Starting phenix.real_space_refine
on Fri Mar 14 03:35:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kxy_23067/03_2025/7kxy_23067.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kxy_23067/03_2025/7kxy_23067.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kxy_23067/03_2025/7kxy_23067.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kxy_23067/03_2025/7kxy_23067.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kxy_23067/03_2025/7kxy_23067.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kxy_23067/03_2025/7kxy_23067.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
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      48      5.16       5
     C    6048      2.51       5
     N    1630      2.21       5
     O    1784      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 67 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9510
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 588, 4704
          Classifications: {'peptide': 588}
          Link IDs: {'PTRANS': 30, 'TRANS': 557}
          Chain breaks: 8
    Chain: "B"
      Number of atoms: 4806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 593, 4806
          Classifications: {'peptide': 593}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 27, 'TRANS': 564}
          Chain breaks: 4
  Time building chain proxies: 5.84, per 1000 atoms: 0.61
  Number of scatterers: 9510
  At special positions: 0
  Unit cell: (85.8, 96.8, 134.2, 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      48     16.00
     O    1784      8.00
     N    1630      7.00
     C    6048      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 139 " - pdb=" SG  CYS A 165 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 220 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 472 " - pdb=" SG  CYS A 498 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1697 " - pdb=" SG  CYS B1723 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1879 " - pdb=" SG  CYS B2033 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B2038 " - pdb=" SG  CYS B2193 " distance=2.02

  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: 2.37
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2206

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 12 sheets defined
      2.4% alpha, 6.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 425 through 429
    Processing helix  chain 'A' and resid 549 through 554
    Processing helix  chain 'A' and resid 640 through 645
      removed outlier: 4.331A  pdb=" N   LYS A 645 " --> pdb=" O   SER A 641 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1779 through 1783
      removed outlier: 3.698A  pdb=" N   MET B1783 " --> pdb=" O   ILE B1780 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1861 through 1866
      removed outlier: 3.506A  pdb=" N   GLN B1864 " --> pdb=" O   GLY B1861 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ARG B1865 " --> pdb=" O   GLU B1862 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13
      removed outlier: 3.980A  pdb=" N   ALA A   9 " --> pdb=" O   ARG A  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 64
      removed outlier: 6.969A  pdb=" N   LEU A  62 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   CYS A 165 " --> pdb=" O   LEU A  62 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   ALA A  64 " --> pdb=" O   CYS A 165 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ILE A 164 " --> pdb=" O   LEU A 140 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 224 through 231
      removed outlier: 3.584A  pdb=" N   ILE A 225 " --> pdb=" O   MET A 270 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ALA A 268 " --> pdb=" O   TRP A 227 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 331 through 334
      removed outlier: 3.869A  pdb=" N   VAL A 331 " --> pdb=" O   LYS A 365 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 394 through 395
      removed outlier: 6.741A  pdb=" N   LEU A 494 " --> pdb=" O   ILE A 395 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 594 through 595
      removed outlier: 3.585A  pdb=" N   LEU A 594 " --> pdb=" O   LEU A 615 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1555 through 1556
    Processing sheet with id=AA8, first strand: chain 'B' and resid 1620 through 1622
      removed outlier: 3.506A  pdb=" N   LEU B1721 " --> pdb=" O   ILE B1620 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   ALA B1622 " --> pdb=" O   LEU B1721 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 1800 through 1801
    Processing sheet with id=AB1, first strand: chain 'B' and resid 1814 through 1816
      removed outlier: 3.744A  pdb=" N   HIS B1815 " --> pdb=" O   ASN B1857 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   ASN B1857 " --> pdb=" O   HIS B1815 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 1896 through 1897
      removed outlier: 4.499A  pdb=" N   LYS B1896 " --> pdb=" O   GLN B1936 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   GLN B1936 " --> pdb=" O   LYS B1896 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 1977 through 1978

    42 hydrogen bonds defined for protein.
    90 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: 2.12

  Time building geometry restraints manager: 2.83 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3065
        1.35 -     1.47: 2405
        1.47 -     1.59: 4197
        1.59 -     1.70: 0
        1.70 -     1.82: 79
  Bond restraints: 9746
  Sorted by residual:
  bond pdb=" C   ILE B2176 "
       pdb=" N   PRO B2177 "
    ideal  model  delta    sigma   weight residual
    1.335  1.356 -0.021 8.70e-03 1.32e+04 5.81e+00
  bond pdb=" CA  THR B2018 "
       pdb=" C   THR B2018 "
    ideal  model  delta    sigma   weight residual
    1.517  1.528 -0.011 6.30e-03 2.52e+04 3.00e+00
  bond pdb=" CA  ARG B2074 "
       pdb=" CB  ARG B2074 "
    ideal  model  delta    sigma   weight residual
    1.528  1.557 -0.029 1.67e-02 3.59e+03 2.95e+00
  bond pdb=" C   GLU A  42 "
       pdb=" N   PRO A  43 "
    ideal  model  delta    sigma   weight residual
    1.332  1.352 -0.020 1.33e-02 5.65e+03 2.32e+00
  bond pdb=" CA  PHE B1872 "
       pdb=" CB  PHE B1872 "
    ideal  model  delta    sigma   weight residual
    1.526  1.549 -0.022 1.53e-02 4.27e+03 2.16e+00
  ... (remaining 9741 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 12597
        1.79 -     3.58: 513
        3.58 -     5.36: 62
        5.36 -     7.15: 8
        7.15 -     8.94: 4
  Bond angle restraints: 13184
  Sorted by residual:
  angle pdb=" CA  THR B2018 "
        pdb=" C   THR B2018 "
        pdb=" N   ARG B2019 "
      ideal   model   delta    sigma   weight residual
     119.46  116.96    2.50 6.10e-01 2.69e+00 1.68e+01
  angle pdb=" C   SER A 262 "
        pdb=" N   ALA A 263 "
        pdb=" CA  ALA A 263 "
      ideal   model   delta    sigma   weight residual
     121.54  128.50   -6.96 1.91e+00 2.74e-01 1.33e+01
  angle pdb=" N   ILE A 390 "
        pdb=" CA  ILE A 390 "
        pdb=" C   ILE A 390 "
      ideal   model   delta    sigma   weight residual
     112.17  108.72    3.45 9.50e-01 1.11e+00 1.32e+01
  angle pdb=" C   TYR B1678 "
        pdb=" CA  TYR B1678 "
        pdb=" CB  TYR B1678 "
      ideal   model   delta    sigma   weight residual
     114.40  109.96    4.44 1.25e+00 6.40e-01 1.26e+01
  angle pdb=" CA  ARG A 445 "
        pdb=" C   ARG A 445 "
        pdb=" N   ALA A 446 "
      ideal   model   delta    sigma   weight residual
     118.27  123.71   -5.44 1.59e+00 3.96e-01 1.17e+01
  ... (remaining 13179 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.54: 5171
       17.54 -    35.07: 505
       35.07 -    52.61: 112
       52.61 -    70.15: 24
       70.15 -    87.68: 11
  Dihedral angle restraints: 5823
    sinusoidal: 2392
      harmonic: 3431
  Sorted by residual:
  dihedral pdb=" CA  VAL A 565 "
           pdb=" C   VAL A 565 "
           pdb=" N   PRO A 566 "
           pdb=" CA  PRO A 566 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.96   28.04     0      5.00e+00 4.00e-02 3.15e+01
  dihedral pdb=" CA  TYR A 415 "
           pdb=" C   TYR A 415 "
           pdb=" N   SER A 416 "
           pdb=" CA  SER A 416 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.06  -24.94     0      5.00e+00 4.00e-02 2.49e+01
  dihedral pdb=" CA  LEU A 403 "
           pdb=" C   LEU A 403 "
           pdb=" N   LYS A 404 "
           pdb=" CA  LYS A 404 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.86   24.14     0      5.00e+00 4.00e-02 2.33e+01
  ... (remaining 5820 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 777
       0.030 -    0.060: 368
       0.060 -    0.090: 165
       0.090 -    0.120: 73
       0.120 -    0.150: 20
  Chirality restraints: 1403
  Sorted by residual:
  chirality pdb=" CA  ILE B2169 "
            pdb=" N   ILE B2169 "
            pdb=" C   ILE B2169 "
            pdb=" CB  ILE B2169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.65e-01
  chirality pdb=" CA  ILE B1890 "
            pdb=" N   ILE B1890 "
            pdb=" C   ILE B1890 "
            pdb=" CB  ILE B1890 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.64e-01
  chirality pdb=" CA  VAL A 206 "
            pdb=" N   VAL A 206 "
            pdb=" C   VAL A 206 "
            pdb=" CB  VAL A 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.64e-01
  ... (remaining 1400 not shown)

  Planarity restraints: 1689
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 565 "    0.048 5.00e-02 4.00e+02   7.14e-02 8.16e+00
        pdb=" N   PRO A 566 "   -0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO A 566 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 566 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 160 "    0.041 5.00e-02 4.00e+02   6.20e-02 6.16e+00
        pdb=" N   PRO A 161 "   -0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO A 161 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 161 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 136 "    0.037 5.00e-02 4.00e+02   5.52e-02 4.87e+00
        pdb=" N   PRO A 137 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 137 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 137 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1686 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 861
        2.74 -     3.28: 9626
        3.28 -     3.82: 15522
        3.82 -     4.36: 18165
        4.36 -     4.90: 29045
  Nonbonded interactions: 73219
  Sorted by model distance:
  nonbonded pdb=" OG  SER B1648 "
            pdb=" OG1 THR B1685 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   ARG B1910 "
            pdb=" NH1 ARG B2027 "
     model   vdw
     2.236 3.120
  nonbonded pdb=" O   LYS A 607 "
            pdb=" OG  SER B1692 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   VAL B1624 "
            pdb=" NZ  LYS B1725 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" OG1 THR B1962 "
            pdb=" O   THR B2025 "
     model   vdw
     2.277 3.040
  ... (remaining 73214 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.860
  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:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.790
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6064
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   9746  Z= 0.237
  Angle     :  0.822   8.939  13184  Z= 0.472
  Chirality :  0.046   0.150   1403
  Planarity :  0.005   0.071   1689
  Dihedral  : 15.126  87.683   3599
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 19.28
  Ramachandran Plot:
    Outliers :  4.16 %
    Allowed  : 26.02 %
    Favored  : 69.82 %
  Rotamer:
    Outliers :  7.18 %
    Allowed  : 11.87 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.90 (0.19), residues: 1153
  helix: -5.24 (0.21), residues: 25
  sheet: -4.15 (0.32), residues: 174
  loop : -4.26 (0.16), residues: 954

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B2094 
 HIS   0.003   0.001   HIS B2128 
 PHE   0.017   0.002   PHE B1872 
 TYR   0.021   0.001   TYR A 144 
 ARG   0.003   0.001   ARG A 306 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 188
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 MET cc_start: 0.5254 (ptm) cc_final: 0.4695 (ptm)
REVERT: A  407 PHE cc_start: 0.3839 (p90) cc_final: 0.3593 (p90)
REVERT: B 1736 MET cc_start: 0.6433 (tpt) cc_final: 0.6158 (tpp)
REVERT: B 1755 TYR cc_start: 0.7567 (p90) cc_final: 0.7337 (p90)
REVERT: B 1801 HIS cc_start: 0.7575 (m-70) cc_final: 0.7226 (m-70)
REVERT: B 1903 TYR cc_start: 0.6273 (t80) cc_final: 0.5725 (t80)
REVERT: B 1905 GLU cc_start: 0.4699 (mt-10) cc_final: 0.4436 (mt-10)
REVERT: B 2075 LEU cc_start: 0.5836 (OUTLIER) cc_final: 0.5570 (pp)
REVERT: B 2120 MET cc_start: 0.2084 (mmp) cc_final: 0.1849 (mmt)
  outliers start: 75
  outliers final: 21
  residues processed: 243
  average time/residue: 0.2037
  time to fit residues: 70.0083
Evaluate side-chains
  156 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 88 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   chunk 30 optimal weight:    7.9990
   chunk 59 optimal weight:    7.9990
   chunk 47 optimal weight:    8.9990
   chunk 91 optimal weight:   20.0000
   chunk 35 optimal weight:    5.9990
   chunk 55 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9980
   chunk 106 optimal weight:    2.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  11 GLN
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 207 ASN
A 211 ASN
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 GLN
A 362 HIS
A 448 GLN
A 516 GLN
A 541 ASN
** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 597 HIS
B1547 ASN
** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1713 HIS
** B1778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B2051 ASN
B2078 GLN
** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.157759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.147219 restraints weight = 28331.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.148874 restraints weight = 19453.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.149918 restraints weight = 14474.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.4224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6320
moved from start:          0.2583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   9746  Z= 0.320
  Angle     :  0.865   9.403  13184  Z= 0.444
  Chirality :  0.052   0.201   1403
  Planarity :  0.007   0.069   1689
  Dihedral  :  7.874  30.757   1282
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 25.78
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 17.35 %
    Favored  : 82.57 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  6.89 %
    Favored  : 92.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 1.75 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.57 (0.20), residues: 1153
  helix: -5.00 (0.39), residues: 27
  sheet: -4.03 (0.32), residues: 195
  loop : -3.96 (0.17), residues: 931

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B2094 
 HIS   0.008   0.002   HIS B1643 
 PHE   0.025   0.002   PHE A 574 
 TYR   0.023   0.002   TYR B2129 
 ARG   0.005   0.001   ARG A 396 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 160
  time to evaluate  : 1.064 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 TYR cc_start: 0.6680 (m-10) cc_final: 0.5686 (m-80)
REVERT: A   90 ARG cc_start: 0.5897 (ptt90) cc_final: 0.5182 (mtm180)
REVERT: A  229 LEU cc_start: 0.6681 (mt) cc_final: 0.6443 (mt)
REVERT: A  232 MET cc_start: 0.6065 (ptm) cc_final: 0.5620 (ptm)
REVERT: A  483 ILE cc_start: 0.7241 (mt) cc_final: 0.6884 (mt)
REVERT: A  551 LYS cc_start: 0.6038 (mttt) cc_final: 0.5628 (mptt)
REVERT: A  609 HIS cc_start: 0.6419 (m170) cc_final: 0.5777 (m170)
REVERT: B 1703 TYR cc_start: 0.4688 (p90) cc_final: 0.4463 (p90)
REVERT: B 1746 MET cc_start: 0.8197 (tpp) cc_final: 0.7942 (tpp)
REVERT: B 1883 MET cc_start: 0.4296 (tmm) cc_final: 0.3890 (tmm)
REVERT: B 1903 TYR cc_start: 0.6169 (t80) cc_final: 0.5869 (t80)
REVERT: B 2120 MET cc_start: 0.3173 (mmp) cc_final: 0.2910 (mmt)
  outliers start: 2
  outliers final: 1
  residues processed: 161
  average time/residue: 0.2439
  time to fit residues: 54.5553
Evaluate side-chains
  123 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 122
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 45 optimal weight:   10.0000
   chunk 29 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 63 optimal weight:    7.9990
   chunk 56 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 101 optimal weight:    9.9990
   chunk 59 optimal weight:    0.7980
   chunk 78 optimal weight:    0.8980
   chunk 51 optimal weight:    0.4980
   chunk 49 optimal weight:   10.0000
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1670 ASN
B1778 HIS
** B1801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.165738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.155152 restraints weight = 28337.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.156830 restraints weight = 18993.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.158191 restraints weight = 13926.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.4327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6094
moved from start:          0.2794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9746  Z= 0.188
  Angle     :  0.733   8.327  13184  Z= 0.372
  Chirality :  0.049   0.208   1403
  Planarity :  0.005   0.057   1689
  Dihedral  :  6.935  29.964   1282
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 20.45
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 17.78 %
    Favored  : 82.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.19 (0.21), residues: 1153
  helix: -4.95 (0.42), residues: 32
  sheet: -3.78 (0.35), residues: 185
  loop : -3.67 (0.17), residues: 936

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B2094 
 HIS   0.007   0.001   HIS B1801 
 PHE   0.017   0.002   PHE B1872 
 TYR   0.020   0.002   TYR A 144 
 ARG   0.002   0.000   ARG A 445 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 1.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 TYR cc_start: 0.6513 (m-10) cc_final: 0.5592 (m-80)
REVERT: A  229 LEU cc_start: 0.6303 (mt) cc_final: 0.6050 (mt)
REVERT: A  312 THR cc_start: 0.4244 (t) cc_final: 0.4022 (t)
REVERT: A  405 ILE cc_start: 0.7895 (mp) cc_final: 0.7550 (mm)
REVERT: A  551 LYS cc_start: 0.6038 (mttt) cc_final: 0.5623 (mptt)
REVERT: B 1809 GLN cc_start: 0.7463 (pm20) cc_final: 0.7016 (pm20)
REVERT: B 1850 LYS cc_start: 0.6287 (mmtt) cc_final: 0.6033 (mmtp)
REVERT: B 1874 ILE cc_start: 0.6791 (mp) cc_final: 0.6391 (mp)
REVERT: B 1903 TYR cc_start: 0.6020 (t80) cc_final: 0.5670 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.2487
  time to fit residues: 55.1403
Evaluate side-chains
  122 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 21 optimal weight:    9.9990
   chunk 77 optimal weight:   10.0000
   chunk 4 optimal weight:    6.9990
   chunk 100 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 66 optimal weight:    8.9990
   chunk 91 optimal weight:    4.9990
   chunk 90 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 251 ASN
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1973 GLN
B2078 GLN
** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B2132 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.155966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.145340 restraints weight = 28538.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.147021 restraints weight = 19168.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.148419 restraints weight = 14144.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.4211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6363
moved from start:          0.3125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9746  Z= 0.318
  Angle     :  0.839   9.390  13184  Z= 0.428
  Chirality :  0.051   0.213   1403
  Planarity :  0.006   0.060   1689
  Dihedral  :  7.638  32.219   1282
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 27.54
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 20.82 %
    Favored  : 79.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 1.75 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.35 (0.21), residues: 1153
  helix: -4.66 (0.57), residues: 32
  sheet: -3.88 (0.33), residues: 205
  loop : -3.77 (0.17), residues: 916

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B2094 
 HIS   0.013   0.002   HIS B1801 
 PHE   0.041   0.002   PHE A 325 
 TYR   0.019   0.002   TYR B1703 
 ARG   0.008   0.001   ARG B1910 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 1.101 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 TYR cc_start: 0.6725 (m-10) cc_final: 0.5747 (m-80)
REVERT: A  203 MET cc_start: 0.4102 (mmp) cc_final: 0.3861 (mmt)
REVERT: A  232 MET cc_start: 0.6287 (ptm) cc_final: 0.5419 (ptm)
REVERT: A  312 THR cc_start: 0.4642 (t) cc_final: 0.4347 (t)
REVERT: B 1734 MET cc_start: 0.6227 (mmt) cc_final: 0.5460 (mmm)
REVERT: B 1809 GLN cc_start: 0.7520 (pm20) cc_final: 0.7066 (pm20)
REVERT: B 1850 LYS cc_start: 0.6765 (mmtt) cc_final: 0.6560 (mmtp)
REVERT: B 1903 TYR cc_start: 0.6061 (t80) cc_final: 0.5623 (t80)
REVERT: B 1948 ILE cc_start: 0.4996 (pt) cc_final: 0.4785 (pt)
REVERT: B 2011 ARG cc_start: 0.2077 (mmt90) cc_final: 0.1858 (mmt180)
REVERT: B 2180 TRP cc_start: 0.7185 (m100) cc_final: 0.6570 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.2155
  time to fit residues: 46.5807
Evaluate side-chains
  122 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 89 optimal weight:    3.9990
   chunk 19 optimal weight:    0.4980
   chunk 106 optimal weight:    4.9990
   chunk 111 optimal weight:    7.9990
   chunk 77 optimal weight:    9.9990
   chunk 116 optimal weight:    0.9990
   chunk 95 optimal weight:    9.9990
   chunk 2 optimal weight:    0.4980
   chunk 22 optimal weight:    0.4980
   chunk 44 optimal weight:    0.7980
   chunk 102 optimal weight:   10.0000
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
** A   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 251 ASN
** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 541 ASN
** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1553 ASN
** B1643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1955 HIS
** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B2181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.166280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.155794 restraints weight = 27702.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.157726 restraints weight = 18349.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.159052 restraints weight = 13175.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.4333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6067
moved from start:          0.3316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   9746  Z= 0.189
  Angle     :  0.716   8.520  13184  Z= 0.362
  Chirality :  0.048   0.218   1403
  Planarity :  0.006   0.075   1689
  Dihedral  :  6.758  34.708   1282
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 18.38
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 13.96 %
    Favored  : 85.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 1.75 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.92 (0.22), residues: 1153
  helix: -4.73 (0.47), residues: 32
  sheet: -3.50 (0.36), residues: 197
  loop : -3.49 (0.18), residues: 924

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B2094 
 HIS   0.017   0.001   HIS A 252 
 PHE   0.027   0.002   PHE A 325 
 TYR   0.017   0.001   TYR A 144 
 ARG   0.007   0.000   ARG B2027 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 1.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 TYR cc_start: 0.6688 (m-10) cc_final: 0.5851 (m-80)
REVERT: A  203 MET cc_start: 0.3713 (mmp) cc_final: 0.2578 (mmt)
REVERT: A  229 LEU cc_start: 0.6166 (mt) cc_final: 0.5926 (mt)
REVERT: B 1734 MET cc_start: 0.5778 (mmt) cc_final: 0.4945 (mmt)
REVERT: B 1809 GLN cc_start: 0.7352 (pm20) cc_final: 0.6843 (pm20)
REVERT: B 1850 LYS cc_start: 0.6536 (mmtt) cc_final: 0.6246 (mmtp)
REVERT: B 1874 ILE cc_start: 0.6710 (mp) cc_final: 0.6389 (mp)
REVERT: B 1903 TYR cc_start: 0.6081 (t80) cc_final: 0.5538 (t80)
REVERT: B 2095 LEU cc_start: 0.6405 (tt) cc_final: 0.6144 (mm)
REVERT: B 2180 TRP cc_start: 0.6591 (m100) cc_final: 0.6136 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.2967
  time to fit residues: 67.8217
Evaluate side-chains
  126 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 91 optimal weight:   20.0000
   chunk 19 optimal weight:    2.9990
   chunk 83 optimal weight:    0.7980
   chunk 45 optimal weight:    9.9990
   chunk 30 optimal weight:    2.9990
   chunk 107 optimal weight:    4.9990
   chunk 44 optimal weight:    9.9990
   chunk 113 optimal weight:    0.3980
   chunk 20 optimal weight:    5.9990
   chunk 31 optimal weight:    0.2980
   chunk 88 optimal weight:    0.9980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** A   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 246 GLN
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 468 ASN
** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B2078 GLN
** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B2181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.166407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.156218 restraints weight = 27974.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.157970 restraints weight = 18787.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.159331 restraints weight = 13577.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.4344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6065
moved from start:          0.3655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9746  Z= 0.180
  Angle     :  0.702   9.060  13184  Z= 0.353
  Chirality :  0.047   0.234   1403
  Planarity :  0.005   0.064   1689
  Dihedral  :  6.525  32.396   1282
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 17.68
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 14.48 %
    Favored  : 85.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 1.75 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.80 (0.22), residues: 1153
  helix: -4.82 (0.49), residues: 25
  sheet: -3.57 (0.36), residues: 188
  loop : -3.37 (0.18), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B2094 
 HIS   0.004   0.001   HIS B2159 
 PHE   0.030   0.001   PHE A 325 
 TYR   0.017   0.002   TYR A 418 
 ARG   0.004   0.000   ARG A  90 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 1.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 TYR cc_start: 0.6619 (m-10) cc_final: 0.5741 (m-80)
REVERT: A  203 MET cc_start: 0.3592 (mmp) cc_final: 0.2473 (mmt)
REVERT: B 1698 ARG cc_start: 0.6790 (ptp90) cc_final: 0.6345 (ptp90)
REVERT: B 1734 MET cc_start: 0.5859 (mmt) cc_final: 0.5118 (mmt)
REVERT: B 1738 MET cc_start: 0.5654 (tpp) cc_final: 0.5450 (tpt)
REVERT: B 1850 LYS cc_start: 0.6455 (mmtt) cc_final: 0.6210 (mmtp)
REVERT: B 1875 MET cc_start: 0.2745 (pmm) cc_final: 0.1226 (ptp)
REVERT: B 1903 TYR cc_start: 0.6031 (t80) cc_final: 0.5398 (t80)
REVERT: B 1948 ILE cc_start: 0.4855 (pt) cc_final: 0.4560 (pt)
REVERT: B 2123 LYS cc_start: 0.8169 (mmmt) cc_final: 0.7765 (mmmt)
REVERT: B 2180 TRP cc_start: 0.6562 (m100) cc_final: 0.6108 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.3030
  time to fit residues: 72.0579
Evaluate side-chains
  127 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 103 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 99 optimal weight:    0.8980
   chunk 51 optimal weight:   10.0000
   chunk 59 optimal weight:    0.4980
   chunk 116 optimal weight:    0.9990
   chunk 45 optimal weight:    8.9990
   chunk 82 optimal weight:    0.6980
   chunk 13 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0980
   chunk 2 optimal weight:   10.0000
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
** A   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 207 ASN
** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B2181 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.170582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.160350 restraints weight = 27984.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.162077 restraints weight = 18746.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.163430 restraints weight = 13565.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.4394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5968
moved from start:          0.3987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9746  Z= 0.172
  Angle     :  0.693   8.544  13184  Z= 0.347
  Chirality :  0.047   0.229   1403
  Planarity :  0.005   0.060   1689
  Dihedral  :  6.233  31.586   1282
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 16.14
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 12.75 %
    Favored  : 87.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 1.75 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.70 (0.22), residues: 1153
  helix: -4.83 (0.35), residues: 37
  sheet: -3.33 (0.36), residues: 196
  loop : -3.30 (0.18), residues: 920

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B2094 
 HIS   0.009   0.001   HIS B1801 
 PHE   0.014   0.001   PHE B1872 
 TYR   0.020   0.001   TYR B2129 
 ARG   0.005   0.000   ARG A  90 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 1.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 TYR cc_start: 0.6583 (m-10) cc_final: 0.5709 (m-80)
REVERT: A  203 MET cc_start: 0.3486 (mmp) cc_final: 0.2814 (mmt)
REVERT: B 1734 MET cc_start: 0.5596 (mmt) cc_final: 0.4864 (mmt)
REVERT: B 1850 LYS cc_start: 0.6400 (mmtt) cc_final: 0.6130 (mmtp)
REVERT: B 1883 MET cc_start: 0.4198 (tmm) cc_final: 0.3590 (tmm)
REVERT: B 2018 THR cc_start: 0.7136 (t) cc_final: 0.6888 (t)
REVERT: B 2095 LEU cc_start: 0.6892 (tt) cc_final: 0.6214 (mp)
REVERT: B 2180 TRP cc_start: 0.6657 (m100) cc_final: 0.6312 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.2676
  time to fit residues: 62.6882
Evaluate side-chains
  129 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 1.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 75 optimal weight:    8.9990
   chunk 2 optimal weight:    9.9990
   chunk 80 optimal weight:    8.9990
   chunk 102 optimal weight:    9.9990
   chunk 50 optimal weight:    2.9990
   chunk 42 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 72 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 7 optimal weight:    8.9990
   overall best weight:    3.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 251 ASN
** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1547 ASN
** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1829 HIS
** B1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1940 GLN
** B2078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.158148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.147300 restraints weight = 29074.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.149050 restraints weight = 19975.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.150340 restraints weight = 14718.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.4240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6311
moved from start:          0.3947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   9746  Z= 0.333
  Angle     :  0.858  10.630  13184  Z= 0.435
  Chirality :  0.052   0.265   1403
  Planarity :  0.007   0.072   1689
  Dihedral  :  7.315  30.464   1282
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 26.53
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 19.34 %
    Favored  : 80.57 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.01 %
    Favored  : 97.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 1.75 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.98 (0.22), residues: 1153
  helix: -4.82 (0.56), residues: 25
  sheet: -3.81 (0.33), residues: 200
  loop : -3.46 (0.18), residues: 928

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP B2094 
 HIS   0.010   0.001   HIS B1801 
 PHE   0.027   0.002   PHE B2163 
 TYR   0.030   0.002   TYR B2129 
 ARG   0.017   0.001   ARG A  90 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 144
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 MET cc_start: 0.6152 (ppp) cc_final: 0.5689 (ptm)
REVERT: A  495 LEU cc_start: 0.8625 (tp) cc_final: 0.8418 (tp)
REVERT: B 1734 MET cc_start: 0.6179 (mmt) cc_final: 0.5505 (mmm)
REVERT: B 1738 MET cc_start: 0.5453 (tpt) cc_final: 0.5086 (tpt)
REVERT: B 1809 GLN cc_start: 0.7416 (pm20) cc_final: 0.6857 (pm20)
  outliers start: 1
  outliers final: 1
  residues processed: 145
  average time/residue: 0.1997
  time to fit residues: 41.8467
Evaluate side-chains
  123 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 122
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 94 optimal weight:    9.9990
   chunk 92 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 13 optimal weight:    8.9990
   chunk 71 optimal weight:    1.9990
   chunk 98 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9980
   chunk 76 optimal weight:    0.0370
   chunk 11 optimal weight:    0.4980
   chunk 58 optimal weight:   10.0000
   chunk 91 optimal weight:   10.0000
   overall best weight:    1.9062

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

Flipped N/Q/H residues before XYZ refinement:
** A   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B2078 GLN
** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B2153 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.163543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.152594 restraints weight = 28266.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.154411 restraints weight = 19465.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.155739 restraints weight = 14229.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.4306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6170
moved from start:          0.4020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9746  Z= 0.221
  Angle     :  0.770   9.559  13184  Z= 0.387
  Chirality :  0.049   0.325   1403
  Planarity :  0.006   0.056   1689
  Dihedral  :  6.898  29.036   1282
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 20.83
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 15.00 %
    Favored  : 84.91 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.57 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.75 (0.22), residues: 1153
  helix: -4.80 (0.55), residues: 25
  sheet: -3.49 (0.37), residues: 181
  loop : -3.36 (0.18), residues: 947

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B2094 
 HIS   0.009   0.001   HIS B1801 
 PHE   0.016   0.002   PHE B1872 
 TYR   0.027   0.002   TYR B2129 
 ARG   0.008   0.001   ARG A  90 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 151
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 MET cc_start: 0.6360 (ppp) cc_final: 0.5746 (ptm)
REVERT: A  233 SER cc_start: 0.8850 (p) cc_final: 0.8151 (m)
REVERT: A  483 ILE cc_start: 0.6570 (mt) cc_final: 0.6359 (mt)
REVERT: B 1738 MET cc_start: 0.5115 (tpt) cc_final: 0.4858 (tpt)
REVERT: B 1809 GLN cc_start: 0.7283 (pm20) cc_final: 0.6703 (pm20)
REVERT: B 1883 MET cc_start: 0.4286 (tmm) cc_final: 0.4058 (tmm)
REVERT: B 1903 TYR cc_start: 0.6116 (t80) cc_final: 0.5495 (t80)
REVERT: B 2123 LYS cc_start: 0.8770 (mmmt) cc_final: 0.8383 (mmmt)
REVERT: B 2180 TRP cc_start: 0.6603 (m100) cc_final: 0.6102 (m100)
  outliers start: 1
  outliers final: 0
  residues processed: 152
  average time/residue: 0.1921
  time to fit residues: 42.4499
Evaluate side-chains
  126 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 101 optimal weight:    9.9990
   chunk 81 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 69 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9990
   chunk 58 optimal weight:    9.9990
   chunk 77 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   chunk 74 optimal weight:    5.9990
   chunk 34 optimal weight:   10.0000
   chunk 85 optimal weight:    0.5980
   overall best weight:    2.9188

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

Flipped N/Q/H residues before XYZ refinement:
** A   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 516 GLN
A 541 ASN
B1547 ASN
** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1829 HIS
** B1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B2078 GLN
** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.159954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.149209 restraints weight = 28951.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.151005 restraints weight = 20016.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.152241 restraints weight = 14717.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.4253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6272
moved from start:          0.4153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   9746  Z= 0.282
  Angle     :  0.836  10.514  13184  Z= 0.420
  Chirality :  0.051   0.317   1403
  Planarity :  0.007   0.098   1689
  Dihedral  :  7.249  32.162   1282
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 25.57
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 18.73 %
    Favored  : 81.18 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.38 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 1.75 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.81 (0.22), residues: 1153
  helix: -4.81 (0.54), residues: 25
  sheet: -3.50 (0.37), residues: 174
  loop : -3.43 (0.18), residues: 954

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP B2094 
 HIS   0.012   0.001   HIS B1801 
 PHE   0.027   0.002   PHE B1816 
 TYR   0.027   0.002   TYR B2129 
 ARG   0.011   0.001   ARG A  90 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 1.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 TYR cc_start: 0.6679 (m-10) cc_final: 0.5846 (m-80)
REVERT: A   93 LYS cc_start: 0.7825 (mmtt) cc_final: 0.7585 (mmtt)
REVERT: A  232 MET cc_start: 0.6430 (ppp) cc_final: 0.5908 (ptm)
REVERT: A  233 SER cc_start: 0.8692 (p) cc_final: 0.8129 (m)
REVERT: A  270 MET cc_start: 0.7204 (mpp) cc_final: 0.6993 (mpp)
REVERT: B 1734 MET cc_start: 0.6331 (mmt) cc_final: 0.5613 (mmm)
REVERT: B 1846 MET cc_start: 0.6431 (ttp) cc_final: 0.6063 (ttp)
REVERT: B 1903 TYR cc_start: 0.6080 (t80) cc_final: 0.5420 (t80)
REVERT: B 2123 LYS cc_start: 0.8855 (mmmt) cc_final: 0.8558 (mmmt)
REVERT: B 2180 TRP cc_start: 0.6626 (m100) cc_final: 0.6391 (m100)
  outliers start: 1
  outliers final: 1
  residues processed: 138
  average time/residue: 0.2359
  time to fit residues: 47.4275
Evaluate side-chains
  121 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 120
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 39 optimal weight:   20.0000
   chunk 53 optimal weight:    7.9990
   chunk 101 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 109 optimal weight:   10.0000
   chunk 90 optimal weight:    3.9990
   chunk 2 optimal weight:    8.9990
   chunk 68 optimal weight:    0.0060
   chunk 33 optimal weight:    0.1980
   chunk 43 optimal weight:    0.5980
   overall best weight:    1.7600

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

Flipped N/Q/H residues before XYZ refinement:
** A   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 251 ASN
** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1829 HIS
** B1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B2085 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.163587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.152936 restraints weight = 28386.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.154737 restraints weight = 19553.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.155827 restraints weight = 14365.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.4299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6167
moved from start:          0.4228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9746  Z= 0.227
  Angle     :  0.779   9.569  13184  Z= 0.392
  Chirality :  0.049   0.292   1403
  Planarity :  0.006   0.089   1689
  Dihedral  :  6.961  31.643   1282
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 21.73
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 15.70 %
    Favored  : 84.22 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.67 %
    Favored  : 99.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 1.75 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.70 (0.22), residues: 1153
  helix: -4.76 (0.56), residues: 25
  sheet: -3.49 (0.37), residues: 163
  loop : -3.34 (0.18), residues: 965

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B2094 
 HIS   0.022   0.002   HIS A 252 
 PHE   0.026   0.002   PHE B2163 
 TYR   0.026   0.002   TYR B2129 
 ARG   0.011   0.001   ARG A 321 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3320.79 seconds
wall clock time: 61 minutes 19.10 seconds (3679.10 seconds total)