Starting phenix.real_space_refine
on Sun Jul 27 16:37:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kxy_23067/07_2025/7kxy_23067.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kxy_23067/07_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_23067/07_2025/7kxy_23067.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kxy_23067/07_2025/7kxy_23067.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kxy_23067/07_2025/7kxy_23067.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kxy_23067/07_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.58, per 1000 atoms: 0.59
  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: 2.24
  Conformation dependent library (CDL) restraints added in 1.1 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: 0.70
  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: 2.19

  Time building geometry restraints manager: 2.67 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:             0.980
  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:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     22.530
  Find NCS groups from input model:        0.140
  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:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.890
-------------------------------------------------------------------------------
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   9752  Z= 0.188
  Angle     :  0.823   8.939  13196  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.31460 (   42)
  hydrogen bonds       : angle      13.93961 (   90)
  SS BOND              : bond        0.00379 (    6)
  SS BOND              : angle       1.66288 (   12)
  covalent geometry    : bond        0.00356 ( 9746)
  covalent geometry    : angle       0.82162 (13184)

*********************** 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  : 1.061 
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: 0.2093
  time to fit residues: 71.5862
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  : 0.955 
-------------------------------------------------------------------------------
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   9752  Z= 0.211
  Angle     :  0.865   9.403  13196  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04387 (   42)
  hydrogen bonds       : angle       9.86947 (   90)
  SS BOND              : bond        0.00574 (    6)
  SS BOND              : angle       1.08033 (   12)
  covalent geometry    : bond        0.00483 ( 9746)
  covalent geometry    : angle       0.86510 (13184)

*********************** 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  : 1.000 
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: 0.2370
  time to fit residues: 52.3871
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  : 0.969 
-------------------------------------------------------------------------------
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   9752  Z= 0.127
  Angle     :  0.733   8.327  13196  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03517 (   42)
  hydrogen bonds       : angle       8.47091 (   90)
  SS BOND              : bond        0.00624 (    6)
  SS BOND              : angle       0.74066 (   12)
  covalent geometry    : bond        0.00284 ( 9746)
  covalent geometry    : angle       0.73290 (13184)

*********************** 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  : 0.991 
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: 0.2627
  time to fit residues: 58.5567
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  : 1.109 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 88 optimal weight:    5.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
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 468 ASN ** 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**
B1940 GLN
B1973 GLN
B2078 GLN
** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B2132 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.155910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.145282 restraints weight = 28559.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.147104 restraints weight = 19309.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.148229 restraints weight = 14007.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.4211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6366
moved from start:          0.3161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9752  Z= 0.207
  Angle     :  0.840   9.473  13196  Z= 0.430
  Chirality :  0.052   0.220   1403
  Planarity :  0.006   0.061   1689
  Dihedral  :  7.664  32.633   1282
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 27.97
  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: -4.67 (0.57), residues: 32
  sheet: -3.89 (0.33), residues: 205
  loop : -3.77 (0.17), residues: 916

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B2094 
 HIS   0.013   0.002   HIS B1801 
 PHE   0.037   0.002   PHE A 325 
 TYR   0.019   0.002   TYR B1703 
 ARG   0.009   0.001   ARG B1910 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04138 (   42)
  hydrogen bonds       : angle       8.58739 (   90)
  SS BOND              : bond        0.00457 (    6)
  SS BOND              : angle       0.99042 (   12)
  covalent geometry    : bond        0.00464 ( 9746)
  covalent geometry    : angle       0.83955 (13184)

*********************** 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  : 1.184 
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: 0.6692 (m-10) cc_final: 0.5738 (m-80)
REVERT: A  232 MET cc_start: 0.6367 (ptm) cc_final: 0.5535 (ptm)
REVERT: A  312 THR cc_start: 0.4605 (t) cc_final: 0.4322 (t)
REVERT: B 1734 MET cc_start: 0.6233 (mmt) cc_final: 0.5460 (mmm)
REVERT: B 1809 GLN cc_start: 0.7484 (pm20) cc_final: 0.7033 (pm20)
REVERT: B 1903 TYR cc_start: 0.6081 (t80) cc_final: 0.5659 (t80)
REVERT: B 2011 ARG cc_start: 0.2128 (mmt90) cc_final: 0.1926 (mmt180)
REVERT: B 2180 TRP cc_start: 0.7210 (m100) cc_final: 0.6604 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.3689
  time to fit residues: 78.2363
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  : 1.265 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 106 optimal weight:    8.9990
   chunk 111 optimal weight:    7.9990
   chunk 77 optimal weight:    1.9990
   chunk 116 optimal weight:    6.9990
   chunk 95 optimal weight:   10.0000
   chunk 2 optimal weight:    9.9990
   chunk 22 optimal weight:    0.3980
   chunk 44 optimal weight:    0.9990
   chunk 102 optimal weight:    5.9990
   overall best weight:    1.4586

-------------------------------------------------------------------------------
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 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**
** B1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B2181 ASN ** 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 = 0.4391 r_free = 0.4391 target = 0.162644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.152726 restraints weight = 28160.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.154523 restraints weight = 18791.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.155757 restraints weight = 13543.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.4293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6150
moved from start:          0.3265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9752  Z= 0.131
  Angle     :  0.738   8.890  13196  Z= 0.373
  Chirality :  0.048   0.215   1403
  Planarity :  0.006   0.059   1689
  Dihedral  :  6.980  31.973   1282
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 20.83
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 15.35 %
    Favored  : 84.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  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: -5.00 (0.21), residues: 1153
  helix: -4.74 (0.48), residues: 32
  sheet: -3.68 (0.36), residues: 184
  loop : -3.53 (0.18), residues: 937

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B2094 
 HIS   0.018   0.001   HIS A 252 
 PHE   0.016   0.002   PHE B1872 
 TYR   0.016   0.002   TYR A 144 
 ARG   0.006   0.000   ARG B2027 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03063 (   42)
  hydrogen bonds       : angle       7.82106 (   90)
  SS BOND              : bond        0.00388 (    6)
  SS BOND              : angle       0.99450 (   12)
  covalent geometry    : bond        0.00295 ( 9746)
  covalent geometry    : angle       0.73778 (13184)

*********************** 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
  160 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.985 
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: 0.6757 (m-10) cc_final: 0.5903 (m-80)
REVERT: A  203 MET cc_start: 0.3794 (mmp) cc_final: 0.2611 (mmt)
REVERT: A  229 LEU cc_start: 0.5997 (mt) cc_final: 0.5736 (mt)
REVERT: A  483 ILE cc_start: 0.6749 (mt) cc_final: 0.6538 (mt)
REVERT: B 1734 MET cc_start: 0.5994 (mmt) cc_final: 0.5106 (mmm)
REVERT: B 1809 GLN cc_start: 0.7385 (pm20) cc_final: 0.6874 (pm20)
REVERT: B 1874 ILE cc_start: 0.6763 (mp) cc_final: 0.6457 (mp)
REVERT: B 1903 TYR cc_start: 0.6100 (t80) cc_final: 0.5503 (t80)
REVERT: B 1948 ILE cc_start: 0.4869 (pt) cc_final: 0.4649 (pt)
REVERT: B 2095 LEU cc_start: 0.6584 (tt) cc_final: 0.6199 (mm)
REVERT: B 2180 TRP cc_start: 0.6392 (m100) cc_final: 0.5913 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.2287
  time to fit residues: 51.7107
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  : 1.093 
-------------------------------------------------------------------------------
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:   30.0000
   chunk 19 optimal weight:    5.9990
   chunk 83 optimal weight:    0.0770
   chunk 45 optimal weight:    9.9990
   chunk 30 optimal weight:    6.9990
   chunk 107 optimal weight:    0.3980
   chunk 44 optimal weight:    2.9990
   chunk 113 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9990
   overall best weight:    1.8944

-------------------------------------------------------------------------------
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 468 ASN
A 556 ASN
** B1643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1683 HIS ** 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 = 0.4394 r_free = 0.4394 target = 0.162584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.152742 restraints weight = 28500.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.154460 restraints weight = 19239.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.155663 restraints weight = 13936.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.4295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6178
moved from start:          0.3486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9752  Z= 0.139
  Angle     :  0.738   9.390  13196  Z= 0.373
  Chirality :  0.048   0.243   1403
  Planarity :  0.006   0.071   1689
  Dihedral  :  6.885  34.013   1282
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 20.88
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 15.96 %
    Favored  : 83.95 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.11 %
    Favored  : 95.79 %
  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: -4.96 (0.22), residues: 1153
  helix: -4.79 (0.56), residues: 25
  sheet: -3.71 (0.34), residues: 200
  loop : -3.48 (0.18), residues: 928

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B2094 
 HIS   0.004   0.001   HIS A 287 
 PHE   0.016   0.002   PHE B1872 
 TYR   0.017   0.002   TYR A 418 
 ARG   0.005   0.001   ARG B1910 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03087 (   42)
  hydrogen bonds       : angle       7.78806 (   90)
  SS BOND              : bond        0.00407 (    6)
  SS BOND              : angle       0.78511 (   12)
  covalent geometry    : bond        0.00319 ( 9746)
  covalent geometry    : angle       0.73830 (13184)

*********************** 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
  162 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 161
  time to evaluate  : 1.077 
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: 0.6747 (m-10) cc_final: 0.5911 (m-80)
REVERT: A  203 MET cc_start: 0.3748 (mmp) cc_final: 0.2729 (mmt)
REVERT: A  229 LEU cc_start: 0.5945 (mt) cc_final: 0.5740 (mt)
REVERT: A  483 ILE cc_start: 0.6992 (mt) cc_final: 0.6657 (mt)
REVERT: B 1698 ARG cc_start: 0.6887 (ptp90) cc_final: 0.6494 (ptp90)
REVERT: B 1700 TRP cc_start: 0.7444 (m100) cc_final: 0.7239 (m100)
REVERT: B 1734 MET cc_start: 0.6006 (mmt) cc_final: 0.5204 (mmm)
REVERT: B 1809 GLN cc_start: 0.7417 (pm20) cc_final: 0.6755 (pm20)
REVERT: B 1875 MET cc_start: 0.2627 (pmm) cc_final: 0.1210 (ptp)
REVERT: B 1903 TYR cc_start: 0.6039 (t80) cc_final: 0.5471 (t80)
REVERT: B 1948 ILE cc_start: 0.4843 (pt) cc_final: 0.4520 (pt)
  outliers start: 1
  outliers final: 0
  residues processed: 162
  average time/residue: 0.2306
  time to fit residues: 53.8601
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  : 1.468 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 73 optimal weight:    0.8980
   chunk 99 optimal weight:    0.0980
   chunk 51 optimal weight:    3.9990
   chunk 59 optimal weight:   10.0000
   chunk 116 optimal weight:    9.9990
   chunk 45 optimal weight:    8.9990
   chunk 82 optimal weight:   10.0000
   chunk 13 optimal weight:    9.9990
   chunk 16 optimal weight:    2.9990
   chunk 2 optimal weight:   10.0000
   overall best weight:    2.9986

-------------------------------------------------------------------------------
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 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1683 HIS ** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.159717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.149600 restraints weight = 28878.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.151265 restraints weight = 19451.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.152583 restraints weight = 14206.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.4251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6266
moved from start:          0.3652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9752  Z= 0.178
  Angle     :  0.800   9.658  13196  Z= 0.407
  Chirality :  0.051   0.255   1403
  Planarity :  0.006   0.072   1689
  Dihedral  :  7.229  32.592   1282
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 23.97
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 18.65 %
    Favored  : 81.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  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: -5.11 (0.21), residues: 1153
  helix: -4.76 (0.48), residues: 32
  sheet: -3.95 (0.34), residues: 177
  loop : -3.57 (0.18), residues: 944

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   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   0.006   0.001   ARG A  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03544 (   42)
  hydrogen bonds       : angle       8.00927 (   90)
  SS BOND              : bond        0.00421 (    6)
  SS BOND              : angle       0.95583 (   12)
  covalent geometry    : bond        0.00411 ( 9746)
  covalent geometry    : angle       0.79996 (13184)

*********************** 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
  150 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 MET cc_start: 0.3737 (mmp) cc_final: 0.2585 (mmt)
REVERT: A  405 ILE cc_start: 0.7701 (mp) cc_final: 0.7435 (mm)
REVERT: A  483 ILE cc_start: 0.7293 (mt) cc_final: 0.7015 (mt)
REVERT: A  516 GLN cc_start: 0.6698 (tp40) cc_final: 0.6403 (tm-30)
REVERT: B 1734 MET cc_start: 0.6307 (mmt) cc_final: 0.5541 (mmm)
REVERT: B 1809 GLN cc_start: 0.7406 (pm20) cc_final: 0.6838 (pm20)
REVERT: B 1875 MET cc_start: 0.2495 (pmm) cc_final: 0.1508 (ptp)
REVERT: B 1903 TYR cc_start: 0.6097 (t80) cc_final: 0.5512 (t80)
REVERT: B 2180 TRP cc_start: 0.6635 (m100) cc_final: 0.6345 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.2183
  time to fit residues: 46.1970
Evaluate side-chains
  121 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
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:    0.0980
   chunk 75 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9990
   chunk 102 optimal weight:    4.9990
   chunk 50 optimal weight:    0.0070
   chunk 42 optimal weight:    0.9980
   chunk 65 optimal weight:    4.9990
   chunk 72 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.5400

-------------------------------------------------------------------------------
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 251 ASN
** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1829 HIS
** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B2153 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.168799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.158543 restraints weight = 28540.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.160345 restraints weight = 19165.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.161519 restraints weight = 13853.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.4365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6001
moved from start:          0.3953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9752  Z= 0.121
  Angle     :  0.740  10.370  13196  Z= 0.368
  Chirality :  0.049   0.292   1403
  Planarity :  0.006   0.058   1689
  Dihedral  :  6.566  30.699   1282
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 18.11
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 13.44 %
    Favored  : 86.47 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.72 %
    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: -4.76 (0.22), residues: 1153
  helix: -4.72 (0.55), residues: 24
  sheet: -3.56 (0.37), residues: 180
  loop : -3.36 (0.18), residues: 949

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B2094 
 HIS   0.021   0.002   HIS A 252 
 PHE   0.029   0.002   PHE B1816 
 TYR   0.024   0.001   TYR B2129 
 ARG   0.006   0.000   ARG A  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02569 (   42)
  hydrogen bonds       : angle       7.20158 (   90)
  SS BOND              : bond        0.00324 (    6)
  SS BOND              : angle       1.32192 (   12)
  covalent geometry    : bond        0.00279 ( 9746)
  covalent geometry    : angle       0.73922 (13184)

*********************** 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
  168 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 167
  time to evaluate  : 1.094 
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: 0.6478 (m-10) cc_final: 0.5697 (m-80)
REVERT: A  203 MET cc_start: 0.3728 (mmp) cc_final: 0.3155 (mmt)
REVERT: A  405 ILE cc_start: 0.7658 (mp) cc_final: 0.7439 (mm)
REVERT: A  483 ILE cc_start: 0.6657 (mt) cc_final: 0.6437 (mt)
REVERT: A  634 MET cc_start: 0.5354 (tmm) cc_final: 0.4901 (tmm)
REVERT: B 1734 MET cc_start: 0.5854 (mmt) cc_final: 0.5125 (mmt)
REVERT: B 2180 TRP cc_start: 0.6612 (m100) cc_final: 0.6264 (m100)
  outliers start: 1
  outliers final: 0
  residues processed: 168
  average time/residue: 0.2179
  time to fit residues: 52.2382
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  : 1.113 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 92 optimal weight:    9.9990
   chunk 27 optimal weight:    8.9990
   chunk 13 optimal weight:    3.9990
   chunk 71 optimal weight:   10.0000
   chunk 98 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 58 optimal weight:    9.9990
   chunk 91 optimal weight:   20.0000
   overall best weight:    2.3990

-------------------------------------------------------------------------------
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
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1547 ASN
B1553 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.162457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.152170 restraints weight = 28559.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.153948 restraints weight = 19299.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.155252 restraints weight = 13932.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.4298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6180
moved from start:          0.3991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9752  Z= 0.161
  Angle     :  0.789   9.757  13196  Z= 0.396
  Chirality :  0.050   0.267   1403
  Planarity :  0.006   0.087   1689
  Dihedral  :  6.909  29.504   1282
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 22.27
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 16.91 %
    Favored  : 83.00 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.15 %
    Favored  : 98.76 %
  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: -4.86 (0.22), residues: 1153
  helix: -4.49 (0.61), residues: 26
  sheet: -3.73 (0.35), residues: 192
  loop : -3.39 (0.18), residues: 935

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B2094 
 HIS   0.007   0.001   HIS B1801 
 PHE   0.021   0.002   PHE A 179 
 TYR   0.025   0.002   TYR B2129 
 ARG   0.008   0.001   ARG B1698 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02973 (   42)
  hydrogen bonds       : angle       7.57230 (   90)
  SS BOND              : bond        0.00541 (    6)
  SS BOND              : angle       1.22333 (   12)
  covalent geometry    : bond        0.00370 ( 9746)
  covalent geometry    : angle       0.78822 (13184)

*********************** 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  : 0.992 
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: 0.6617 (m-10) cc_final: 0.5850 (m-80)
REVERT: A  374 GLU cc_start: 0.5111 (mp0) cc_final: 0.4900 (mp0)
REVERT: B 1547 ASN cc_start: 0.7923 (OUTLIER) cc_final: 0.7654 (t0)
REVERT: B 1700 TRP cc_start: 0.7467 (m100) cc_final: 0.7186 (m100)
REVERT: B 1809 GLN cc_start: 0.7359 (pm20) cc_final: 0.6651 (pm20)
REVERT: B 1829 HIS cc_start: 0.5389 (t-90) cc_final: 0.4993 (t-90)
REVERT: B 2123 LYS cc_start: 0.8369 (mmpt) cc_final: 0.8080 (mmmt)
REVERT: B 2180 TRP cc_start: 0.6528 (m100) cc_final: 0.5920 (m100)
  outliers start: 1
  outliers final: 0
  residues processed: 152
  average time/residue: 0.2156
  time to fit residues: 46.1883
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  : 1.113 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 53 optimal weight:    9.9990
   chunk 69 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 58 optimal weight:    9.9990
   chunk 77 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 34 optimal weight:   10.0000
   chunk 85 optimal weight:    0.7980
   overall best weight:    2.5588

-------------------------------------------------------------------------------
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
A 251 ASN
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1683 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 = 0.4381 r_free = 0.4381 target = 0.161223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.150992 restraints weight = 28770.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.152724 restraints weight = 19608.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.154017 restraints weight = 14308.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.4279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6206
moved from start:          0.4071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9752  Z= 0.165
  Angle     :  0.814  10.608  13196  Z= 0.407
  Chirality :  0.050   0.272   1403
  Planarity :  0.006   0.085   1689
  Dihedral  :  7.114  31.444   1282
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 23.12
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 17.61 %
    Favored  : 82.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  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: -4.76 (0.22), residues: 1153
  helix: -4.48 (0.63), residues: 26
  sheet: -3.41 (0.38), residues: 169
  loop : -3.41 (0.18), residues: 958

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B2094 
 HIS   0.009   0.001   HIS B1801 
 PHE   0.018   0.002   PHE A 616 
 TYR   0.027   0.002   TYR B2129 
 ARG   0.007   0.001   ARG B1698 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02930 (   42)
  hydrogen bonds       : angle       7.63003 (   90)
  SS BOND              : bond        0.00608 (    6)
  SS BOND              : angle       1.27577 (   12)
  covalent geometry    : bond        0.00379 ( 9746)
  covalent geometry    : angle       0.81320 (13184)

********************** 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
  150 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 1.087 
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: 0.6624 (m-10) cc_final: 0.5890 (m-80)
REVERT: A   90 ARG cc_start: 0.6312 (ptt90) cc_final: 0.5972 (ptt180)
REVERT: A  374 GLU cc_start: 0.5909 (mp0) cc_final: 0.5672 (mp0)
REVERT: A  483 ILE cc_start: 0.6760 (mt) cc_final: 0.6547 (mt)
REVERT: B 1700 TRP cc_start: 0.7420 (m100) cc_final: 0.7172 (m100)
REVERT: B 1734 MET cc_start: 0.6476 (mmt) cc_final: 0.5713 (mmm)
REVERT: B 1903 TYR cc_start: 0.6063 (t80) cc_final: 0.5424 (t80)
REVERT: B 2123 LYS cc_start: 0.8353 (mmpt) cc_final: 0.8141 (mmmt)
REVERT: B 2180 TRP cc_start: 0.6475 (m100) cc_final: 0.5924 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.2254
  time to fit residues: 47.2548
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  : 0.953 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 39 optimal weight:   20.0000
   chunk 53 optimal weight:    8.9990
   chunk 101 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 109 optimal weight:   10.0000
   chunk 90 optimal weight:    5.9990
   chunk 2 optimal weight:    9.9990
   chunk 68 optimal weight:    0.0470
   chunk 33 optimal weight:    8.9990
   chunk 43 optimal weight:    7.9990
   overall best weight:    4.4086

-------------------------------------------------------------------------------
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 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B2085 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.155379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.145541 restraints weight = 29337.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.147215 restraints weight = 20140.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.148424 restraints weight = 14635.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.4206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6363
moved from start:          0.4091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   9752  Z= 0.234
  Angle     :  0.919  12.584  13196  Z= 0.463
  Chirality :  0.054   0.276   1403
  Planarity :  0.007   0.087   1689
  Dihedral  :  7.834  31.120   1282
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 29.72
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 21.77 %
    Favored  : 78.14 %
  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 : 0.09 %

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: -5.08 (0.21), residues: 1153
  helix: -4.48 (0.65), residues: 26
  sheet: -3.77 (0.36), residues: 163
  loop : -3.63 (0.17), residues: 964

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.003   TRP B2094 
 HIS   0.022   0.002   HIS A 252 
 PHE   0.024   0.003   PHE B1816 
 TYR   0.032   0.003   TYR B2129 
 ARG   0.009   0.001   ARG B1698 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03756 (   42)
  hydrogen bonds       : angle       8.30387 (   90)
  SS BOND              : bond        0.00648 (    6)
  SS BOND              : angle       1.35483 (   12)
  covalent geometry    : bond        0.00536 ( 9746)
  covalent geometry    : angle       0.91899 (13184)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3121.91 seconds
wall clock time: 57 minutes 2.69 seconds (3422.69 seconds total)