Starting phenix.real_space_refine
on Tue Feb  3 16:26:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ndt_49277/02_2026/9ndt_49277_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ndt_49277/02_2026/9ndt_49277.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ndt_49277/02_2026/9ndt_49277_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ndt_49277/02_2026/9ndt_49277_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ndt_49277/02_2026/9ndt_49277.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ndt_49277/02_2026/9ndt_49277.map"
  }
  resolution = 3.8
  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=   0.016
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      18      5.16       5
     C    3121      2.51       5
     N     853      2.21       5
     O     880      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s

  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: 4872
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 347, 2735
          Classifications: {'peptide': 347}
          Link IDs: {'PTRANS': 20, 'TRANS': 326}
          Chain breaks: 12
    Chain: "B"
      Number of atoms: 2137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 269, 2137
          Classifications: {'peptide': 269}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 255}
          Chain breaks: 3
  Time building chain proxies: 0.83, per 1000 atoms: 0.17
  Number of scatterers: 4872
  At special positions: 0
  Unit cell: (86.751, 69.255, 108.621, 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      18     16.00
     O     880      8.00
     N     853      7.00
     C    3121      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: 0.23
  Conformation dependent library (CDL) restraints added in 263.0 milliseconds
  

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1166

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 2 sheets defined
      64.0% alpha, 4.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 31 through 36
    Processing helix  chain 'A' and resid 67 through 78
      removed outlier: 3.570A  pdb=" N   TYR A  78 " --> pdb=" O   SER A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 134
    Processing helix  chain 'A' and resid 222 through 226
      removed outlier: 4.324A  pdb=" N   ALA A 225 " --> pdb=" O   TYR A 222 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   GLN A 226 " --> pdb=" O   GLY A 223 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 222 through 226'
    Processing helix  chain 'A' and resid 227 through 235
    Processing helix  chain 'A' and resid 238 through 251
      removed outlier: 4.135A  pdb=" N   THR A 246 " --> pdb=" O   LEU A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 257
    Processing helix  chain 'A' and resid 258 through 262
    Processing helix  chain 'A' and resid 264 through 274
      removed outlier: 3.787A  pdb=" N   THR A 274 " --> pdb=" O   ASP A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 304 through 308
      removed outlier: 3.750A  pdb=" N   ARG A 308 " --> pdb=" O   GLN A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 344
      Proline residue:  A 316  - end of helix
      removed outlier: 4.229A  pdb=" N   CYS A 343 " --> pdb=" O   HIS A 339 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   LEU A 344 " --> pdb=" O   ASP A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 362
    Processing helix  chain 'A' and resid 364 through 376
    Processing helix  chain 'A' and resid 391 through 399
    Processing helix  chain 'A' and resid 400 through 408
    Processing helix  chain 'A' and resid 410 through 418
    Processing helix  chain 'A' and resid 641 through 661
    Processing helix  chain 'A' and resid 779 through 794
      removed outlier: 3.576A  pdb=" N   ASP A 794 " --> pdb=" O   ALA A 790 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 794 through 802
      removed outlier: 3.965A  pdb=" N   VAL A 798 " --> pdb=" O   ASP A 794 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 803 through 805
      No H-bonds generated for 'chain 'A' and resid 803 through 805'
    Processing helix  chain 'B' and resid 40 through 45
    Processing helix  chain 'B' and resid 45 through 58
      removed outlier: 3.527A  pdb=" N   GLN B  58 " --> pdb=" O   GLU B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 77
      removed outlier: 3.767A  pdb=" N   PHE B  71 " --> pdb=" O   HIS B  67 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU B  77 " --> pdb=" O   ASP B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 3.704A  pdb=" N   GLY B  82 " --> pdb=" O   SER B  79 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 114
    Processing helix  chain 'B' and resid 122 through 135
      removed outlier: 3.572A  pdb=" N   GLY B 135 " --> pdb=" O   ALA B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 150
    Processing helix  chain 'B' and resid 152 through 156
    Processing helix  chain 'B' and resid 173 through 185
    Processing helix  chain 'B' and resid 185 through 198
    Processing helix  chain 'B' and resid 238 through 242
    Processing helix  chain 'B' and resid 251 through 254
    Processing helix  chain 'B' and resid 255 through 273
      removed outlier: 3.636A  pdb=" N   LEU B 259 " --> pdb=" O   GLY B 255 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   THR B 260 " --> pdb=" O   ARG B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 280
    Processing helix  chain 'B' and resid 316 through 324
    Processing helix  chain 'B' and resid 324 through 331
    Processing helix  chain 'B' and resid 866 through 875
    Processing sheet with id=AA1, first strand: chain 'A' and resid 419 through 421
    Processing sheet with id=AA2, first strand: chain 'B' and resid 143 through 144
      removed outlier: 4.477A  pdb=" N   ASN B 143 " --> pdb=" O   VAL B 118 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ASP B 249 " --> pdb=" O   THR B 119 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ILE B 246 " --> pdb=" O   VAL B 287 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   VAL B 289 " --> pdb=" O   ILE B 246 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   ILE B 248 " --> pdb=" O   VAL B 289 " (cutoff:3.500A)
      removed outlier: 8.537A  pdb=" N   ALA B 338 " --> pdb=" O   VAL B  92 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   LEU B  94 " --> pdb=" O   ALA B 338 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   PHE B 340 " --> pdb=" O   LEU B  94 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   THR B  96 " --> pdb=" O   PHE B 340 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   TRP B 337 " --> pdb=" O   VAL B 879 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   VAL B 881 " --> pdb=" O   TRP B 337 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   ILE B 339 " --> pdb=" O   VAL B 881 " (cutoff:3.500A)

    242 hydrogen bonds defined for protein.
    693 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: 0.48

  Time building geometry restraints manager: 0.32 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: 1586
        1.34 -     1.46: 971
        1.46 -     1.58: 2398
        1.58 -     1.69: 0
        1.69 -     1.81: 23
  Bond restraints: 4978
  Sorted by residual:
  bond pdb=" CG1 ILE A 323 "
       pdb=" CD1 ILE A 323 "
    ideal  model  delta    sigma   weight residual
    1.513  1.458  0.055 3.90e-02 6.57e+02 1.99e+00
  bond pdb=" CA  TYR A 222 "
       pdb=" CB  TYR A 222 "
    ideal  model  delta    sigma   weight residual
    1.535  1.556 -0.021 1.64e-02 3.72e+03 1.61e+00
  bond pdb=" CA  GLU B  78 "
       pdb=" CB  GLU B  78 "
    ideal  model  delta    sigma   weight residual
    1.530  1.549 -0.019 1.69e-02 3.50e+03 1.29e+00
  bond pdb=" CB  ARG A 341 "
       pdb=" CG  ARG A 341 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 3.00e-02 1.11e+03 1.26e+00
  bond pdb=" CA  ILE A 277 "
       pdb=" CB  ILE A 277 "
    ideal  model  delta    sigma   weight residual
    1.537  1.526  0.011 1.29e-02 6.01e+03 7.64e-01
  ... (remaining 4973 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 6492
        1.56 -     3.12: 229
        3.12 -     4.69: 32
        4.69 -     6.25: 4
        6.25 -     7.81: 3
  Bond angle restraints: 6760
  Sorted by residual:
  angle pdb=" CA  GLY A 889 "
        pdb=" C   GLY A 889 "
        pdb=" N   ASP A 890 "
      ideal   model   delta    sigma   weight residual
     114.23  117.47   -3.24 8.80e-01 1.29e+00 1.35e+01
  angle pdb=" C   ARG A  70 "
        pdb=" N   PHE A  71 "
        pdb=" CA  PHE A  71 "
      ideal   model   delta    sigma   weight residual
     120.31  114.91    5.40 1.52e+00 4.33e-01 1.26e+01
  angle pdb=" N   ALA A 132 "
        pdb=" CA  ALA A 132 "
        pdb=" C   ALA A 132 "
      ideal   model   delta    sigma   weight residual
     114.31  110.03    4.28 1.29e+00 6.01e-01 1.10e+01
  angle pdb=" CA  GLY A 889 "
        pdb=" C   GLY A 889 "
        pdb=" O   GLY A 889 "
      ideal   model   delta    sigma   weight residual
     122.33  119.98    2.35 8.10e-01 1.52e+00 8.42e+00
  angle pdb=" N   PHE A  71 "
        pdb=" CA  PHE A  71 "
        pdb=" CB  PHE A  71 "
      ideal   model   delta    sigma   weight residual
     110.28  114.20   -3.92 1.55e+00 4.16e-01 6.40e+00
  ... (remaining 6755 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.54: 2685
       16.54 -    33.09: 203
       33.09 -    49.63: 49
       49.63 -    66.17: 11
       66.17 -    82.71: 8
  Dihedral angle restraints: 2956
    sinusoidal: 1161
      harmonic: 1795
  Sorted by residual:
  dihedral pdb=" CA  TYR B 185 "
           pdb=" C   TYR B 185 "
           pdb=" N   TRP B 186 "
           pdb=" CA  TRP B 186 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.45  -21.55     0      5.00e+00 4.00e-02 1.86e+01
  dihedral pdb=" CA  ARG A 341 "
           pdb=" C   ARG A 341 "
           pdb=" N   SER A 342 "
           pdb=" CA  SER A 342 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.04  -18.96     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  LEU A 633 "
           pdb=" C   LEU A 633 "
           pdb=" N   LYS A 634 "
           pdb=" CA  LYS A 634 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.49   18.51     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 2953 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 425
       0.026 -    0.051: 212
       0.051 -    0.077: 71
       0.077 -    0.103: 43
       0.103 -    0.129: 21
  Chirality restraints: 772
  Sorted by residual:
  chirality pdb=" CA  VAL B 287 "
            pdb=" N   VAL B 287 "
            pdb=" C   VAL B 287 "
            pdb=" CB  VAL B 287 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.13e-01
  chirality pdb=" CA  ILE B  95 "
            pdb=" N   ILE B  95 "
            pdb=" C   ILE B  95 "
            pdb=" CB  ILE B  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.12e-01
  chirality pdb=" CA  PHE B 149 "
            pdb=" N   PHE B 149 "
            pdb=" C   PHE B 149 "
            pdb=" CB  PHE B 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.05e-01
  ... (remaining 769 not shown)

  Planarity restraints: 862
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  71 "    0.015 2.00e-02 2.50e+03   2.17e-02 8.28e+00
        pdb=" CG  PHE B  71 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  71 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  71 "    0.021 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  71 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  71 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  71 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  79 "   -0.039 5.00e-02 4.00e+02   5.83e-02 5.44e+00
        pdb=" N   PRO B  80 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO B  80 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B  80 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 269 "    0.011 2.00e-02 2.50e+03   2.25e-02 5.08e+00
        pdb=" C   ILE B 269 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   ILE B 269 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ASN B 270 "    0.013 2.00e-02 2.50e+03
  ... (remaining 859 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 484
        2.75 -     3.29: 5001
        3.29 -     3.82: 7963
        3.82 -     4.36: 9013
        4.36 -     4.90: 15640
  Nonbonded interactions: 38101
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 107 "
            pdb=" O   ASN B 111 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" O   ARG A 421 "
            pdb=" N   HIS A 885 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" NH2 ARG A 651 "
            pdb=" OD2 ASP A 796 "
     model   vdw
     2.281 3.120
  nonbonded pdb=" OG1 THR A 262 "
            pdb=" OE1 GLN B  46 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" NH1 ARG A 651 "
            pdb=" OD2 ASP A 794 "
     model   vdw
     2.377 3.120
  ... (remaining 38096 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:             6.530
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     4.350
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5694
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   0.055   4978  Z= 0.161
  Angle     :  0.687   7.810   6760  Z= 0.400
  Chirality :  0.041   0.129    772
  Planarity :  0.006   0.058    862
  Dihedral  : 13.639  82.713   1790
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.58 (0.33), residues: 582
  helix:  0.22 (0.29), residues: 324
  sheet: -1.19 (0.84), residues: 31
  loop : -1.03 (0.38), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 874 
 TYR   0.029   0.002   TYR B 320 
 PHE   0.049   0.002   PHE B  71 
 TRP   0.021   0.003   TRP A 230 
 HIS   0.009   0.001   HIS B 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 4978)
  covalent geometry    : angle       0.68682 ( 6760)
  hydrogen bonds       : bond        0.16347 (  242)
  hydrogen bonds       : angle       7.21251 (  693)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
REVERT: A  319 VAL cc_start: 0.6812 (t) cc_final: 0.6548 (t)
REVERT: A  344 LEU cc_start: 0.8367 (tp) cc_final: 0.8034 (tp)
REVERT: B   46 GLN cc_start: 0.6933 (mm-40) cc_final: 0.6583 (mm110)
REVERT: B  130 TYR cc_start: 0.6249 (t80) cc_final: 0.6027 (t80)
REVERT: B  139 SER cc_start: 0.7939 (t) cc_final: 0.7696 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.0934
  time to fit residues: 17.5580
Evaluate side-chains
  130 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    0.0770
   chunk 24 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0970
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.2980
   chunk 25 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.3936

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
B  43 HIS
** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 277 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.156244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.138680 restraints weight = 8933.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.143158 restraints weight = 5137.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.146247 restraints weight = 3278.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.148314 restraints weight = 2240.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.149868 restraints weight = 1625.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6415
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4978  Z= 0.150
  Angle     :  0.590   7.747   6760  Z= 0.308
  Chirality :  0.041   0.124    772
  Planarity :  0.005   0.041    862
  Dihedral  :  4.442  16.653    676
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  :  8.90 %
    Favored  : 88.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.20 (0.34), residues: 582
  helix:  0.54 (0.28), residues: 328
  sheet: -1.63 (0.82), residues: 33
  loop : -0.78 (0.41), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 322 
 TYR   0.019   0.002   TYR B 184 
 PHE   0.022   0.002   PHE B 149 
 TRP   0.030   0.003   TRP A 230 
 HIS   0.006   0.001   HIS B 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 4978)
  covalent geometry    : angle       0.58958 ( 6760)
  hydrogen bonds       : bond        0.04755 (  242)
  hydrogen bonds       : angle       5.47481 (  693)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 134
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: A  651 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6886 (ttp80)
REVERT: A  788 GLN cc_start: 0.7147 (tt0) cc_final: 0.6918 (tt0)
REVERT: A  793 LEU cc_start: 0.7461 (mt) cc_final: 0.7248 (mt)
REVERT: A  796 ASP cc_start: 0.7482 (m-30) cc_final: 0.7242 (m-30)
REVERT: A  810 LEU cc_start: 0.7801 (mm) cc_final: 0.7528 (mt)
REVERT: B  139 SER cc_start: 0.8333 (t) cc_final: 0.8039 (t)
REVERT: B  289 VAL cc_start: 0.7914 (t) cc_final: 0.7427 (m)
REVERT: B  320 TYR cc_start: 0.6981 (t80) cc_final: 0.6744 (t80)
REVERT: B  324 ASN cc_start: 0.7650 (t0) cc_final: 0.7264 (t0)
REVERT: B  332 ARG cc_start: 0.7526 (mtp85) cc_final: 0.7256 (mtp85)
  outliers start: 12
  outliers final: 9
  residues processed: 138
  average time/residue: 0.0856
  time to fit residues: 14.1344
Evaluate side-chains
  137 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 127
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue  282 ARG
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  651 ARG
Chi-restraints excluded: chain A residue  803 SER
Chi-restraints excluded: chain B residue  132 LYS
Chi-restraints excluded: chain B residue  341 ILE
Chi-restraints excluded: chain B residue  877 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0870
   chunk 50 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0010
   chunk 56 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 8 optimal weight:    0.3980
   overall best weight:    0.4564

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

Flipped N/Q/H residues before XYZ refinement:
B  46 GLN
** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 257 HIS
B 277 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.154480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.136958 restraints weight = 8885.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.141455 restraints weight = 5118.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.144533 restraints weight = 3278.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.146743 restraints weight = 2254.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.148343 restraints weight = 1625.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6461
moved from start:          0.2943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   4978  Z= 0.158
  Angle     :  0.577   7.946   6760  Z= 0.299
  Chirality :  0.040   0.131    772
  Planarity :  0.005   0.040    862
  Dihedral  :  4.459  16.619    676
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 13.54 %
    Favored  : 83.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.27 (0.34), residues: 582
  helix:  0.45 (0.28), residues: 335
  sheet: -1.78 (0.84), residues: 31
  loop : -0.78 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 874 
 TYR   0.017   0.002   TYR B 320 
 PHE   0.020   0.002   PHE B 149 
 TRP   0.021   0.003   TRP A 230 
 HIS   0.008   0.001   HIS B  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 4978)
  covalent geometry    : angle       0.57665 ( 6760)
  hydrogen bonds       : bond        0.04633 (  242)
  hydrogen bonds       : angle       5.35065 (  693)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
REVERT: A  247 ARG cc_start: 0.7142 (mtp85) cc_final: 0.6857 (ttt90)
REVERT: A  282 ARG cc_start: 0.6738 (OUTLIER) cc_final: 0.6515 (ttt-90)
REVERT: A  368 LEU cc_start: 0.7588 (mm) cc_final: 0.7320 (mp)
REVERT: A  651 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6899 (ttp80)
REVERT: A  788 GLN cc_start: 0.7249 (tt0) cc_final: 0.7007 (tt0)
REVERT: A  793 LEU cc_start: 0.7586 (mt) cc_final: 0.7354 (mt)
REVERT: A  795 ARG cc_start: 0.7145 (ptm160) cc_final: 0.6863 (ptm160)
REVERT: A  796 ASP cc_start: 0.7745 (m-30) cc_final: 0.7467 (m-30)
REVERT: A  810 LEU cc_start: 0.7836 (mm) cc_final: 0.7588 (mt)
REVERT: B  281 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7431 (mtm-85)
REVERT: B  285 VAL cc_start: 0.6831 (t) cc_final: 0.6247 (m)
REVERT: B  289 VAL cc_start: 0.7914 (t) cc_final: 0.7401 (m)
REVERT: B  332 ARG cc_start: 0.7479 (mtp85) cc_final: 0.7207 (mtp85)
  outliers start: 14
  outliers final: 9
  residues processed: 140
  average time/residue: 0.0863
  time to fit residues: 14.4156
Evaluate side-chains
  144 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 133
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue   71 PHE
Chi-restraints excluded: chain A residue  282 ARG
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  651 ARG
Chi-restraints excluded: chain A residue  803 SER
Chi-restraints excluded: chain A residue  811 ILE
Chi-restraints excluded: chain B residue  877 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 47 optimal weight:    0.2980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 226 GLN
** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 416 HIS
** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 277 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.150750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.133785 restraints weight = 9001.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.138248 restraints weight = 5109.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.141289 restraints weight = 3240.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.143398 restraints weight = 2207.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.144868 restraints weight = 1592.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6527
moved from start:          0.3970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077   4978  Z= 0.252
  Angle     :  0.666   9.282   6760  Z= 0.350
  Chirality :  0.044   0.162    772
  Planarity :  0.005   0.040    862
  Dihedral  :  5.184  19.784    676
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 13.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 15.86 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.90 (0.34), residues: 582
  helix: -0.07 (0.27), residues: 336
  sheet: -1.96 (0.76), residues: 36
  loop : -1.01 (0.44), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 195 
 TYR   0.019   0.003   TYR B 184 
 PHE   0.035   0.003   PHE A 336 
 TRP   0.030   0.003   TRP B 186 
 HIS   0.008   0.002   HIS A 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00524 ( 4978)
  covalent geometry    : angle       0.66619 ( 6760)
  hydrogen bonds       : bond        0.05583 (  242)
  hydrogen bonds       : angle       5.81360 (  693)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 154
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  323 ILE cc_start: 0.8317 (mp) cc_final: 0.8047 (mp)
REVERT: A  348 ASP cc_start: 0.7379 (m-30) cc_final: 0.6917 (m-30)
REVERT: A  350 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6682 (pt0)
REVERT: A  419 THR cc_start: 0.8502 (p) cc_final: 0.7523 (m)
REVERT: A  651 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6866 (ttp80)
REVERT: A  788 GLN cc_start: 0.7358 (tt0) cc_final: 0.7133 (tt0)
REVERT: A  796 ASP cc_start: 0.7969 (m-30) cc_final: 0.7452 (m-30)
REVERT: B   69 GLN cc_start: 0.7678 (tp40) cc_final: 0.7123 (tp40)
REVERT: B   95 ILE cc_start: 0.8428 (mt) cc_final: 0.8103 (mm)
REVERT: B  185 TYR cc_start: 0.6764 (OUTLIER) cc_final: 0.5058 (t80)
REVERT: B  281 ARG cc_start: 0.7870 (mtm-85) cc_final: 0.7489 (mtm-85)
REVERT: B  285 VAL cc_start: 0.6806 (t) cc_final: 0.6297 (m)
REVERT: B  289 VAL cc_start: 0.7964 (t) cc_final: 0.7413 (m)
REVERT: B  324 ASN cc_start: 0.7554 (t0) cc_final: 0.7140 (t0)
REVERT: B  332 ARG cc_start: 0.7512 (mtp85) cc_final: 0.7241 (mtp85)
  outliers start: 18
  outliers final: 13
  residues processed: 162
  average time/residue: 0.0783
  time to fit residues: 15.3656
Evaluate side-chains
  155 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 140
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue   71 PHE
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  651 ARG
Chi-restraints excluded: chain A residue  803 SER
Chi-restraints excluded: chain A residue  811 ILE
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  181 ASP
Chi-restraints excluded: chain B residue  185 TYR
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  870 LEU
Chi-restraints excluded: chain B residue  877 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 10 optimal weight:    0.1980
   chunk 9 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0980
   chunk 42 optimal weight:    0.6980
   chunk 47 optimal weight:    0.3980
   chunk 52 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 23 optimal weight:    0.1980
   chunk 19 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0980
   chunk 53 optimal weight:    0.4980
   overall best weight:    0.1980

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

Flipped N/Q/H residues before XYZ refinement:
A 305 GLN
** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  46 GLN
B 155 HIS
B 277 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.154441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 21)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.137093 restraints weight = 9014.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.141636 restraints weight = 5096.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.144773 restraints weight = 3219.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.146677 restraints weight = 2195.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.148420 restraints weight = 1613.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6450
moved from start:          0.3960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4978  Z= 0.116
  Angle     :  0.546   7.400   6760  Z= 0.281
  Chirality :  0.040   0.169    772
  Planarity :  0.005   0.044    862
  Dihedral  :  4.428  16.493    676
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 18.96 %
    Favored  : 77.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.32 (0.34), residues: 582
  helix:  0.43 (0.27), residues: 335
  sheet: -1.96 (0.86), residues: 31
  loop : -0.80 (0.44), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 874 
 TYR   0.030   0.001   TYR B 320 
 PHE   0.020   0.002   PHE B 149 
 TRP   0.022   0.002   TRP B 186 
 HIS   0.005   0.001   HIS A 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 4978)
  covalent geometry    : angle       0.54650 ( 6760)
  hydrogen bonds       : bond        0.04241 (  242)
  hydrogen bonds       : angle       5.18803 (  693)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 142
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7173 (mt-10)
REVERT: A  323 ILE cc_start: 0.8182 (mp) cc_final: 0.7966 (mp)
REVERT: A  348 ASP cc_start: 0.7305 (m-30) cc_final: 0.6847 (m-30)
REVERT: A  350 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6803 (pt0)
REVERT: A  368 LEU cc_start: 0.7657 (mm) cc_final: 0.7398 (mp)
REVERT: A  419 THR cc_start: 0.8435 (p) cc_final: 0.7442 (m)
REVERT: A  651 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6790 (ttp80)
REVERT: A  788 GLN cc_start: 0.7197 (tt0) cc_final: 0.6984 (tt0)
REVERT: A  796 ASP cc_start: 0.7702 (m-30) cc_final: 0.7310 (m-30)
REVERT: B  132 LYS cc_start: 0.7336 (mtpt) cc_final: 0.7124 (mtpt)
REVERT: B  244 ASN cc_start: 0.7464 (p0) cc_final: 0.7250 (p0)
REVERT: B  268 MET cc_start: 0.5008 (tmm) cc_final: 0.3702 (tmm)
REVERT: B  285 VAL cc_start: 0.6857 (t) cc_final: 0.6356 (m)
REVERT: B  289 VAL cc_start: 0.7952 (t) cc_final: 0.7495 (m)
  outliers start: 17
  outliers final: 10
  residues processed: 150
  average time/residue: 0.0816
  time to fit residues: 14.7875
Evaluate side-chains
  151 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 140
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue   71 PHE
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  416 HIS
Chi-restraints excluded: chain A residue  651 ARG
Chi-restraints excluded: chain A residue  803 SER
Chi-restraints excluded: chain B residue  870 LEU
Chi-restraints excluded: chain B residue  877 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 1 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 416 HIS
A 417 ASN
B 868 HIS
B 877 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.150192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.133067 restraints weight = 9104.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.137519 restraints weight = 5182.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.140613 restraints weight = 3295.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.142728 restraints weight = 2254.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.144003 restraints weight = 1630.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6547
moved from start:          0.4632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   4978  Z= 0.248
  Angle     :  0.680   9.189   6760  Z= 0.355
  Chirality :  0.045   0.182    772
  Planarity :  0.005   0.047    862
  Dihedral  :  5.114  20.461    676
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 16.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 18.96 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.87 (0.34), residues: 582
  helix: -0.05 (0.26), residues: 340
  sheet: -1.99 (0.78), residues: 36
  loop : -0.99 (0.47), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 195 
 TYR   0.033   0.002   TYR B 320 
 PHE   0.027   0.003   PHE A  51 
 TRP   0.035   0.003   TRP B 186 
 HIS   0.012   0.002   HIS A 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 ( 4978)
  covalent geometry    : angle       0.67984 ( 6760)
  hydrogen bonds       : bond        0.05429 (  242)
  hydrogen bonds       : angle       5.72510 (  693)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 157
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7288 (mt-10)
REVERT: A  318 TYR cc_start: 0.6735 (t80) cc_final: 0.6475 (t80)
REVERT: A  323 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8063 (mp)
REVERT: A  348 ASP cc_start: 0.7308 (m-30) cc_final: 0.6854 (m-30)
REVERT: A  350 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6878 (pt0)
REVERT: A  404 VAL cc_start: 0.1398 (OUTLIER) cc_final: 0.1124 (p)
REVERT: A  419 THR cc_start: 0.8423 (p) cc_final: 0.8000 (t)
REVERT: A  651 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6857 (ttp80)
REVERT: A  788 GLN cc_start: 0.7331 (tt0) cc_final: 0.7114 (tt0)
REVERT: A  796 ASP cc_start: 0.7920 (m-30) cc_final: 0.7393 (m-30)
REVERT: B   69 GLN cc_start: 0.7685 (tp40) cc_final: 0.7124 (tp40)
REVERT: B   83 LEU cc_start: 0.7838 (tt) cc_final: 0.7549 (mp)
REVERT: B   95 ILE cc_start: 0.8448 (mt) cc_final: 0.8118 (mm)
REVERT: B  132 LYS cc_start: 0.7328 (mtpt) cc_final: 0.7065 (mtpt)
REVERT: B  192 LEU cc_start: 0.7458 (mt) cc_final: 0.7241 (mt)
REVERT: B  268 MET cc_start: 0.5087 (OUTLIER) cc_final: 0.3601 (tmm)
REVERT: B  285 VAL cc_start: 0.6880 (t) cc_final: 0.6364 (m)
REVERT: B  289 VAL cc_start: 0.8038 (t) cc_final: 0.7523 (m)
REVERT: B  325 ARG cc_start: 0.6357 (mmp80) cc_final: 0.6076 (mmp80)
  outliers start: 22
  outliers final: 15
  residues processed: 168
  average time/residue: 0.0834
  time to fit residues: 16.8111
Evaluate side-chains
  174 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 155
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 GLU
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   71 PHE
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  347 SER
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  651 ARG
Chi-restraints excluded: chain A residue  803 SER
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  181 ASP
Chi-restraints excluded: chain B residue  268 MET
Chi-restraints excluded: chain B residue  870 LEU
Chi-restraints excluded: chain B residue  877 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 16 optimal weight:    0.0980
   chunk 45 optimal weight:    0.8980
   chunk 58 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    6.9990
   chunk 5 optimal weight:    0.0770
   chunk 42 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 44 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
A 416 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.152569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.135440 restraints weight = 8983.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.139927 restraints weight = 5102.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.142997 restraints weight = 3247.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.145163 restraints weight = 2226.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.146606 restraints weight = 1604.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6494
moved from start:          0.4661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4978  Z= 0.160
  Angle     :  0.615   8.387   6760  Z= 0.317
  Chirality :  0.043   0.299    772
  Planarity :  0.005   0.050    862
  Dihedral  :  4.701  17.817    676
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 20.12 %
    Favored  : 75.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.68 (0.34), residues: 582
  helix:  0.13 (0.26), residues: 340
  sheet: -1.75 (0.78), residues: 36
  loop : -1.01 (0.46), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 874 
 TYR   0.039   0.002   TYR B 320 
 PHE   0.021   0.002   PHE B 149 
 TRP   0.035   0.003   TRP B 186 
 HIS   0.009   0.001   HIS A 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 4978)
  covalent geometry    : angle       0.61503 ( 6760)
  hydrogen bonds       : bond        0.04652 (  242)
  hydrogen bonds       : angle       5.35974 (  693)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 152
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7245 (mt-10)
REVERT: A  323 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.8041 (mp)
REVERT: A  348 ASP cc_start: 0.7265 (m-30) cc_final: 0.6789 (m-30)
REVERT: A  350 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6812 (pt0)
REVERT: A  404 VAL cc_start: 0.1236 (OUTLIER) cc_final: 0.0997 (p)
REVERT: A  419 THR cc_start: 0.8409 (p) cc_final: 0.8019 (t)
REVERT: A  651 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6783 (ttp80)
REVERT: A  788 GLN cc_start: 0.7249 (tt0) cc_final: 0.7040 (tt0)
REVERT: A  796 ASP cc_start: 0.7787 (m-30) cc_final: 0.7311 (m-30)
REVERT: B   95 ILE cc_start: 0.8434 (mt) cc_final: 0.8106 (mm)
REVERT: B  132 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.7072 (mtpt)
REVERT: B  185 TYR cc_start: 0.6668 (OUTLIER) cc_final: 0.5705 (t80)
REVERT: B  256 ARG cc_start: 0.7109 (ptp90) cc_final: 0.6861 (ptp90)
REVERT: B  285 VAL cc_start: 0.6909 (t) cc_final: 0.6434 (m)
REVERT: B  289 VAL cc_start: 0.8011 (t) cc_final: 0.7514 (m)
REVERT: B  295 THR cc_start: 0.5401 (OUTLIER) cc_final: 0.5130 (p)
REVERT: B  325 ARG cc_start: 0.6322 (mmp80) cc_final: 0.6034 (mmp80)
  outliers start: 25
  outliers final: 13
  residues processed: 163
  average time/residue: 0.0886
  time to fit residues: 17.5075
Evaluate side-chains
  167 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 148
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 GLU
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue   71 PHE
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  347 SER
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  416 HIS
Chi-restraints excluded: chain A residue  651 ARG
Chi-restraints excluded: chain A residue  803 SER
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  132 LYS
Chi-restraints excluded: chain B residue  185 TYR
Chi-restraints excluded: chain B residue  295 THR
Chi-restraints excluded: chain B residue  870 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 38 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0060
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
A 416 HIS
B 277 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.151670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.134519 restraints weight = 9045.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.138948 restraints weight = 5148.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.142011 restraints weight = 3286.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.144072 restraints weight = 2257.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.145619 restraints weight = 1648.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6510
moved from start:          0.4913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4978  Z= 0.201
  Angle     :  0.680   8.726   6760  Z= 0.348
  Chirality :  0.045   0.270    772
  Planarity :  0.005   0.053    862
  Dihedral  :  4.884  18.020    676
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 15.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 20.70 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.75 (0.34), residues: 582
  helix:  0.11 (0.27), residues: 333
  sheet: -1.85 (0.76), residues: 36
  loop : -1.05 (0.45), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 874 
 TYR   0.034   0.002   TYR B 320 
 PHE   0.022   0.002   PHE B 149 
 TRP   0.044   0.004   TRP B 186 
 HIS   0.009   0.002   HIS A 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 4978)
  covalent geometry    : angle       0.67991 ( 6760)
  hydrogen bonds       : bond        0.05129 (  242)
  hydrogen bonds       : angle       5.58108 (  693)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 151
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7241 (mt-10)
REVERT: A  318 TYR cc_start: 0.6778 (t80) cc_final: 0.6455 (t80)
REVERT: A  323 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8034 (mp)
REVERT: A  350 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6768 (pt0)
REVERT: A  368 LEU cc_start: 0.7665 (mm) cc_final: 0.7409 (mp)
REVERT: A  404 VAL cc_start: 0.1367 (OUTLIER) cc_final: 0.1071 (p)
REVERT: A  419 THR cc_start: 0.8410 (p) cc_final: 0.8015 (t)
REVERT: A  651 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6788 (ttp80)
REVERT: A  796 ASP cc_start: 0.7862 (m-30) cc_final: 0.7362 (m-30)
REVERT: B   95 ILE cc_start: 0.8439 (mt) cc_final: 0.8120 (mm)
REVERT: B  132 LYS cc_start: 0.7338 (mtpt) cc_final: 0.7051 (mtpt)
REVERT: B  185 TYR cc_start: 0.6680 (OUTLIER) cc_final: 0.5800 (t80)
REVERT: B  285 VAL cc_start: 0.6952 (t) cc_final: 0.6477 (m)
REVERT: B  289 VAL cc_start: 0.8050 (t) cc_final: 0.7550 (m)
REVERT: B  295 THR cc_start: 0.5358 (OUTLIER) cc_final: 0.5088 (p)
  outliers start: 25
  outliers final: 18
  residues processed: 164
  average time/residue: 0.1002
  time to fit residues: 19.9399
Evaluate side-chains
  173 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 150
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 GLU
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   71 PHE
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  347 SER
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  416 HIS
Chi-restraints excluded: chain A residue  417 ASN
Chi-restraints excluded: chain A residue  651 ARG
Chi-restraints excluded: chain A residue  795 ARG
Chi-restraints excluded: chain A residue  803 SER
Chi-restraints excluded: chain A residue  811 ILE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  185 TYR
Chi-restraints excluded: chain B residue  295 THR
Chi-restraints excluded: chain B residue  870 LEU
Chi-restraints excluded: chain B residue  877 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 17 optimal weight:    0.1980
   chunk 45 optimal weight:    0.5980
   chunk 46 optimal weight:    0.6980
   chunk 40 optimal weight:    0.1980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 416 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.152474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.135428 restraints weight = 8902.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.139822 restraints weight = 5090.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.142886 restraints weight = 3260.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.144930 restraints weight = 2241.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.146412 restraints weight = 1636.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6496
moved from start:          0.4997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4978  Z= 0.174
  Angle     :  0.659   8.582   6760  Z= 0.336
  Chirality :  0.045   0.261    772
  Planarity :  0.005   0.053    862
  Dihedral  :  4.803  17.916    676
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 14.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 20.89 %
    Favored  : 74.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.70 (0.34), residues: 582
  helix:  0.18 (0.27), residues: 335
  sheet: -1.83 (0.77), residues: 36
  loop : -1.09 (0.45), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 255 
 TYR   0.028   0.002   TYR B 320 
 PHE   0.023   0.002   PHE A 336 
 TRP   0.053   0.004   TRP B 186 
 HIS   0.009   0.001   HIS A 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 4978)
  covalent geometry    : angle       0.65915 ( 6760)
  hydrogen bonds       : bond        0.04781 (  242)
  hydrogen bonds       : angle       5.43989 (  693)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 148
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7236 (mt-10)
REVERT: A  138 GLN cc_start: 0.6609 (OUTLIER) cc_final: 0.6002 (mm110)
REVERT: A  323 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7995 (mp)
REVERT: A  350 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6813 (pt0)
REVERT: A  404 VAL cc_start: 0.1285 (OUTLIER) cc_final: 0.1020 (p)
REVERT: A  651 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6795 (ttp80)
REVERT: A  796 ASP cc_start: 0.7783 (m-30) cc_final: 0.7279 (m-30)
REVERT: B   95 ILE cc_start: 0.8424 (mt) cc_final: 0.8086 (mm)
REVERT: B  132 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.7050 (mtpt)
REVERT: B  285 VAL cc_start: 0.6964 (t) cc_final: 0.6490 (m)
REVERT: B  289 VAL cc_start: 0.8023 (t) cc_final: 0.7530 (m)
REVERT: B  295 THR cc_start: 0.5365 (OUTLIER) cc_final: 0.5083 (p)
  outliers start: 25
  outliers final: 14
  residues processed: 158
  average time/residue: 0.0857
  time to fit residues: 16.2160
Evaluate side-chains
  167 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 147
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 GLU
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue   71 PHE
Chi-restraints excluded: chain A residue  138 GLN
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  347 SER
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  651 ARG
Chi-restraints excluded: chain A residue  803 SER
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  132 LYS
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  295 THR
Chi-restraints excluded: chain B residue  870 LEU
Chi-restraints excluded: chain B residue  877 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 17 optimal weight:    0.0870
   chunk 58 optimal weight:    0.0870
   chunk 9 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0980
   chunk 28 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9990
   chunk 40 optimal weight:    0.4980
   chunk 18 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.2336

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

Flipped N/Q/H residues before XYZ refinement:
A 416 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.150540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.134279 restraints weight = 8925.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.138567 restraints weight = 5173.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.141463 restraints weight = 3316.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.143417 restraints weight = 2283.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.144919 restraints weight = 1668.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6433
moved from start:          0.4934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4978  Z= 0.129
  Angle     :  0.625   8.587   6760  Z= 0.317
  Chirality :  0.043   0.257    772
  Planarity :  0.005   0.051    862
  Dihedral  :  4.425  17.170    676
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 22.44 %
    Favored  : 74.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.42 (0.34), residues: 582
  helix:  0.36 (0.27), residues: 336
  sheet: -1.50 (0.80), residues: 36
  loop : -0.96 (0.45), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 328 
 TYR   0.024   0.001   TYR B 320 
 PHE   0.018   0.002   PHE B 149 
 TRP   0.056   0.004   TRP B 186 
 HIS   0.007   0.001   HIS A 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 4978)
  covalent geometry    : angle       0.62457 ( 6760)
  hydrogen bonds       : bond        0.04154 (  242)
  hydrogen bonds       : angle       5.16516 (  693)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 147
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7157 (mt-10)
REVERT: A  323 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7953 (mp)
REVERT: A  350 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6797 (pt0)
REVERT: A  404 VAL cc_start: 0.1245 (OUTLIER) cc_final: 0.1004 (p)
REVERT: A  419 THR cc_start: 0.8415 (p) cc_final: 0.8017 (t)
REVERT: A  651 ARG cc_start: 0.7057 (ttp80) cc_final: 0.6667 (ttp80)
REVERT: A  796 ASP cc_start: 0.7638 (m-30) cc_final: 0.7198 (m-30)
REVERT: B   95 ILE cc_start: 0.8439 (mt) cc_final: 0.8119 (mm)
REVERT: B  132 LYS cc_start: 0.7328 (mtpt) cc_final: 0.7070 (mtpt)
REVERT: B  285 VAL cc_start: 0.7025 (t) cc_final: 0.6555 (m)
REVERT: B  289 VAL cc_start: 0.8015 (t) cc_final: 0.7524 (m)
  outliers start: 17
  outliers final: 12
  residues processed: 153
  average time/residue: 0.0820
  time to fit residues: 15.3461
Evaluate side-chains
  156 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 142
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   71 PHE
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  347 SER
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  795 ARG
Chi-restraints excluded: chain A residue  803 SER
Chi-restraints excluded: chain B residue   54 GLU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  870 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 48 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0870
   chunk 39 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 17 optimal weight:    0.1980
   chunk 3 optimal weight:    0.0970
   chunk 44 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0970
   overall best weight:    0.2154

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

Flipped N/Q/H residues before XYZ refinement:
A 409 ASN
A 416 HIS
B 277 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.150796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.134486 restraints weight = 9097.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.138825 restraints weight = 5201.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.141687 restraints weight = 3305.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.143751 restraints weight = 2267.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.145219 restraints weight = 1626.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6418
moved from start:          0.5008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4978  Z= 0.123
  Angle     :  0.610   8.632   6760  Z= 0.308
  Chirality :  0.043   0.235    772
  Planarity :  0.005   0.049    862
  Dihedral  :  4.295  17.789    676
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 23.40 %
    Favored  : 73.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.27 (0.34), residues: 582
  helix:  0.45 (0.27), residues: 337
  sheet: -1.18 (0.80), residues: 36
  loop : -0.88 (0.44), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 328 
 TYR   0.021   0.001   TYR B 320 
 PHE   0.021   0.002   PHE A 649 
 TRP   0.051   0.004   TRP B 186 
 HIS   0.007   0.001   HIS A 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 4978)
  covalent geometry    : angle       0.61009 ( 6760)
  hydrogen bonds       : bond        0.04055 (  242)
  hydrogen bonds       : angle       5.09351 (  693)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1029.28 seconds
wall clock time: 18 minutes 29.34 seconds (1109.34 seconds total)