Starting phenix.real_space_refine
on Wed Sep 17 15:51:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kxy_23067/09_2025/7kxy_23067.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kxy_23067/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kxy_23067/09_2025/7kxy_23067.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kxy_23067/09_2025/7kxy_23067.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kxy_23067/09_2025/7kxy_23067.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kxy_23067/09_2025/7kxy_23067.map"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.29, per 1000 atoms: 0.24
  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: 0.81
  Conformation dependent library (CDL) restraints added in 420.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.17
  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: 1.19

  Time building geometry restraints manager: 1.08 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:             1.090
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.950
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.510
-------------------------------------------------------------------------------
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 : 19.23
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.003   0.001   ARG A 306 
 TYR   0.021   0.001   TYR A 144 
 PHE   0.017   0.002   PHE B1872 
 TRP   0.021   0.001   TRP B2094 
 HIS   0.003   0.001   HIS B2128 

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

*********************** 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  : 0.293 
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: symmetry clash
REVERT: A  232 MET cc_start: 0.5254 (ptm) cc_final: 0.4691 (ptm)
REVERT: A  407 PHE cc_start: 0.3839 (p90) cc_final: 0.3588 (p90)
REVERT: B 1736 MET cc_start: 0.6433 (tpt) cc_final: 0.6162 (tpp)
REVERT: B 1755 TYR cc_start: 0.7567 (p90) cc_final: 0.7322 (p90)
REVERT: B 1801 HIS cc_start: 0.7575 (m-70) cc_final: 0.7238 (m-70)
REVERT: B 1903 TYR cc_start: 0.6273 (t80) cc_final: 0.5722 (t80)
REVERT: B 1905 GLU cc_start: 0.4699 (mt-10) cc_final: 0.4443 (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: 0.1855 (mmt)
  outliers start: 75
  outliers final: 21
  residues processed: 243
  average time/residue: 0.0843
  time to fit residues: 29.1170
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  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    9.9990
   chunk 113 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    9.9990
   chunk 100 optimal weight:    0.5980
   overall best weight:    2.4386

-------------------------------------------------------------------------------
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 251 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
B1713 HIS
** B1778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B2051 ASN
B2078 GLN
B2181 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.161199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.150378 restraints weight = 28344.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.152174 restraints weight = 19230.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.153470 restraints weight = 14051.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.154402 restraints weight = 10865.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.155145 restraints weight = 8851.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.4292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6194
moved from start:          0.2466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9752  Z= 0.174
  Angle     :  0.809   9.218  13196  Z= 0.414
  Chirality :  0.051   0.186   1403
  Planarity :  0.006   0.067   1689
  Dihedral  :  7.504  30.179   1282
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 23.49
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 16.83 %
    Favored  : 83.09 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  6.32 %
    Favored  : 93.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 1.75 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.53 (0.20), residues: 1153
  helix: -5.01 (0.38), residues: 27
  sheet: -4.04 (0.31), residues: 211
  loop : -3.89 (0.17), residues: 915

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 396 
 TYR   0.019   0.002   TYR B1966 
 PHE   0.032   0.002   PHE A 574 
 TRP   0.026   0.002   TRP B2094 
 HIS   0.007   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 9746)
  covalent geometry    : angle       0.80869 (13184)
  SS BOND              : bond        0.00275 (    6)
  SS BOND              : angle       0.81091 (   12)
  hydrogen bonds       : bond        0.04445 (   42)
  hydrogen bonds       : angle       9.75078 (   90)

*********************** 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
  168 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 167
  time to evaluate  : 0.356 
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: 0.6678 (m-10) cc_final: 0.5657 (m-80)
REVERT: A   90 ARG cc_start: 0.5675 (ptt90) cc_final: 0.5242 (mtm180)
REVERT: A  232 MET cc_start: 0.5892 (ptm) cc_final: 0.5689 (ptm)
REVERT: A  551 LYS cc_start: 0.6172 (mttt) cc_final: 0.5769 (mptt)
REVERT: A  609 HIS cc_start: 0.6369 (m170) cc_final: 0.5808 (m170)
REVERT: B 1703 TYR cc_start: 0.4612 (p90) cc_final: 0.4328 (p90)
REVERT: B 1734 MET cc_start: 0.6123 (mmt) cc_final: 0.5430 (mmm)
REVERT: B 1746 MET cc_start: 0.8219 (tpp) cc_final: 0.7934 (tpp)
REVERT: B 1846 MET cc_start: 0.6891 (mtm) cc_final: 0.6654 (mtt)
REVERT: B 1903 TYR cc_start: 0.6149 (t80) cc_final: 0.5813 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 167
  average time/residue: 0.1055
  time to fit residues: 23.8924
Evaluate side-chains
  126 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 60 optimal weight:    9.9990
   chunk 72 optimal weight:    3.9990
   chunk 116 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 31 optimal weight:    0.1980
   chunk 98 optimal weight:    5.9990
   chunk 94 optimal weight:   10.0000
   chunk 65 optimal weight:    4.9990
   chunk 104 optimal weight:    0.9990
   overall best weight:    2.2388

-------------------------------------------------------------------------------
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**
** B1801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B2153 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.161325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.150863 restraints weight = 28435.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.152663 restraints weight = 19356.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.153865 restraints weight = 14026.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.154836 restraints weight = 10889.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.155553 restraints weight = 8744.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.4298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6187
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   0.035   9752  Z= 0.153
  Angle     :  0.758   9.096  13196  Z= 0.387
  Chirality :  0.049   0.215   1403
  Planarity :  0.006   0.060   1689
  Dihedral  :  7.210  30.424   1282
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 22.85
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 19.69 %
    Favored  : 80.23 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  6.79 %
    Favored  : 93.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 1.75 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.29 (0.21), residues: 1153
  helix: -4.91 (0.42), residues: 32
  sheet: -4.03 (0.32), residues: 199
  loop : -3.68 (0.17), residues: 922

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B1910 
 TYR   0.018   0.002   TYR B2129 
 PHE   0.037   0.002   PHE A 325 
 TRP   0.025   0.002   TRP B2094 
 HIS   0.007   0.001   HIS B1801 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 9746)
  covalent geometry    : angle       0.75817 (13184)
  SS BOND              : bond        0.00397 (    6)
  SS BOND              : angle       0.82657 (   12)
  hydrogen bonds       : bond        0.04075 (   42)
  hydrogen bonds       : angle       8.83507 (   90)

*********************** 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
  159 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 158
  time to evaluate  : 0.381 
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: 0.6644 (m-10) cc_final: 0.5738 (m-80)
REVERT: A  229 LEU cc_start: 0.6528 (mt) cc_final: 0.6318 (mt)
REVERT: A  475 ARG cc_start: 0.7870 (mtt90) cc_final: 0.7511 (ttp-110)
REVERT: A  551 LYS cc_start: 0.6299 (mttt) cc_final: 0.5914 (mptt)
REVERT: B 1734 MET cc_start: 0.6216 (mmt) cc_final: 0.5290 (mmm)
REVERT: B 1801 HIS cc_start: 0.7543 (m-70) cc_final: 0.7086 (m-70)
REVERT: B 1809 GLN cc_start: 0.7485 (pm20) cc_final: 0.7081 (pm20)
REVERT: B 1850 LYS cc_start: 0.6404 (mmtt) cc_final: 0.6141 (mmtp)
REVERT: B 1874 ILE cc_start: 0.6724 (mp) cc_final: 0.6261 (mp)
REVERT: B 1903 TYR cc_start: 0.6005 (t80) cc_final: 0.5633 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 159
  average time/residue: 0.0864
  time to fit residues: 19.4450
Evaluate side-chains
  125 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 6 optimal weight:    0.1980
   chunk 50 optimal weight:    0.4980
   chunk 80 optimal weight:    9.9990
   chunk 67 optimal weight:    0.0010
   chunk 17 optimal weight:    6.9990
   chunk 13 optimal weight:    0.7980
   chunk 39 optimal weight:    9.9990
   chunk 91 optimal weight:    6.9990
   chunk 84 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 82 optimal weight:    9.9990
   overall best weight:    1.0988

-------------------------------------------------------------------------------
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 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 468 ASN
A 556 ASN
** B1643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1940 GLN
** B1955 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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.165862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.155570 restraints weight = 28005.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.157358 restraints weight = 18756.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.158544 restraints weight = 13363.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.159553 restraints weight = 10260.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.160240 restraints weight = 8138.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.4360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6057
moved from start:          0.3116

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= 0.127
  Angle     :  0.732   9.329  13196  Z= 0.370
  Chirality :  0.049   0.200   1403
  Planarity :  0.005   0.057   1689
  Dihedral  :  6.809  33.640   1282
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 20.30
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 13.96 %
    Favored  : 85.95 %
  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 : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.04 (0.21), residues: 1153
  helix: -4.97 (0.43), residues: 31
  sheet: -3.90 (0.35), residues: 180
  loop : -3.51 (0.17), residues: 942

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B1910 
 TYR   0.017   0.002   TYR A 144 
 PHE   0.021   0.002   PHE B1872 
 TRP   0.017   0.001   TRP B1976 
 HIS   0.010   0.001   HIS B2159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 9746)
  covalent geometry    : angle       0.73240 (13184)
  SS BOND              : bond        0.00312 (    6)
  SS BOND              : angle       0.63033 (   12)
  hydrogen bonds       : bond        0.03138 (   42)
  hydrogen bonds       : angle       7.92986 (   90)

*********************** 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
  166 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 165
  time to evaluate  : 0.255 
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: 0.6588 (m-10) cc_final: 0.5652 (m-80)
REVERT: A  203 MET cc_start: 0.3887 (mmp) cc_final: 0.2828 (mmt)
REVERT: A  229 LEU cc_start: 0.6236 (mt) cc_final: 0.6016 (mt)
REVERT: A  312 THR cc_start: 0.3537 (t) cc_final: 0.3292 (t)
REVERT: A  405 ILE cc_start: 0.7154 (mm) cc_final: 0.6738 (mm)
REVERT: A  475 ARG cc_start: 0.7797 (mtt90) cc_final: 0.7593 (ttm110)
REVERT: B 1743 LEU cc_start: 0.7359 (mp) cc_final: 0.6956 (mp)
REVERT: B 1801 HIS cc_start: 0.7413 (m-70) cc_final: 0.6958 (m-70)
REVERT: B 1809 GLN cc_start: 0.7384 (pm20) cc_final: 0.6715 (pm20)
REVERT: B 1850 LYS cc_start: 0.6372 (mmtt) cc_final: 0.6164 (mmtp)
REVERT: B 1874 ILE cc_start: 0.6376 (mp) cc_final: 0.6036 (mp)
REVERT: B 1903 TYR cc_start: 0.6010 (t80) cc_final: 0.5455 (t80)
REVERT: B 2018 THR cc_start: 0.7838 (t) cc_final: 0.7608 (t)
REVERT: B 2123 LYS cc_start: 0.8145 (mmmt) cc_final: 0.7733 (mmmt)
  outliers start: 1
  outliers final: 0
  residues processed: 166
  average time/residue: 0.0908
  time to fit residues: 20.9186
Evaluate side-chains
  132 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 95 optimal weight:    9.9990
   chunk 80 optimal weight:    9.9990
   chunk 47 optimal weight:    0.6980
   chunk 76 optimal weight:    0.5980
   chunk 104 optimal weight:    3.9990
   chunk 65 optimal weight:    9.9990
   chunk 96 optimal weight:    7.9990
   chunk 45 optimal weight:    7.9990
   chunk 105 optimal weight:    6.9990
   chunk 79 optimal weight:   10.0000
   chunk 3 optimal weight:    5.9990
   overall best weight:    3.6586

-------------------------------------------------------------------------------
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**
A 468 ASN
** B1801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B2078 GLN
** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B2132 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.156895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.146802 restraints weight = 28959.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.148515 restraints weight = 19765.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.149682 restraints weight = 14438.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.150613 restraints weight = 11281.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.151146 restraints weight = 9115.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.4241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6312
moved from start:          0.3286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   9752  Z= 0.200
  Angle     :  0.823   9.722  13196  Z= 0.420
  Chirality :  0.051   0.223   1403
  Planarity :  0.006   0.082   1689
  Dihedral  :  7.453  31.725   1282
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 26.10
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 20.12 %
    Favored  : 79.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 1.75 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.17 (0.21), residues: 1153
  helix: -4.76 (0.62), residues: 25
  sheet: -3.98 (0.34), residues: 188
  loop : -3.62 (0.17), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  90 
 TYR   0.017   0.002   TYR A  44 
 PHE   0.023   0.002   PHE A 325 
 TRP   0.034   0.002   TRP B2094 
 HIS   0.007   0.001   HIS B1643 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 9746)
  covalent geometry    : angle       0.82270 (13184)
  SS BOND              : bond        0.00540 (    6)
  SS BOND              : angle       0.94549 (   12)
  hydrogen bonds       : bond        0.04088 (   42)
  hydrogen bonds       : angle       8.46075 (   90)

*********************** 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
  151 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 TYR cc_start: 0.6784 (m-10) cc_final: 0.5917 (m-80)
REVERT: A  229 LEU cc_start: 0.6415 (mt) cc_final: 0.6163 (mt)
REVERT: A  312 THR cc_start: 0.4562 (t) cc_final: 0.4318 (t)
REVERT: A  410 MET cc_start: 0.7264 (mmp) cc_final: 0.7022 (tpt)
REVERT: B 1734 MET cc_start: 0.6577 (mmt) cc_final: 0.5794 (mmm)
REVERT: B 1809 GLN cc_start: 0.7449 (pm20) cc_final: 0.6917 (pm20)
REVERT: B 1850 LYS cc_start: 0.6726 (mmtt) cc_final: 0.6508 (mmtp)
REVERT: B 1903 TYR cc_start: 0.6141 (t80) cc_final: 0.5562 (t80)
REVERT: B 2123 LYS cc_start: 0.8436 (mmmt) cc_final: 0.7772 (mmmt)
REVERT: B 2180 TRP cc_start: 0.6599 (m100) cc_final: 0.5990 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 151
  average time/residue: 0.0909
  time to fit residues: 19.0669
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  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 83 optimal weight:    0.0370
   chunk 28 optimal weight:    0.2980
   chunk 59 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 73 optimal weight:    8.9990
   chunk 39 optimal weight:    8.9990
   chunk 69 optimal weight:    9.9990
   chunk 107 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0980
   chunk 62 optimal weight:   10.0000
   overall best weight:    0.4258

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

Flipped N/Q/H residues before XYZ refinement:
A 207 ASN
A 251 ASN
A 468 ASN
B1553 ASN
** B1643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1801 HIS
B1955 HIS
B1991 ASN
** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.169651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.159105 restraints weight = 27635.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.160971 restraints weight = 18405.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.162292 restraints weight = 13057.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.163013 restraints weight = 9909.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.163880 restraints weight = 8220.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.4408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5952
moved from start:          0.3608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9752  Z= 0.124
  Angle     :  0.720   9.479  13196  Z= 0.361
  Chirality :  0.048   0.237   1403
  Planarity :  0.005   0.063   1689
  Dihedral  :  6.556  34.281   1282
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 16.57
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 12.40 %
    Favored  : 87.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 1.75 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.81 (0.22), residues: 1153
  helix: -4.76 (0.42), residues: 30
  sheet: -3.66 (0.36), residues: 187
  loop : -3.35 (0.18), residues: 936

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  90 
 TYR   0.016   0.001   TYR B1702 
 PHE   0.022   0.002   PHE B1872 
 TRP   0.014   0.001   TRP A 633 
 HIS   0.012   0.001   HIS B1801 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 9746)
  covalent geometry    : angle       0.71962 (13184)
  SS BOND              : bond        0.00654 (    6)
  SS BOND              : angle       0.90746 (   12)
  hydrogen bonds       : bond        0.02711 (   42)
  hydrogen bonds       : angle       7.51224 (   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
  169 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 TYR cc_start: 0.6566 (m-10) cc_final: 0.5742 (m-80)
REVERT: A  270 MET cc_start: 0.6744 (mpp) cc_final: 0.6396 (mmm)
REVERT: A  312 THR cc_start: 0.4188 (t) cc_final: 0.3952 (t)
REVERT: A  405 ILE cc_start: 0.7002 (mm) cc_final: 0.6696 (mm)
REVERT: B 1698 ARG cc_start: 0.6856 (ptp90) cc_final: 0.6563 (ptp90)
REVERT: B 1743 LEU cc_start: 0.7263 (mp) cc_final: 0.6909 (mp)
REVERT: B 1850 LYS cc_start: 0.6281 (mmtt) cc_final: 0.5988 (mmtp)
REVERT: B 1874 ILE cc_start: 0.6512 (mp) cc_final: 0.6153 (mp)
REVERT: B 1883 MET cc_start: 0.3723 (tmm) cc_final: 0.3510 (tmm)
REVERT: B 1903 TYR cc_start: 0.5989 (t80) cc_final: 0.5401 (t80)
REVERT: B 1948 ILE cc_start: 0.4828 (pt) cc_final: 0.4605 (pt)
REVERT: B 2095 LEU cc_start: 0.6602 (tt) cc_final: 0.6242 (mm)
REVERT: B 2123 LYS cc_start: 0.8092 (mmmt) cc_final: 0.7738 (mmmt)
REVERT: B 2180 TRP cc_start: 0.6603 (m100) cc_final: 0.6045 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.0935
  time to fit residues: 22.4394
Evaluate side-chains
  126 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 37 optimal weight:    9.9990
   chunk 52 optimal weight:    9.9990
   chunk 99 optimal weight:   20.0000
   chunk 53 optimal weight:   10.0000
   chunk 75 optimal weight:   10.0000
   chunk 69 optimal weight:    9.9990
   chunk 86 optimal weight:    9.9990
   chunk 114 optimal weight:    0.8980
   chunk 7 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9980
   chunk 57 optimal weight:    5.9990
   overall best weight:    5.5786

-------------------------------------------------------------------------------
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**
A 315 GLN
** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1936 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 = 0.4280 r_free = 0.4280 target = 0.152718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.142329 restraints weight = 28893.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.144061 restraints weight = 19624.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.145292 restraints weight = 14317.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.146209 restraints weight = 11074.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.146899 restraints weight = 8950.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.4195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6420
moved from start:          0.3768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.071   9752  Z= 0.277
  Angle     :  0.946  10.073  13196  Z= 0.483
  Chirality :  0.055   0.251   1403
  Planarity :  0.007   0.085   1689
  Dihedral  :  8.053  33.298   1282
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 30.95
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 22.38 %
    Favored  : 77.36 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.73 %
    Favored  : 96.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 1.75 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.34 (0.20), residues: 1153
  helix: -4.59 (0.58), residues: 26
  sheet: -3.74 (0.33), residues: 199
  loop : -3.84 (0.17), residues: 928

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.025   0.001   ARG A 321 
 TYR   0.035   0.003   TYR B2129 
 PHE   0.030   0.003   PHE B1872 
 TRP   0.050   0.003   TRP B2094 
 HIS   0.008   0.002   HIS B1801 

Details of bonding type rmsd
  covalent geometry    : bond        0.00637 ( 9746)
  covalent geometry    : angle       0.94568 (13184)
  SS BOND              : bond        0.00800 (    6)
  SS BOND              : angle       1.35371 (   12)
  hydrogen bonds       : bond        0.04750 (   42)
  hydrogen bonds       : angle       8.77817 (   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
  146 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 ASP cc_start: 0.6780 (t0) cc_final: 0.6268 (p0)
REVERT: A  312 THR cc_start: 0.3424 (t) cc_final: 0.3217 (t)
REVERT: A  417 ILE cc_start: 0.7685 (mp) cc_final: 0.7460 (mp)
REVERT: B 1738 MET cc_start: 0.6186 (tpp) cc_final: 0.5740 (tpt)
REVERT: B 1809 GLN cc_start: 0.7482 (pm20) cc_final: 0.6919 (pm20)
REVERT: B 1883 MET cc_start: 0.4304 (tmm) cc_final: 0.4016 (tmm)
REVERT: B 1903 TYR cc_start: 0.6208 (t80) cc_final: 0.5679 (t80)
REVERT: B 2123 LYS cc_start: 0.8688 (mmmt) cc_final: 0.8141 (mmmt)
REVERT: B 2180 TRP cc_start: 0.6850 (m100) cc_final: 0.6314 (m100)
  outliers start: 1
  outliers final: 0
  residues processed: 146
  average time/residue: 0.0930
  time to fit residues: 19.3818
Evaluate side-chains
  115 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 72 optimal weight:   20.0000
   chunk 64 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 115 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0010
   chunk 18 optimal weight:    6.9990
   chunk 59 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.7994

-------------------------------------------------------------------------------
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**
** B1643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1936 GLN
B2085 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.161531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.151130 restraints weight = 28416.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.152845 restraints weight = 19173.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.154112 restraints weight = 13893.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.155018 restraints weight = 10688.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.155572 restraints weight = 8663.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.4301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6185
moved from start:          0.3803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9752  Z= 0.150
  Angle     :  0.792   9.707  13196  Z= 0.400
  Chirality :  0.050   0.234   1403
  Planarity :  0.006   0.077   1689
  Dihedral  :  7.304  34.058   1282
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 21.47
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 15.00 %
    Favored  : 84.91 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.53 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 1.75 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.06 (0.21), residues: 1153
  helix: -4.71 (0.54), residues: 25
  sheet: -3.88 (0.34), residues: 192
  loop : -3.54 (0.18), residues: 936

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 321 
 TYR   0.030   0.002   TYR B2129 
 PHE   0.032   0.002   PHE A 325 
 TRP   0.029   0.002   TRP B2094 
 HIS   0.004   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 9746)
  covalent geometry    : angle       0.79069 (13184)
  SS BOND              : bond        0.00472 (    6)
  SS BOND              : angle       1.42892 (   12)
  hydrogen bonds       : bond        0.03154 (   42)
  hydrogen bonds       : angle       7.93465 (   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
  155 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 154
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 TYR cc_start: 0.6687 (m-10) cc_final: 0.5895 (m-80)
REVERT: A  270 MET cc_start: 0.6839 (mpp) cc_final: 0.6572 (mpp)
REVERT: A  410 MET cc_start: 0.6969 (mmp) cc_final: 0.6717 (tpt)
REVERT: A  483 ILE cc_start: 0.6646 (mt) cc_final: 0.6401 (mt)
REVERT: B 1734 MET cc_start: 0.6365 (mmt) cc_final: 0.5576 (mmm)
REVERT: B 1743 LEU cc_start: 0.7645 (mp) cc_final: 0.7287 (mp)
REVERT: B 1809 GLN cc_start: 0.7338 (pm20) cc_final: 0.6691 (pm20)
REVERT: B 1875 MET cc_start: 0.2781 (pmm) cc_final: 0.1409 (ptp)
REVERT: B 1883 MET cc_start: 0.3845 (tmm) cc_final: 0.3552 (tmm)
REVERT: B 1903 TYR cc_start: 0.6135 (t80) cc_final: 0.5501 (t80)
REVERT: B 1948 ILE cc_start: 0.5012 (pt) cc_final: 0.4672 (pt)
REVERT: B 1987 VAL cc_start: 0.6977 (t) cc_final: 0.6322 (t)
REVERT: B 2085 GLN cc_start: 0.4493 (OUTLIER) cc_final: 0.3760 (pp30)
REVERT: B 2180 TRP cc_start: 0.6487 (m100) cc_final: 0.5193 (m100)
  outliers start: 1
  outliers final: 0
  residues processed: 155
  average time/residue: 0.0873
  time to fit residues: 19.7162
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  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 27 optimal weight:    7.9990
   chunk 8 optimal weight:   10.0000
   chunk 105 optimal weight:   10.0000
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.9988

-------------------------------------------------------------------------------
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**
** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.161058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.150194 restraints weight = 28114.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.152018 restraints weight = 18987.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.153136 restraints weight = 13792.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.154157 restraints weight = 10928.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.154764 restraints weight = 8866.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.4294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6195
moved from start:          0.3945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9752  Z= 0.151
  Angle     :  0.795   9.299  13196  Z= 0.399
  Chirality :  0.050   0.331   1403
  Planarity :  0.006   0.068   1689
  Dihedral  :  7.172  32.540   1282
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 22.32
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 17.95 %
    Favored  : 81.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 1.75 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.98 (0.22), residues: 1153
  helix: -4.71 (0.54), residues: 25
  sheet: -3.81 (0.34), residues: 192
  loop : -3.48 (0.18), residues: 936

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B1698 
 TYR   0.027   0.002   TYR B2129 
 PHE   0.027   0.002   PHE A 574 
 TRP   0.028   0.002   TRP B2094 
 HIS   0.022   0.002   HIS A 252 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 9746)
  covalent geometry    : angle       0.79494 (13184)
  SS BOND              : bond        0.00466 (    6)
  SS BOND              : angle       1.15184 (   12)
  hydrogen bonds       : bond        0.03201 (   42)
  hydrogen bonds       : angle       7.73265 (   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
  146 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.356 
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: 0.6604 (m-10) cc_final: 0.5831 (m-80)
REVERT: A  270 MET cc_start: 0.7000 (mpp) cc_final: 0.6677 (mpp)
REVERT: A  410 MET cc_start: 0.6955 (mmp) cc_final: 0.6688 (tpt)
REVERT: A  483 ILE cc_start: 0.6609 (mt) cc_final: 0.6336 (mt)
REVERT: B 1734 MET cc_start: 0.6497 (mmt) cc_final: 0.5632 (mmm)
REVERT: B 1738 MET cc_start: 0.5603 (tpt) cc_final: 0.5355 (tpt)
REVERT: B 1743 LEU cc_start: 0.7540 (mp) cc_final: 0.7228 (mp)
REVERT: B 1755 TYR cc_start: 0.7882 (p90) cc_final: 0.7600 (p90)
REVERT: B 1875 MET cc_start: 0.2828 (pmm) cc_final: 0.1442 (ptp)
REVERT: B 1972 ASN cc_start: 0.8082 (p0) cc_final: 0.7875 (p0)
REVERT: B 2123 LYS cc_start: 0.8464 (mmpt) cc_final: 0.8095 (mmmt)
REVERT: B 2180 TRP cc_start: 0.6589 (m100) cc_final: 0.6090 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.0867
  time to fit residues: 18.5202
Evaluate side-chains
  125 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 94 optimal weight:    8.9990
   chunk 63 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 80 optimal weight:    9.9990
   chunk 96 optimal weight:    3.9990
   chunk 59 optimal weight:    7.9990
   chunk 113 optimal weight:    8.9990
   chunk 19 optimal weight:    8.9990
   chunk 105 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 35 optimal weight:    0.2980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 224 HIS
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**
** B1801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4437 r_free = 0.4437 target = 0.165286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.154478 restraints weight = 28064.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.156253 restraints weight = 19008.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.157545 restraints weight = 13870.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.158404 restraints weight = 10749.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.159127 restraints weight = 8823.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.4351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6064
moved from start:          0.4129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9752  Z= 0.128
  Angle     :  0.755   9.878  13196  Z= 0.376
  Chirality :  0.048   0.298   1403
  Planarity :  0.006   0.062   1689
  Dihedral  :  6.769  30.259   1282
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 18.48
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 13.96 %
    Favored  : 85.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 1.75 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.77 (0.22), residues: 1153
  helix: -4.73 (0.53), residues: 24
  sheet: -3.70 (0.34), residues: 192
  loop : -3.31 (0.18), residues: 937

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B1698 
 TYR   0.024   0.002   TYR B2129 
 PHE   0.024   0.002   PHE B1872 
 TRP   0.019   0.001   TRP B2094 
 HIS   0.011   0.001   HIS B1643 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9746)
  covalent geometry    : angle       0.75479 (13184)
  SS BOND              : bond        0.00399 (    6)
  SS BOND              : angle       1.12911 (   12)
  hydrogen bonds       : bond        0.02711 (   42)
  hydrogen bonds       : angle       7.36580 (   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
  154 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.366 
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: 0.6439 (m-10) cc_final: 0.5762 (m-80)
REVERT: A  270 MET cc_start: 0.6855 (mpp) cc_final: 0.6636 (mpp)
REVERT: A  410 MET cc_start: 0.6831 (mmp) cc_final: 0.6612 (tpt)
REVERT: B 1743 LEU cc_start: 0.7267 (mp) cc_final: 0.6933 (mp)
REVERT: B 1875 MET cc_start: 0.2551 (pmm) cc_final: 0.1334 (ptp)
REVERT: B 1972 ASN cc_start: 0.8078 (p0) cc_final: 0.7863 (p0)
REVERT: B 2123 LYS cc_start: 0.8296 (mmpt) cc_final: 0.7976 (mmmt)
REVERT: B 2180 TRP cc_start: 0.6671 (m100) cc_final: 0.6254 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.0865
  time to fit residues: 19.2941
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  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 87 optimal weight:    8.9990
   chunk 3 optimal weight:    5.9990
   chunk 59 optimal weight:    2.9990
   chunk 111 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 45 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 85 optimal weight:    0.0970
   chunk 69 optimal weight:    8.9990
   overall best weight:    3.0186

-------------------------------------------------------------------------------
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 224 HIS
A 251 ASN
** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B2078 GLN
** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.158543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.148204 restraints weight = 28466.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.149852 restraints weight = 19422.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.151054 restraints weight = 14334.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.151790 restraints weight = 11176.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.152496 restraints weight = 9306.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.4271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6246
moved from start:          0.4170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9752  Z= 0.186
  Angle     :  0.824   9.674  13196  Z= 0.416
  Chirality :  0.051   0.307   1403
  Planarity :  0.006   0.070   1689
  Dihedral  :  7.296  31.807   1282
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 24.72
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 19.08 %
    Favored  : 80.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 1.75 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.82 (0.22), residues: 1153
  helix: -4.73 (0.55), residues: 25
  sheet: -3.61 (0.35), residues: 190
  loop : -3.39 (0.18), residues: 938

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  90 
 TYR   0.027   0.002   TYR B2129 
 PHE   0.027   0.002   PHE B1872 
 TRP   0.038   0.002   TRP B2094 
 HIS   0.012   0.001   HIS B1801 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 9746)
  covalent geometry    : angle       0.82341 (13184)
  SS BOND              : bond        0.00542 (    6)
  SS BOND              : angle       1.14880 (   12)
  hydrogen bonds       : bond        0.03283 (   42)
  hydrogen bonds       : angle       7.75512 (   90)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1364.84 seconds
wall clock time: 24 minutes 41.06 seconds (1481.06 seconds total)