Starting phenix.real_space_refine
on Thu Feb 13 23:51:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kxy_23067/02_2025/7kxy_23067.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kxy_23067/02_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_23067/02_2025/7kxy_23067.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kxy_23067/02_2025/7kxy_23067.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kxy_23067/02_2025/7kxy_23067.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kxy_23067/02_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-5592/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: 5.80, 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: 2.29
  Conformation dependent library (CDL) restraints added in 1.0 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: 0.83
  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: 2.43

  Time building geometry restraints manager: 2.71 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:             1.900
  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:             0.000
  Extract box with map and model:          0.710
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     22.700
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.140
-------------------------------------------------------------------------------
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  : 1.043 
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: 0.2158
  time to fit residues: 73.7461
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  : 1.092 
-------------------------------------------------------------------------------
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 = 0.157760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.147181 restraints weight = 28331.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.148867 restraints weight = 19583.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.149911 restraints weight = 14492.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.4224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6321
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  : 1.063 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 TYR cc_start: 0.6679 (m-10) cc_final: 0.5688 (m-80)
REVERT: A   90 ARG cc_start: 0.5900 (ptt90) cc_final: 0.5185 (mtm180)
REVERT: A  229 LEU cc_start: 0.6684 (mt) cc_final: 0.6446 (mt)
REVERT: A  232 MET cc_start: 0.6062 (ptm) cc_final: 0.5618 (ptm)
REVERT: A  483 ILE cc_start: 0.7243 (mt) cc_final: 0.6885 (mt)
REVERT: A  551 LYS cc_start: 0.6040 (mttt) cc_final: 0.5630 (mptt)
REVERT: A  609 HIS cc_start: 0.6419 (m170) cc_final: 0.5777 (m170)
REVERT: B 1703 TYR cc_start: 0.4685 (p90) cc_final: 0.4462 (p90)
REVERT: B 1746 MET cc_start: 0.8197 (tpp) cc_final: 0.7939 (tpp)
REVERT: B 1883 MET cc_start: 0.4297 (tmm) cc_final: 0.3892 (tmm)
REVERT: B 1903 TYR cc_start: 0.6169 (t80) cc_final: 0.5867 (t80)
REVERT: B 2120 MET cc_start: 0.3171 (mmp) cc_final: 0.2910 (mmt)
  outliers start: 2
  outliers final: 1
  residues processed: 161
  average time/residue: 0.2478
  time to fit residues: 54.4912
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  : 1.114 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 63 optimal weight:    7.9990
   chunk 56 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 101 optimal weight:    9.9990
   chunk 59 optimal weight:    0.7980
   chunk 78 optimal weight:    0.0980
   chunk 51 optimal weight:    2.9990
   chunk 49 optimal weight:   10.0000
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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**
** B1955 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 = 0.4418 r_free = 0.4418 target = 0.164000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.153453 restraints weight = 28416.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.155231 restraints weight = 19253.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.156521 restraints weight = 13966.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.4312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6134
moved from start:          0.2777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9746  Z= 0.198
  Angle     :  0.740   8.186  13184  Z= 0.376
  Chirality :  0.049   0.211   1403
  Planarity :  0.005   0.057   1689
  Dihedral  :  7.018  30.133   1282
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 20.88
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 18.47 %
    Favored  : 81.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  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: -5.23 (0.21), residues: 1153
  helix: -4.96 (0.42), residues: 32
  sheet: -3.83 (0.34), residues: 187
  loop : -3.69 (0.17), residues: 934

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B2094 
 HIS   0.006   0.001   HIS B1801 
 PHE   0.018   0.002   PHE B1872 
 TYR   0.019   0.002   TYR A 144 
 ARG   0.002   0.000   ARG A 396 

*********************** 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
  160 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 1.037 
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: 0.6593 (m-10) cc_final: 0.5680 (m-80)
REVERT: A  229 LEU cc_start: 0.6422 (mt) cc_final: 0.6157 (mt)
REVERT: A  312 THR cc_start: 0.4269 (t) cc_final: 0.4023 (t)
REVERT: A  405 ILE cc_start: 0.7852 (mp) cc_final: 0.7621 (mm)
REVERT: A  551 LYS cc_start: 0.6082 (mttt) cc_final: 0.5668 (mptt)
REVERT: B 1809 GLN cc_start: 0.7477 (pm20) cc_final: 0.7045 (pm20)
REVERT: B 1850 LYS cc_start: 0.6406 (mmtt) cc_final: 0.6163 (mmtp)
REVERT: B 1874 ILE cc_start: 0.6815 (mp) cc_final: 0.6400 (mp)
REVERT: B 1903 TYR cc_start: 0.6039 (t80) cc_final: 0.5676 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.2647
  time to fit residues: 59.6523
Evaluate side-chains
  120 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 1.167 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 77 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 100 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9980
   chunk 66 optimal weight:    8.9990
   chunk 91 optimal weight:   10.0000
   chunk 90 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9980
   overall best weight:    1.9782

-------------------------------------------------------------------------------
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 468 ASN
** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1973 GLN
B2078 GLN
** 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 = 0.4394 r_free = 0.4394 target = 0.162078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.151665 restraints weight = 28113.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.153321 restraints weight = 18969.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.154677 restraints weight = 13941.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.4287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6198
moved from start:          0.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9746  Z= 0.219
  Angle     :  0.747   9.617  13184  Z= 0.379
  Chirality :  0.049   0.201   1403
  Planarity :  0.006   0.056   1689
  Dihedral  :  7.059  30.941   1282
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 21.36
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 17.52 %
    Favored  : 82.39 %
  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 : 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: -5.17 (0.21), residues: 1153
  helix: -4.69 (0.53), residues: 32
  sheet: -3.94 (0.33), residues: 207
  loop : -3.58 (0.18), residues: 914

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B2094 
 HIS   0.012   0.001   HIS B1801 
 PHE   0.036   0.002   PHE A 325 
 TYR   0.017   0.002   TYR B1966 
 ARG   0.004   0.000   ARG A 445 

*********************** 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
  154 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 1.142 
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: 0.6595 (m-10) cc_final: 0.5626 (m-80)
REVERT: A  229 LEU cc_start: 0.6321 (mt) cc_final: 0.6086 (mt)
REVERT: A  312 THR cc_start: 0.4514 (t) cc_final: 0.4254 (t)
REVERT: A  321 ARG cc_start: 0.6193 (ttt180) cc_final: 0.5963 (ttt180)
REVERT: B 1809 GLN cc_start: 0.7486 (pm20) cc_final: 0.7012 (pm20)
REVERT: B 1850 LYS cc_start: 0.6541 (mmtt) cc_final: 0.6289 (mmtp)
REVERT: B 1883 MET cc_start: 0.4757 (tmm) cc_final: 0.4414 (tmm)
REVERT: B 1903 TYR cc_start: 0.5917 (t80) cc_final: 0.5440 (t80)
REVERT: B 2018 THR cc_start: 0.8121 (t) cc_final: 0.7903 (t)
REVERT: B 2180 TRP cc_start: 0.7007 (m100) cc_final: 0.6472 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.2373
  time to fit residues: 51.0756
Evaluate side-chains
  128 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 106 optimal weight:    0.9990
   chunk 111 optimal weight:    6.9990
   chunk 77 optimal weight:    8.9990
   chunk 116 optimal weight:    6.9990
   chunk 95 optimal weight:    9.9990
   chunk 2 optimal weight:    0.0060
   chunk 22 optimal weight:    7.9990
   chunk 44 optimal weight:    6.9990
   chunk 102 optimal weight:    6.9990
   overall best weight:    4.4004

-------------------------------------------------------------------------------
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 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1553 ASN
B2078 GLN
** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B2132 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.153914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.144115 restraints weight = 28834.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.145703 restraints weight = 20017.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.146860 restraints weight = 14829.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.4181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6400
moved from start:          0.3341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   9746  Z= 0.351
  Angle     :  0.867   9.982  13184  Z= 0.444
  Chirality :  0.052   0.227   1403
  Planarity :  0.007   0.084   1689
  Dihedral  :  7.831  31.269   1282
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 28.98
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 21.94 %
    Favored  : 77.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  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: -5.33 (0.20), residues: 1153
  helix: -4.69 (0.55), residues: 32
  sheet: -3.62 (0.36), residues: 175
  loop : -3.86 (0.17), residues: 946

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.003   TRP B2094 
 HIS   0.023   0.002   HIS A 252 
 PHE   0.024   0.003   PHE A 325 
 TYR   0.019   0.002   TYR A  44 
 ARG   0.007   0.001   ARG A 475 

*********************** 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
  142 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 1.018 
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: 0.6789 (m-10) cc_final: 0.5995 (m-80)
REVERT: A  312 THR cc_start: 0.4183 (t) cc_final: 0.3907 (t)
REVERT: A  410 MET cc_start: 0.7357 (mmp) cc_final: 0.7128 (tpt)
REVERT: B 1734 MET cc_start: 0.6352 (mmt) cc_final: 0.5591 (mmm)
REVERT: B 1809 GLN cc_start: 0.7374 (pm20) cc_final: 0.6999 (pm20)
REVERT: B 1883 MET cc_start: 0.5147 (tmm) cc_final: 0.4844 (tmm)
REVERT: B 1903 TYR cc_start: 0.6054 (t80) cc_final: 0.5550 (t80)
REVERT: B 1948 ILE cc_start: 0.4758 (pt) cc_final: 0.4546 (pt)
REVERT: B 2180 TRP cc_start: 0.6841 (m100) cc_final: 0.6361 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.2277
  time to fit residues: 45.5688
Evaluate side-chains
  118 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 83 optimal weight:    0.7980
   chunk 45 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 107 optimal weight:    0.8980
   chunk 44 optimal weight:    8.9990
   chunk 113 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 516 GLN
** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1991 ASN
** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B2181 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.163865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.152737 restraints weight = 27618.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.154762 restraints weight = 18315.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.156166 restraints weight = 13021.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.4303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6153
moved from start:          0.3450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9746  Z= 0.200
  Angle     :  0.739   8.878  13184  Z= 0.373
  Chirality :  0.049   0.251   1403
  Planarity :  0.006   0.065   1689
  Dihedral  :  6.961  31.240   1282
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 19.44
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 14.74 %
    Favored  : 85.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  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: -5.00 (0.22), residues: 1153
  helix: -4.77 (0.46), residues: 32
  sheet: -3.77 (0.34), residues: 200
  loop : -3.48 (0.18), residues: 921

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B2094 
 HIS   0.017   0.001   HIS A 252 
 PHE   0.031   0.002   PHE B1816 
 TYR   0.020   0.002   TYR A 418 
 ARG   0.008   0.001   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
  163 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.969 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 TYR cc_start: 0.6752 (m-10) cc_final: 0.5901 (m-80)
REVERT: A  312 THR cc_start: 0.4040 (t) cc_final: 0.3814 (t)
REVERT: A  405 ILE cc_start: 0.8036 (mp) cc_final: 0.7815 (mm)
REVERT: B 1698 ARG cc_start: 0.6770 (ptp90) cc_final: 0.6479 (ptp90)
REVERT: B 1700 TRP cc_start: 0.7478 (m100) cc_final: 0.7236 (m100)
REVERT: B 1734 MET cc_start: 0.5999 (mmt) cc_final: 0.5167 (mmm)
REVERT: B 1801 HIS cc_start: 0.7893 (m-70) cc_final: 0.7689 (m170)
REVERT: B 1809 GLN cc_start: 0.7350 (pm20) cc_final: 0.6831 (pm20)
REVERT: B 1850 LYS cc_start: 0.6483 (mmtt) cc_final: 0.6252 (mmtp)
REVERT: B 1903 TYR cc_start: 0.6066 (t80) cc_final: 0.5485 (t80)
REVERT: B 2018 THR cc_start: 0.7728 (t) cc_final: 0.7502 (t)
REVERT: B 2123 LYS cc_start: 0.8571 (mmmt) cc_final: 0.8126 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.2387
  time to fit residues: 54.0132
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  : 1.097 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 99 optimal weight:    0.0770
   chunk 51 optimal weight:    9.9990
   chunk 59 optimal weight:    2.9990
   chunk 116 optimal weight:    5.9990
   chunk 45 optimal weight:    5.9990
   chunk 82 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    1.8146

-------------------------------------------------------------------------------
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**
A 516 GLN
** B1643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4410 r_free = 0.4410 target = 0.163053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.152745 restraints weight = 28297.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.154558 restraints weight = 18925.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.155839 restraints weight = 13597.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.4304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6175
moved from start:          0.3634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   9746  Z= 0.219
  Angle     :  0.755   9.489  13184  Z= 0.381
  Chirality :  0.049   0.244   1403
  Planarity :  0.006   0.074   1689
  Dihedral  :  6.903  33.660   1282
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 21.79
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 17.78 %
    Favored  : 82.13 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.30 %
    Favored  : 97.61 %
  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: -4.93 (0.22), residues: 1153
  helix: -4.73 (0.56), residues: 25
  sheet: -3.89 (0.35), residues: 191
  loop : -3.42 (0.18), residues: 937

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B2094 
 HIS   0.004   0.001   HIS B1955 
 PHE   0.015   0.002   PHE B1872 
 TYR   0.023   0.002   TYR B2129 
 ARG   0.008   0.001   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
  156 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 155
  time to evaluate  : 1.118 
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  312 THR cc_start: 0.4247 (t) cc_final: 0.4000 (t)
REVERT: A  405 ILE cc_start: 0.8085 (mp) cc_final: 0.7831 (mm)
REVERT: B 1700 TRP cc_start: 0.7441 (m100) cc_final: 0.7235 (m100)
REVERT: B 1734 MET cc_start: 0.6180 (mmt) cc_final: 0.5293 (mmm)
REVERT: B 1801 HIS cc_start: 0.7721 (m-70) cc_final: 0.7404 (m170)
REVERT: B 1809 GLN cc_start: 0.7419 (pm20) cc_final: 0.6821 (pm20)
REVERT: B 2123 LYS cc_start: 0.8741 (mmmt) cc_final: 0.8422 (mmmt)
REVERT: B 2180 TRP cc_start: 0.6670 (m100) cc_final: 0.6469 (m100)
  outliers start: 1
  outliers final: 0
  residues processed: 156
  average time/residue: 0.2529
  time to fit residues: 56.6654
Evaluate side-chains
  128 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 1.118 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 75 optimal weight:    5.9990
   chunk 2 optimal weight:    0.8980
   chunk 80 optimal weight:    5.9990
   chunk 102 optimal weight:    9.9990
   chunk 50 optimal weight:    0.6980
   chunk 42 optimal weight:    0.6980
   chunk 65 optimal weight:   10.0000
   chunk 72 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 7 optimal weight:    5.9990
   overall best weight:    1.4582

-------------------------------------------------------------------------------
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 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1547 ASN
** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B2078 GLN
** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.164948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.154426 restraints weight = 28483.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.156217 restraints weight = 19187.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.157503 restraints weight = 13745.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.4329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6120
moved from start:          0.3824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9746  Z= 0.207
  Angle     :  0.745   9.639  13184  Z= 0.374
  Chirality :  0.049   0.308   1403
  Planarity :  0.006   0.063   1689
  Dihedral  :  6.772  32.988   1282
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 19.50
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 15.09 %
    Favored  : 84.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  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: -4.67 (0.55), residues: 25
  sheet: -3.78 (0.35), residues: 193
  loop : -3.33 (0.18), residues: 935

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B2094 
 HIS   0.006   0.001   HIS B2159 
 PHE   0.015   0.002   PHE A 190 
 TYR   0.023   0.002   TYR B2129 
 ARG   0.008   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
  150 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 1.099 
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: 0.6665 (m-10) cc_final: 0.5881 (m-80)
REVERT: A   93 LYS cc_start: 0.7748 (mmtt) cc_final: 0.7526 (mmtt)
REVERT: A  312 THR cc_start: 0.4171 (t) cc_final: 0.3949 (t)
REVERT: A  405 ILE cc_start: 0.7927 (mp) cc_final: 0.7688 (mm)
REVERT: B 1734 MET cc_start: 0.6213 (mmt) cc_final: 0.5316 (mmm)
REVERT: B 1883 MET cc_start: 0.4237 (tmm) cc_final: 0.3749 (tmm)
REVERT: B 1972 ASN cc_start: 0.8044 (p0) cc_final: 0.7825 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.2201
  time to fit residues: 46.5233
Evaluate side-chains
  123 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 92 optimal weight:    0.8980
   chunk 27 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   chunk 71 optimal weight:    9.9990
   chunk 98 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9980
   chunk 76 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 58 optimal weight:    9.9990
   chunk 91 optimal weight:    5.9990
   overall best weight:    1.9786

-------------------------------------------------------------------------------
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**
** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1729 HIS
B1829 HIS
B2078 GLN
** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.163684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.152932 restraints weight = 28117.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.154826 restraints weight = 18766.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.156211 restraints weight = 13509.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.4315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6164
moved from start:          0.3939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9746  Z= 0.229
  Angle     :  0.777   9.976  13184  Z= 0.390
  Chirality :  0.050   0.278   1403
  Planarity :  0.006   0.066   1689
  Dihedral  :  6.905  32.173   1282
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 21.63
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 18.39 %
    Favored  : 81.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    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: -4.75 (0.22), residues: 1153
  helix: -4.66 (0.58), residues: 25
  sheet: -3.70 (0.37), residues: 178
  loop : -3.32 (0.18), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B2094 
 HIS   0.011   0.001   HIS B1801 
 PHE   0.016   0.002   PHE A 179 
 TYR   0.024   0.002   TYR B2129 
 ARG   0.009   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
  149 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 1.107 
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: 0.6635 (m-10) cc_final: 0.5888 (m-80)
REVERT: A  312 THR cc_start: 0.4263 (t) cc_final: 0.4022 (t)
REVERT: A  483 ILE cc_start: 0.6612 (mt) cc_final: 0.6372 (mt)
REVERT: B 1734 MET cc_start: 0.6191 (mmt) cc_final: 0.5582 (mmm)
REVERT: B 1883 MET cc_start: 0.4366 (tmm) cc_final: 0.3864 (tmm)
REVERT: B 2123 LYS cc_start: 0.8757 (mmmt) cc_final: 0.8207 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.2164
  time to fit residues: 46.0518
Evaluate side-chains
  124 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 81 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 69 optimal weight:    7.9990
   chunk 22 optimal weight:    0.0570
   chunk 58 optimal weight:   10.0000
   chunk 77 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0870
   chunk 34 optimal weight:    9.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    1.8282

-------------------------------------------------------------------------------
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 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1547 ASN
** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B2078 GLN
** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.164087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.152848 restraints weight = 28194.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.154981 restraints weight = 18520.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.156397 restraints weight = 13069.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.4319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6156
moved from start:          0.4053

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= 0.218
  Angle     :  0.765   9.265  13184  Z= 0.383
  Chirality :  0.050   0.257   1403
  Planarity :  0.006   0.060   1689
  Dihedral  :  6.865  31.597   1282
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 21.15
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 15.70 %
    Favored  : 84.22 %
  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 : 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: -4.69 (0.22), residues: 1153
  helix: -4.67 (0.56), residues: 25
  sheet: -3.71 (0.37), residues: 175
  loop : -3.27 (0.18), residues: 953

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B2094 
 HIS   0.010   0.001   HIS B1643 
 PHE   0.022   0.002   PHE A 598 
 TYR   0.024   0.002   TYR B2129 
 ARG   0.008   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
  147 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 146
  time to evaluate  : 1.067 
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: A   63 TYR cc_start: 0.6647 (m-10) cc_final: 0.5856 (m-80)
REVERT: A  483 ILE cc_start: 0.6626 (mt) cc_final: 0.6385 (mt)
REVERT: B 1700 TRP cc_start: 0.7409 (m100) cc_final: 0.7163 (m100)
REVERT: B 1734 MET cc_start: 0.6500 (mmt) cc_final: 0.5757 (mmm)
REVERT: B 1868 MET cc_start: 0.7322 (mpp) cc_final: 0.7059 (mpp)
REVERT: B 1883 MET cc_start: 0.4059 (tmm) cc_final: 0.3613 (tmm)
REVERT: B 2123 LYS cc_start: 0.8815 (mmmt) cc_final: 0.8252 (mmmt)
  outliers start: 1
  outliers final: 1
  residues processed: 147
  average time/residue: 0.2126
  time to fit residues: 44.3964
Evaluate side-chains
  127 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 39 optimal weight:    9.9990
   chunk 53 optimal weight:    4.9990
   chunk 101 optimal weight:    5.9990
   chunk 23 optimal weight:    4.9990
   chunk 109 optimal weight:   10.0000
   chunk 90 optimal weight:    4.9990
   chunk 2 optimal weight:   10.0000
   chunk 68 optimal weight:   10.0000
   chunk 33 optimal weight:    7.9990
   chunk 43 optimal weight:    9.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 251 ASN
** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B2078 GLN
B2085 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.152616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.142496 restraints weight = 29269.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.144275 restraints weight = 19753.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.145568 restraints weight = 14287.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.4181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6448
moved from start:          0.4085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.065   9746  Z= 0.447
  Angle     :  1.000  15.756  13184  Z= 0.505
  Chirality :  0.057   0.290   1403
  Planarity :  0.007   0.070   1689
  Dihedral  :  8.276  32.563   1282
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 33.13
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 23.16 %
    Favored  : 76.76 %
  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 : 3.51 %
    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: -5.21 (0.21), residues: 1153
  helix: -4.68 (0.55), residues: 26
  sheet: -3.70 (0.32), residues: 204
  loop : -3.71 (0.17), residues: 923

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.003   TRP B2094 
 HIS   0.014   0.002   HIS B1801 
 PHE   0.026   0.003   PHE A 179 
 TYR   0.035   0.003   TYR B2129 
 ARG   0.011   0.001   ARG A  90 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2579.98 seconds
wall clock time: 47 minutes 49.30 seconds (2869.30 seconds total)