 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  285 ARG
Chi-restraints excluded: chain A residue  322 SER
Chi-restraints excluded: chain A residue  342 ARG
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  959 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 81 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 141 ASN
A 492 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.205734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.142238 restraints weight = 9033.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 2.27
r_work: 0.3446 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3290 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.2924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8203  Z= 0.142
  Angle     :  0.576   8.032  11092  Z= 0.297
  Chirality :  0.043   0.150   1197
  Planarity :  0.004   0.058   1418
  Dihedral  :  4.248  20.046   1086
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.17 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 16.55 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.27), residues: 978
  helix:  1.46 (0.24), residues: 461
  sheet: -0.56 (0.43), residues: 128
  loop : -0.45 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 978 
 TYR   0.009   0.001   TYR A 927 
 PHE   0.017   0.001   PHE A 782 
 TRP   0.016   0.001   TRP A 856 
 HIS   0.003   0.001   HIS A 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8203)
  covalent geometry    : angle       0.57630 (11092)
  hydrogen bonds       : bond        0.03889 (  426)
  hydrogen bonds       : angle       4.90405 ( 1221)

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 TYR cc_start: 0.8004 (m-80) cc_final: 0.7660 (m-80)
REVERT: A   89 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7583 (pt)
REVERT: A   97 TYR cc_start: 0.7870 (p90) cc_final: 0.6978 (p90)
REVERT: A  127 LYS cc_start: 0.8335 (tppp) cc_final: 0.7915 (tptt)
REVERT: A  144 TYR cc_start: 0.7787 (m-80) cc_final: 0.7432 (m-80)
REVERT: A  208 MET cc_start: 0.8746 (ttp) cc_final: 0.8490 (ttm)
REVERT: A  306 GLU cc_start: 0.7602 (tp30) cc_final: 0.7361 (tp30)
REVERT: A  344 LYS cc_start: 0.8290 (tppt) cc_final: 0.7490 (ttpt)
REVERT: A  378 GLU cc_start: 0.6286 (pm20) cc_final: 0.5819 (pm20)
REVERT: A  407 GLU cc_start: 0.6785 (mt-10) cc_final: 0.6049 (mm-30)
REVERT: A  487 ARG cc_start: 0.8085 (ttm110) cc_final: 0.7818 (ttm110)
REVERT: A  586 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8315 (mt)
REVERT: A  601 LYS cc_start: 0.7739 (tppt) cc_final: 0.7486 (tppt)
REVERT: A  730 LYS cc_start: 0.8012 (tmmt) cc_final: 0.7709 (tptp)
REVERT: A  744 ARG cc_start: 0.7893 (ttp80) cc_final: 0.6983 (ttp-110)
REVERT: A  768 LYS cc_start: 0.8177 (mppt) cc_final: 0.7861 (mttt)
  outliers start: 22
  outliers final: 5
  residues processed: 127
  average time/residue: 0.5514
  time to fit residues: 74.1804
Evaluate side-chains
  108 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  322 SER
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  948 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 70 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A  27 GLN
A  57 ASN
A  94 ASN
A 492 HIS
A 776 HIS
A 844 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.203145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.138690 restraints weight = 8960.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 2.26
r_work: 0.3404 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.3256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8203  Z= 0.183
  Angle     :  0.600   7.798  11092  Z= 0.307
  Chirality :  0.044   0.152   1197
  Planarity :  0.004   0.055   1418
  Dihedral  :  4.294  20.724   1086
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.97 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 17.46 %
    Favored  : 79.59 %
  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:  0.48 (0.27), residues: 978
  helix:  1.38 (0.24), residues: 461
  sheet: -0.95 (0.41), residues: 140
  loop : -0.39 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 809 
 TYR   0.011   0.001   TYR A 495 
 PHE   0.021   0.002   PHE A 782 
 TRP   0.015   0.001   TRP A 856 
 HIS   0.005   0.001   HIS A 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 ( 8203)
  covalent geometry    : angle       0.59960 (11092)
  hydrogen bonds       : bond        0.04002 (  426)
  hydrogen bonds       : angle       4.86814 ( 1221)

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 110
  time to evaluate  : 0.189 
Fit side-chains
REVERT: A   44 TYR cc_start: 0.7998 (m-80) cc_final: 0.7641 (m-80)
REVERT: A   89 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7563 (pt)
REVERT: A   97 TYR cc_start: 0.7972 (p90) cc_final: 0.7052 (p90)
REVERT: A  127 LYS cc_start: 0.8353 (tppp) cc_final: 0.8002 (tptt)
REVERT: A  144 TYR cc_start: 0.7837 (m-80) cc_final: 0.7547 (m-80)
REVERT: A  285 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7593 (ptp90)
REVERT: A  306 GLU cc_start: 0.7634 (tp30) cc_final: 0.7351 (tp30)
REVERT: A  344 LYS cc_start: 0.8314 (tppt) cc_final: 0.7486 (ttpt)
REVERT: A  369 MET cc_start: 0.8222 (mmp) cc_final: 0.7487 (mmp)
REVERT: A  378 GLU cc_start: 0.6304 (pm20) cc_final: 0.5931 (pm20)
REVERT: A  407 GLU cc_start: 0.6765 (mt-10) cc_final: 0.6049 (mm-30)
REVERT: A  601 LYS cc_start: 0.7766 (tppt) cc_final: 0.7516 (tppt)
REVERT: A  730 LYS cc_start: 0.8043 (tmmt) cc_final: 0.7738 (tptp)
REVERT: A  744 ARG cc_start: 0.7890 (ttp80) cc_final: 0.7005 (ttp-110)
REVERT: A  768 LYS cc_start: 0.8250 (mppt) cc_final: 0.7024 (tptt)
REVERT: A  813 GLU cc_start: 0.8663 (mm-30) cc_final: 0.7921 (tm-30)
REVERT: A  872 MET cc_start: 0.4651 (tpt) cc_final: 0.3914 (ptt)
  outliers start: 26
  outliers final: 8
  residues processed: 127
  average time/residue: 0.5702
  time to fit residues: 76.4132
Evaluate side-chains
  113 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  237 MET
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  285 ARG
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  822 ASP
Chi-restraints excluded: chain A residue  948 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 86 optimal weight:   20.0000
   chunk 51 optimal weight:    4.9990
   chunk 41 optimal weight:    5.9990
   chunk 89 optimal weight:    0.0170
   chunk 13 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 35 optimal weight:    0.3980
   chunk 80 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.8622

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

Flipped N/Q/H residues before XYZ refinement:
A  27 GLN
A 141 ASN
A 492 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.204668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.140477 restraints weight = 8785.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 2.24
r_work: 0.3422 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3270 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.3439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8203  Z= 0.146
  Angle     :  0.578   7.819  11092  Z= 0.298
  Chirality :  0.043   0.156   1197
  Planarity :  0.004   0.053   1418
  Dihedral  :  4.180  20.300   1086
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.76 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 18.14 %
    Favored  : 79.48 %
  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:  0.49 (0.27), residues: 978
  helix:  1.44 (0.24), residues: 462
  sheet: -0.93 (0.41), residues: 140
  loop : -0.48 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 490 
 TYR   0.010   0.001   TYR A 673 
 PHE   0.018   0.001   PHE A 782 
 TRP   0.015   0.001   TRP A 856 
 HIS   0.003   0.001   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 8203)
  covalent geometry    : angle       0.57786 (11092)
  hydrogen bonds       : bond        0.03799 (  426)
  hydrogen bonds       : angle       4.74244 ( 1221)

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLN cc_start: 0.8622 (mt0) cc_final: 0.8406 (mm110)
REVERT: A   44 TYR cc_start: 0.7991 (m-80) cc_final: 0.7653 (m-80)
REVERT: A   89 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7498 (pt)
REVERT: A   97 TYR cc_start: 0.7996 (p90) cc_final: 0.7146 (p90)
REVERT: A  127 LYS cc_start: 0.8339 (tppp) cc_final: 0.8012 (tptt)
REVERT: A  144 TYR cc_start: 0.7944 (m-80) cc_final: 0.7614 (m-80)
REVERT: A  208 MET cc_start: 0.8814 (ttp) cc_final: 0.8566 (ttm)
REVERT: A  285 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7493 (ptp90)
REVERT: A  306 GLU cc_start: 0.7660 (tp30) cc_final: 0.7338 (tp30)
REVERT: A  344 LYS cc_start: 0.8307 (tppt) cc_final: 0.7550 (ttpt)
REVERT: A  378 GLU cc_start: 0.6303 (pm20) cc_final: 0.5917 (pm20)
REVERT: A  407 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6085 (mm-30)
REVERT: A  601 LYS cc_start: 0.7793 (tppt) cc_final: 0.7557 (tppt)
REVERT: A  730 LYS cc_start: 0.8061 (tmmt) cc_final: 0.7768 (tptp)
REVERT: A  744 ARG cc_start: 0.7941 (ttp80) cc_final: 0.7058 (ttp-110)
REVERT: A  768 LYS cc_start: 0.8240 (mppt) cc_final: 0.7036 (tptt)
REVERT: A  809 ARG cc_start: 0.7658 (ttp-170) cc_final: 0.7331 (ttm110)
REVERT: A  813 GLU cc_start: 0.8653 (mm-30) cc_final: 0.7974 (tm-30)
  outliers start: 21
  outliers final: 8
  residues processed: 123
  average time/residue: 0.6010
  time to fit residues: 78.3623
Evaluate side-chains
  114 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   29 ASN
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  237 MET
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  285 ARG
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  822 ASP
Chi-restraints excluded: chain A residue  948 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 96 optimal weight:    8.9990
   chunk 90 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   chunk 69 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 80 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 46 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 492 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.205064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.140746 restraints weight = 8937.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 2.26
r_work: 0.3431 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.3558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8203  Z= 0.139
  Angle     :  0.577   7.533  11092  Z= 0.296
  Chirality :  0.043   0.157   1197
  Planarity :  0.004   0.051   1418
  Dihedral  :  4.128  20.221   1086
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.97 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 18.03 %
    Favored  : 79.48 %
  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:  0.52 (0.27), residues: 978
  helix:  1.49 (0.24), residues: 461
  sheet: -0.98 (0.42), residues: 140
  loop : -0.46 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 185 
 TYR   0.009   0.001   TYR A 673 
 PHE   0.016   0.001   PHE A 782 
 TRP   0.015   0.001   TRP A 856 
 HIS   0.003   0.001   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 8203)
  covalent geometry    : angle       0.57740 (11092)
  hydrogen bonds       : bond        0.03739 (  426)
  hydrogen bonds       : angle       4.68325 ( 1221)

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 TYR cc_start: 0.7972 (m-80) cc_final: 0.7649 (m-80)
REVERT: A   89 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7491 (pt)
REVERT: A   97 TYR cc_start: 0.8019 (p90) cc_final: 0.7156 (p90)
REVERT: A  127 LYS cc_start: 0.8308 (tppp) cc_final: 0.7979 (tptt)
REVERT: A  140 ASN cc_start: 0.6550 (m110) cc_final: 0.6318 (m-40)
REVERT: A  144 TYR cc_start: 0.7993 (m-80) cc_final: 0.7638 (m-80)
REVERT: A  285 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7480 (ptp90)
REVERT: A  306 GLU cc_start: 0.7655 (tp30) cc_final: 0.7385 (tp30)
REVERT: A  344 LYS cc_start: 0.8340 (tppt) cc_final: 0.7580 (ttpt)
REVERT: A  378 GLU cc_start: 0.6258 (pm20) cc_final: 0.5881 (pm20)
REVERT: A  407 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6136 (mm-30)
REVERT: A  601 LYS cc_start: 0.7779 (tppt) cc_final: 0.7557 (tppt)
REVERT: A  703 VAL cc_start: 0.8287 (t) cc_final: 0.8008 (m)
REVERT: A  719 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8301 (mm-40)
REVERT: A  723 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8210 (mm-30)
REVERT: A  730 LYS cc_start: 0.8041 (tmmt) cc_final: 0.7738 (tptp)
REVERT: A  733 SER cc_start: 0.8488 (t) cc_final: 0.8125 (m)
REVERT: A  744 ARG cc_start: 0.7917 (ttp80) cc_final: 0.7024 (ttp-110)
REVERT: A  768 LYS cc_start: 0.8210 (mppt) cc_final: 0.7891 (mttt)
REVERT: A  809 ARG cc_start: 0.7550 (ttp-170) cc_final: 0.7275 (ttm110)
REVERT: A  813 GLU cc_start: 0.8667 (mm-30) cc_final: 0.7968 (tm-30)
  outliers start: 22
  outliers final: 8
  residues processed: 129
  average time/residue: 0.5396
  time to fit residues: 73.7909
Evaluate side-chains
  117 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   29 ASN
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  285 ARG
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  822 ASP
Chi-restraints excluded: chain A residue  948 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 37 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 14 optimal weight:    6.9990
   chunk 68 optimal weight:    0.7980
   chunk 49 optimal weight:    0.4980
   chunk 85 optimal weight:    7.9990
   chunk 10 optimal weight:    4.9990
   chunk 84 optimal weight:    8.9990
   chunk 8 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    2.2584

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

Flipped N/Q/H residues before XYZ refinement:
A  27 GLN
A 141 ASN
A 492 HIS
A 841 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.200696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.135744 restraints weight = 8832.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 2.25
r_work: 0.3352 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.3877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061   8203  Z= 0.264
  Angle     :  0.687   7.378  11092  Z= 0.352
  Chirality :  0.047   0.214   1197
  Planarity :  0.005   0.050   1418
  Dihedral  :  4.446  21.131   1086
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.17 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.16 %
    Favored  : 78.57 %
  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:  0.22 (0.26), residues: 978
  helix:  1.14 (0.24), residues: 461
  sheet: -1.02 (0.42), residues: 141
  loop : -0.51 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 185 
 TYR   0.019   0.002   TYR A 477 
 PHE   0.022   0.002   PHE A 637 
 TRP   0.015   0.001   TRP A 856 
 HIS   0.005   0.001   HIS A 243 

Details of bonding type rmsd
  covalent geometry    : bond        0.00647 ( 8203)
  covalent geometry    : angle       0.68684 (11092)
  hydrogen bonds       : bond        0.04335 (  426)
  hydrogen bonds       : angle       4.90533 ( 1221)

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 TYR cc_start: 0.8042 (m-80) cc_final: 0.7702 (m-80)
REVERT: A   89 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7597 (pt)
REVERT: A   97 TYR cc_start: 0.8124 (p90) cc_final: 0.7194 (p90)
REVERT: A  100 LEU cc_start: 0.7707 (mm) cc_final: 0.7452 (mm)
REVERT: A  127 LYS cc_start: 0.8294 (tppp) cc_final: 0.7932 (tptt)
REVERT: A  140 ASN cc_start: 0.7100 (m110) cc_final: 0.6844 (m-40)
REVERT: A  144 TYR cc_start: 0.8069 (m-80) cc_final: 0.7763 (m-80)
REVERT: A  208 MET cc_start: 0.8912 (ttp) cc_final: 0.8711 (ttm)
REVERT: A  285 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7407 (ptp90)
REVERT: A  306 GLU cc_start: 0.7680 (tp30) cc_final: 0.7365 (tp30)
REVERT: A  344 LYS cc_start: 0.8425 (tppt) cc_final: 0.7654 (ttpt)
REVERT: A  369 MET cc_start: 0.8233 (mmp) cc_final: 0.7553 (mmp)
REVERT: A  378 GLU cc_start: 0.6236 (pm20) cc_final: 0.5800 (pm20)
REVERT: A  407 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6184 (mm-30)
REVERT: A  427 ARG cc_start: 0.6902 (mmt180) cc_final: 0.6688 (mmt-90)
REVERT: A  555 TYR cc_start: 0.8983 (t80) cc_final: 0.8727 (t80)
REVERT: A  601 LYS cc_start: 0.7848 (tppt) cc_final: 0.7153 (ttpp)
REVERT: A  703 VAL cc_start: 0.8339 (t) cc_final: 0.8090 (m)
REVERT: A  719 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8374 (mm-40)
REVERT: A  730 LYS cc_start: 0.8095 (tmmt) cc_final: 0.7818 (tptp)
REVERT: A  733 SER cc_start: 0.8499 (t) cc_final: 0.8132 (m)
REVERT: A  744 ARG cc_start: 0.8005 (ttp80) cc_final: 0.7179 (ttp-110)
REVERT: A  768 LYS cc_start: 0.8266 (mppt) cc_final: 0.7975 (mttt)
REVERT: A  809 ARG cc_start: 0.7693 (ttp-170) cc_final: 0.7355 (ttm110)
  outliers start: 20
  outliers final: 9
  residues processed: 126
  average time/residue: 0.6622
  time to fit residues: 88.0288
Evaluate side-chains
  120 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   29 ASN
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  237 MET
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  285 ARG
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  822 ASP
Chi-restraints excluded: chain A residue  948 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 84 optimal weight:    9.9990
   chunk 41 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 90 optimal weight:    0.0020
   chunk 58 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 46 optimal weight:    0.5980
   overall best weight:    0.5788

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

Flipped N/Q/H residues before XYZ refinement:
A  27 GLN
A 492 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.205261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.141182 restraints weight = 8735.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 2.26
r_work: 0.3412 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3257 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.3883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8203  Z= 0.136
  Angle     :  0.611   7.853  11092  Z= 0.312
  Chirality :  0.044   0.191   1197
  Planarity :  0.004   0.049   1418
  Dihedral  :  4.262  20.278   1086
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.86 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 20.07 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.38 (0.27), residues: 978
  helix:  1.36 (0.24), residues: 461
  sheet: -1.02 (0.43), residues: 140
  loop : -0.53 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 185 
 TYR   0.012   0.001   TYR A 673 
 PHE   0.016   0.001   PHE A 782 
 TRP   0.016   0.001   TRP A 856 
 HIS   0.004   0.001   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8203)
  covalent geometry    : angle       0.61109 (11092)
  hydrogen bonds       : bond        0.03815 (  426)
  hydrogen bonds       : angle       4.72702 ( 1221)

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 TYR cc_start: 0.8015 (m-80) cc_final: 0.7680 (m-80)
REVERT: A   89 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7586 (pt)
REVERT: A   97 TYR cc_start: 0.8123 (p90) cc_final: 0.7177 (p90)
REVERT: A  100 LEU cc_start: 0.7661 (mm) cc_final: 0.7396 (mm)
REVERT: A  127 LYS cc_start: 0.8255 (tppp) cc_final: 0.7907 (tptt)
REVERT: A  140 ASN cc_start: 0.6493 (m110) cc_final: 0.6257 (m-40)
REVERT: A  144 TYR cc_start: 0.8058 (m-80) cc_final: 0.7774 (m-80)
REVERT: A  285 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7474 (ptp90)
REVERT: A  306 GLU cc_start: 0.7687 (tp30) cc_final: 0.7362 (tp30)
REVERT: A  342 ARG cc_start: 0.7269 (ttm-80) cc_final: 0.6948 (mmm-85)
REVERT: A  344 LYS cc_start: 0.8381 (tppt) cc_final: 0.7661 (ttpt)
REVERT: A  378 GLU cc_start: 0.6224 (pm20) cc_final: 0.5742 (pm20)
REVERT: A  407 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6120 (mm-30)
REVERT: A  434 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8211 (ptm160)
REVERT: A  601 LYS cc_start: 0.7817 (tppt) cc_final: 0.7131 (ttpp)
REVERT: A  703 VAL cc_start: 0.8330 (t) cc_final: 0.8118 (m)
REVERT: A  719 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8352 (mm-40)
REVERT: A  730 LYS cc_start: 0.8032 (tmmt) cc_final: 0.7758 (tptp)
REVERT: A  733 SER cc_start: 0.8463 (t) cc_final: 0.8135 (m)
REVERT: A  744 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7037 (ttp-110)
REVERT: A  768 LYS cc_start: 0.8197 (mppt) cc_final: 0.7903 (mttt)
REVERT: A  809 ARG cc_start: 0.7566 (ttp-170) cc_final: 0.7279 (ttm110)
REVERT: A  813 GLU cc_start: 0.8587 (tp30) cc_final: 0.8262 (tm-30)
  outliers start: 17
  outliers final: 7
  residues processed: 127
  average time/residue: 0.6521
  time to fit residues: 87.4007
Evaluate side-chains
  119 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   29 ASN
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  285 ARG
Chi-restraints excluded: chain A residue  434 ARG
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  822 ASP
Chi-restraints excluded: chain A residue  948 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 31 optimal weight:    0.0170
   chunk 47 optimal weight:    0.9980
   chunk 97 optimal weight:    8.9990
   chunk 76 optimal weight:    0.0030
   chunk 62 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 94 optimal weight:    0.3980
   chunk 86 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   chunk 95 optimal weight:    2.9990
   overall best weight:    0.3828

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

Flipped N/Q/H residues before XYZ refinement:
A  27 GLN
A 492 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.205966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.142838 restraints weight = 8836.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 2.23
r_work: 0.3447 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.3918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8203  Z= 0.126
  Angle     :  0.600   8.089  11092  Z= 0.308
  Chirality :  0.043   0.189   1197
  Planarity :  0.004   0.049   1418
  Dihedral  :  4.175  19.858   1086
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.86 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 21.43 %
    Favored  : 77.21 %
  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:  0.44 (0.27), residues: 978
  helix:  1.46 (0.24), residues: 462
  sheet: -1.04 (0.42), residues: 140
  loop : -0.56 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 342 
 TYR   0.011   0.001   TYR A 673 
 PHE   0.014   0.001   PHE A 782 
 TRP   0.016   0.001   TRP A 856 
 HIS   0.004   0.001   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 8203)
  covalent geometry    : angle       0.59990 (11092)
  hydrogen bonds       : bond        0.03655 (  426)
  hydrogen bonds       : angle       4.62329 ( 1221)

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A   44 TYR cc_start: 0.8049 (m-80) cc_final: 0.7733 (m-80)
REVERT: A   89 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7533 (pt)
REVERT: A   97 TYR cc_start: 0.8115 (p90) cc_final: 0.7219 (p90)
REVERT: A  127 LYS cc_start: 0.8306 (tppp) cc_final: 0.7965 (tptt)
REVERT: A  140 ASN cc_start: 0.6303 (m110) cc_final: 0.5963 (m-40)
REVERT: A  144 TYR cc_start: 0.8092 (m-80) cc_final: 0.7778 (m-80)
REVERT: A  285 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7480 (ptp90)
REVERT: A  306 GLU cc_start: 0.7700 (tp30) cc_final: 0.7375 (tp30)
REVERT: A  342 ARG cc_start: 0.7337 (ttm-80) cc_final: 0.6995 (mmm-85)
REVERT: A  344 LYS cc_start: 0.8412 (tppt) cc_final: 0.7674 (ttpt)
REVERT: A  378 GLU cc_start: 0.6196 (pm20) cc_final: 0.5718 (pm20)
REVERT: A  407 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6116 (mm-30)
REVERT: A  434 ARG cc_start: 0.8397 (ptm160) cc_final: 0.8194 (ptm160)
REVERT: A  601 LYS cc_start: 0.7831 (tppt) cc_final: 0.7157 (ttpp)
REVERT: A  719 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8367 (mm-40)
REVERT: A  730 LYS cc_start: 0.8046 (tmmt) cc_final: 0.7793 (tptp)
REVERT: A  733 SER cc_start: 0.8498 (t) cc_final: 0.8164 (m)
REVERT: A  744 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7064 (ttp-110)
REVERT: A  768 LYS cc_start: 0.8196 (mppt) cc_final: 0.7066 (tptt)
REVERT: A  809 ARG cc_start: 0.7634 (ttp-170) cc_final: 0.7336 (ttm110)
REVERT: A  872 MET cc_start: 0.4464 (tpt) cc_final: 0.3941 (ptp)
  outliers start: 12
  outliers final: 6
  residues processed: 125
  average time/residue: 0.5524
  time to fit residues: 73.0734
Evaluate side-chains
  117 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   29 ASN
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  285 ARG
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  822 ASP
Chi-restraints excluded: chain A residue  948 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 14 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9990
   chunk 79 optimal weight:    6.9990
   chunk 52 optimal weight:    0.8980
   chunk 77 optimal weight:    0.8980
   chunk 85 optimal weight:   20.0000
   chunk 56 optimal weight:    5.9990
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A  27 GLN
A 492 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.205137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.141227 restraints weight = 8756.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 2.25
r_work: 0.3429 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3283 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.3972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8203  Z= 0.152
  Angle     :  0.616   7.953  11092  Z= 0.314
  Chirality :  0.044   0.183   1197
  Planarity :  0.004   0.049   1418
  Dihedral  :  4.166  20.502   1086
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.97 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 21.88 %
    Favored  : 76.30 %
  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:  0.39 (0.26), residues: 978
  helix:  1.40 (0.24), residues: 462
  sheet: -1.04 (0.43), residues: 140
  loop : -0.56 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 342 
 TYR   0.008   0.001   TYR A 673 
 PHE   0.016   0.001   PHE A 782 
 TRP   0.015   0.001   TRP A 856 
 HIS   0.004   0.001   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 8203)
  covalent geometry    : angle       0.61638 (11092)
  hydrogen bonds       : bond        0.03722 (  426)
  hydrogen bonds       : angle       4.65451 ( 1221)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3513.44 seconds
wall clock time: 60 minutes 35.18 seconds (3635.18 seconds total)