Starting phenix.real_space_refine
on Fri Aug 22 15:07:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u1b_41806/08_2025/8u1b_41806.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u1b_41806/08_2025/8u1b_41806.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u1b_41806/08_2025/8u1b_41806.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u1b_41806/08_2025/8u1b_41806.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u1b_41806/08_2025/8u1b_41806.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u1b_41806/08_2025/8u1b_41806.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.021
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      26      5.16       5
     C    2933      2.51       5
     N     774      2.21       5
     O     851      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4584
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3496
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 461, 3496
          Classifications: {'peptide': 461}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 14, 'TRANS': 446}
          Chain breaks: 11
          Unresolved non-hydrogen bonds: 124
          Unresolved non-hydrogen angles: 143
          Unresolved non-hydrogen dihedrals: 107
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 4, 'GLU:plan': 5, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 72
    Chain: "C"
      Number of atoms: 1088
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 150, 1088
          Classifications: {'peptide': 150}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 4, 'TRANS': 145}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 36
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 25
  Time building chain proxies: 1.20, per 1000 atoms: 0.26
  Number of scatterers: 4584
  At special positions: 0
  Unit cell: (89.32, 81.2, 91.64, 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      26     16.00
     O     851      8.00
     N     774      7.00
     C    2933      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A2452 " - pdb=" SG  CYS A2492 " distance=2.03

  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: 0.38
  Conformation dependent library (CDL) restraints added in 200.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1142

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 8 sheets defined
      35.8% alpha, 14.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1956 through 1961
    Processing helix  chain 'A' and resid 1967 through 1988
      removed outlier: 3.672A  pdb=" N   ARG A1973 " --> pdb=" O   THR A1969 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ILE A1974 " --> pdb=" O   LEU A1970 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ALA A1975 " --> pdb=" O   GLN A1971 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   LEU A1976 " --> pdb=" O   HIS A1972 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   TYR A1984 " --> pdb=" O   ASP A1980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1996 through 2000
    Processing helix  chain 'A' and resid 2053 through 2068
      removed outlier: 3.695A  pdb=" N   TYR A2057 " --> pdb=" O   GLN A2053 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   SER A2058 " --> pdb=" O   ALA A2054 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2094 through 2099
    Processing helix  chain 'A' and resid 2107 through 2115
      removed outlier: 4.016A  pdb=" N   LYS A2112 " --> pdb=" O   GLU A2108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2124 through 2133
    Processing helix  chain 'A' and resid 2134 through 2139
    Processing helix  chain 'A' and resid 2208 through 2211
    Processing helix  chain 'A' and resid 2276 through 2280
      removed outlier: 4.016A  pdb=" N   VAL A2280 " --> pdb=" O   ASP A2277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2337 through 2344
      removed outlier: 3.818A  pdb=" N   THR A2340 " --> pdb=" O   GLU A2337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2346 through 2351
    Processing helix  chain 'A' and resid 2389 through 2394
    Processing helix  chain 'A' and resid 2499 through 2521
    Processing helix  chain 'C' and resid 17 through 27
      removed outlier: 3.817A  pdb=" N   ARG C  25 " --> pdb=" O   LEU C  21 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ALA C  26 " --> pdb=" O   GLU C  22 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 60
      removed outlier: 3.587A  pdb=" N   ASP C  58 " --> pdb=" O   HIS C  54 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   SER C  59 " --> pdb=" O   LEU C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 68
    Processing helix  chain 'C' and resid 86 through 93
    Processing helix  chain 'C' and resid 95 through 105
      removed outlier: 3.741A  pdb=" N   LYS C 103 " --> pdb=" O   GLU C  99 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ALA C 104 " --> pdb=" O   VAL C 100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 117 through 125
    Processing helix  chain 'C' and resid 127 through 137
    Processing helix  chain 'C' and resid 150 through 158
    Processing helix  chain 'C' and resid 160 through 171
      removed outlier: 3.607A  pdb=" N   ALA C 164 " --> pdb=" O   ASN C 160 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   VAL C 166 " --> pdb=" O   ASP C 162 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2142 through 2145
      removed outlier: 3.524A  pdb=" N   MET A2459 " --> pdb=" O   LEU A2471 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 2154 through 2156
      removed outlier: 3.844A  pdb=" N   CYS A2154 " --> pdb=" O   GLY A2170 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 2199 through 2207
      removed outlier: 3.982A  pdb=" N   CYS A2201 " --> pdb=" O   GLY A2218 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   TRP A2214 " --> pdb=" O   VAL A2205 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLU A2212 " --> pdb=" O   LEU A2207 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   SER A2217 " --> pdb=" O   LEU A2225 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 2247 through 2249
    Processing sheet with id=AA5, first strand: chain 'A' and resid 2272 through 2274
      removed outlier: 3.776A  pdb=" N   ILE A2274 " --> pdb=" O   LYS A2289 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   LYS A2289 " --> pdb=" O   ILE A2274 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 2304 through 2305
      removed outlier: 4.070A  pdb=" N   GLY A2317 " --> pdb=" O   PHE A2324 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 2354 through 2359
      removed outlier: 6.861A  pdb=" N   ALA A2366 " --> pdb=" O   ILE A2355 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   VAL A2357 " --> pdb=" O   TYR A2364 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   TYR A2364 " --> pdb=" O   VAL A2357 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL A2359 " --> pdb=" O   ALA A2362 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   ALA A2362 " --> pdb=" O   VAL A2359 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ILE A2365 " --> pdb=" O   GLU A2374 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLU A2374 " --> pdb=" O   ILE A2365 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   LYS A2367 " --> pdb=" O   VAL A2372 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   VAL A2372 " --> pdb=" O   LYS A2367 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   ASP A2377 " --> pdb=" O   LEU A2383 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   LEU A2383 " --> pdb=" O   ASP A2377 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 2417 through 2419

    169 hydrogen bonds defined for protein.
    438 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.74

  Time building geometry restraints manager: 0.54 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1277
        1.33 -     1.45: 676
        1.45 -     1.57: 2666
        1.57 -     1.69: 0
        1.69 -     1.81: 37
  Bond restraints: 4656
  Sorted by residual:
  bond pdb=" CA  ARG C  33 "
       pdb=" C   ARG C  33 "
    ideal  model  delta    sigma   weight residual
    1.530  1.506  0.024 1.08e-02 8.57e+03 5.07e+00
  bond pdb=" CA  VAL C  32 "
       pdb=" CB  VAL C  32 "
    ideal  model  delta    sigma   weight residual
    1.540  1.565 -0.024 1.36e-02 5.41e+03 3.24e+00
  bond pdb=" C   GLU C  31 "
       pdb=" O   GLU C  31 "
    ideal  model  delta    sigma   weight residual
    1.237  1.216  0.021 1.17e-02 7.31e+03 3.09e+00
  bond pdb=" C   ARG C  33 "
       pdb=" O   ARG C  33 "
    ideal  model  delta    sigma   weight residual
    1.233  1.214  0.019 1.12e-02 7.97e+03 2.73e+00
  bond pdb=" CA  ARG C  33 "
       pdb=" CB  ARG C  33 "
    ideal  model  delta    sigma   weight residual
    1.522  1.539 -0.017 1.27e-02 6.20e+03 1.82e+00
  ... (remaining 4651 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.43: 6226
        2.43 -     4.86: 87
        4.86 -     7.28: 12
        7.28 -     9.71: 7
        9.71 -    12.14: 2
  Bond angle restraints: 6334
  Sorted by residual:
  angle pdb=" N   ARG C  33 "
        pdb=" CA  ARG C  33 "
        pdb=" C   ARG C  33 "
      ideal   model   delta    sigma   weight residual
     107.32  119.46  -12.14 1.65e+00 3.67e-01 5.41e+01
  angle pdb=" N   ASP C  30 "
        pdb=" CA  ASP C  30 "
        pdb=" C   ASP C  30 "
      ideal   model   delta    sigma   weight residual
     111.36  118.53   -7.17 1.09e+00 8.42e-01 4.32e+01
  angle pdb=" N   VAL A2107 "
        pdb=" CA  VAL A2107 "
        pdb=" C   VAL A2107 "
      ideal   model   delta    sigma   weight residual
     112.12  106.79    5.33 8.40e-01 1.42e+00 4.02e+01
  angle pdb=" N   LEU C  86 "
        pdb=" CA  LEU C  86 "
        pdb=" C   LEU C  86 "
      ideal   model   delta    sigma   weight residual
     114.04  106.70    7.34 1.24e+00 6.50e-01 3.51e+01
  angle pdb=" C   ARG C  33 "
        pdb=" CA  ARG C  33 "
        pdb=" CB  ARG C  33 "
      ideal   model   delta    sigma   weight residual
     111.70  104.87    6.83 1.31e+00 5.83e-01 2.72e+01
  ... (remaining 6329 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.05: 2351
       18.05 -    36.09: 309
       36.09 -    54.14: 77
       54.14 -    72.19: 15
       72.19 -    90.24: 7
  Dihedral angle restraints: 2759
    sinusoidal: 1005
      harmonic: 1754
  Sorted by residual:
  dihedral pdb=" CB  CYS A2452 "
           pdb=" SG  CYS A2452 "
           pdb=" SG  CYS A2492 "
           pdb=" CB  CYS A2492 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  179.37  -86.37     1      1.00e+01 1.00e-02 8.99e+01
  dihedral pdb=" C   VAL C  32 "
           pdb=" N   VAL C  32 "
           pdb=" CA  VAL C  32 "
           pdb=" CB  VAL C  32 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -139.19   17.19     0      2.50e+00 1.60e-01 4.73e+01
  dihedral pdb=" N   VAL C  32 "
           pdb=" C   VAL C  32 "
           pdb=" CA  VAL C  32 "
           pdb=" CB  VAL C  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  137.58  -14.18     0      2.50e+00 1.60e-01 3.22e+01
  ... (remaining 2756 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.104: 753
       0.104 -    0.208: 28
       0.208 -    0.313: 0
       0.313 -    0.417: 0
       0.417 -    0.521: 1
  Chirality restraints: 782
  Sorted by residual:
  chirality pdb=" CA  VAL C  32 "
            pdb=" N   VAL C  32 "
            pdb=" C   VAL C  32 "
            pdb=" CB  VAL C  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.92    0.52 2.00e-01 2.50e+01 6.79e+00
  chirality pdb=" CA  ARG C  33 "
            pdb=" N   ARG C  33 "
            pdb=" C   ARG C  33 "
            pdb=" CB  ARG C  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.82e-01
  chirality pdb=" CA  ASP C  30 "
            pdb=" N   ASP C  30 "
            pdb=" C   ASP C  30 "
            pdb=" CB  ASP C  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.31e-01
  ... (remaining 779 not shown)

  Planarity restraints: 789
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A2104 "   -0.041 5.00e-02 4.00e+02   6.19e-02 6.13e+00
        pdb=" N   PRO A2105 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO A2105 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A2105 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A2214 "    0.014 2.00e-02 2.50e+03   1.37e-02 4.70e+00
        pdb=" CG  TRP A2214 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP A2214 "    0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP A2214 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A2214 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A2214 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A2214 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A2214 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A2214 "    0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A2214 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU C  31 "   -0.009 2.00e-02 2.50e+03   1.78e-02 3.17e+00
        pdb=" C   GLU C  31 "    0.031 2.00e-02 2.50e+03
        pdb=" O   GLU C  31 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   VAL C  32 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 786 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 242
        2.72 -     3.27: 4735
        3.27 -     3.81: 7432
        3.81 -     4.36: 8753
        4.36 -     4.90: 14867
  Nonbonded interactions: 36029
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C 150 "
            pdb=" OD1 ASP C 153 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" OG1 THR A2267 "
            pdb=" OD1 ASP A2269 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" O   GLY A2430 "
            pdb=" OG  SER A2454 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" OD1 ASN A2295 "
            pdb=" OG  SER A2297 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" NE2 HIS C  54 "
            pdb=" O   PHE C  83 "
     model   vdw
     2.222 3.120
  ... (remaining 36024 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:             1.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.620
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7284
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4657  Z= 0.158
  Angle     :  0.753  12.139   6336  Z= 0.411
  Chirality :  0.047   0.521    782
  Planarity :  0.004   0.062    789
  Dihedral  : 17.967  90.235   1614
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  8.06 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  : 37.21 %
    Favored  : 62.58 %
  Cbeta Deviations :  0.18 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.52 (0.36), residues: 583
  helix: -0.73 (0.37), residues: 200
  sheet: -0.12 (0.59), residues: 80
  loop : -1.43 (0.37), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A2122 
 TYR   0.013   0.001   TYR A2189 
 PHE   0.008   0.001   PHE A2181 
 TRP   0.037   0.002   TRP A2214 
 HIS   0.002   0.001   HIS C  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 4656)
  covalent geometry    : angle       0.75291 ( 6334)
  SS BOND              : bond        0.00052 (    1)
  SS BOND              : angle       0.15181 (    2)
  hydrogen bonds       : bond        0.23042 (  169)
  hydrogen bonds       : angle       9.33195 (  438)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.204 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 77
  average time/residue: 0.0628
  time to fit residues: 6.5738
Evaluate side-chains
  69 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    0.0470
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    0.0050
   chunk 56 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.4092

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.151261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.129498 restraints weight = 7935.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.132815 restraints weight = 5223.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.134965 restraints weight = 3808.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.136746 restraints weight = 3016.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.137824 restraints weight = 2496.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
moved from start:          0.0967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4657  Z= 0.129
  Angle     :  0.652   9.779   6336  Z= 0.327
  Chirality :  0.043   0.165    782
  Planarity :  0.004   0.051    789
  Dihedral  :  4.985  24.362    629
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  7.89 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 32.22 %
    Favored  : 62.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.49 (0.35), residues: 583
  helix: -0.36 (0.38), residues: 198
  sheet: -0.74 (0.53), residues: 84
  loop : -1.46 (0.38), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  25 
 TYR   0.012   0.001   TYR A2006 
 PHE   0.016   0.001   PHE C  83 
 TRP   0.020   0.001   TRP A2214 
 HIS   0.005   0.001   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 4656)
  covalent geometry    : angle       0.65184 ( 6334)
  SS BOND              : bond        0.00060 (    1)
  SS BOND              : angle       0.13098 (    2)
  hydrogen bonds       : bond        0.03897 (  169)
  hydrogen bonds       : angle       6.55996 (  438)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A 1955 LEU cc_start: 0.5829 (OUTLIER) cc_final: 0.5443 (tt)
REVERT: A 2155 MET cc_start: 0.8000 (ptm) cc_final: 0.7664 (ptm)
REVERT: A 2225 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8153 (mm)
REVERT: A 2226 VAL cc_start: 0.7434 (t) cc_final: 0.7229 (p)
REVERT: A 2459 MET cc_start: 0.8011 (pmm) cc_final: 0.7673 (pmm)
REVERT: A 2470 MET cc_start: 0.7697 (tpp) cc_final: 0.7495 (tpp)
REVERT: C  103 LYS cc_start: 0.8488 (ttmt) cc_final: 0.8158 (ptmt)
  outliers start: 23
  outliers final: 11
  residues processed: 104
  average time/residue: 0.0712
  time to fit residues: 9.5893
Evaluate side-chains
  91 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1955 LEU
Chi-restraints excluded: chain A residue 1959 LEU
Chi-restraints excluded: chain A residue 2140 LEU
Chi-restraints excluded: chain A residue 2189 TYR
Chi-restraints excluded: chain A residue 2209 VAL
Chi-restraints excluded: chain A residue 2225 LEU
Chi-restraints excluded: chain A residue 2359 VAL
Chi-restraints excluded: chain A residue 2390 VAL
Chi-restraints excluded: chain A residue 2506 ASN
Chi-restraints excluded: chain A residue 2521 MET
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain C residue  150 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0040
   chunk 51 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0970
   chunk 20 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.4190

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

Flipped N/Q/H residues before XYZ refinement:
** A1977 HIS ** 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 = 0.3954 r_free = 0.3954 target = 0.151404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.129524 restraints weight = 7896.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.133030 restraints weight = 5070.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.135420 restraints weight = 3648.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.137156 restraints weight = 2833.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.138278 restraints weight = 2330.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.1284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4657  Z= 0.125
  Angle     :  0.638   9.504   6336  Z= 0.317
  Chirality :  0.043   0.145    782
  Planarity :  0.004   0.042    789
  Dihedral  :  4.874  21.963    629
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  7.72 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  6.24 %
    Allowed  : 32.85 %
    Favored  : 60.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.51 (0.35), residues: 583
  helix: -0.32 (0.37), residues: 198
  sheet: -0.86 (0.52), residues: 84
  loop : -1.49 (0.37), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A2514 
 TYR   0.012   0.001   TYR A2006 
 PHE   0.017   0.001   PHE C  83 
 TRP   0.018   0.001   TRP A2214 
 HIS   0.004   0.001   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 4656)
  covalent geometry    : angle       0.63771 ( 6334)
  SS BOND              : bond        0.00040 (    1)
  SS BOND              : angle       0.15363 (    2)
  hydrogen bonds       : bond        0.03494 (  169)
  hydrogen bonds       : angle       6.01798 (  438)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 84
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A 1955 LEU cc_start: 0.5965 (OUTLIER) cc_final: 0.5579 (tt)
REVERT: A 2117 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7986 (tp30)
REVERT: A 2276 GLU cc_start: 0.6121 (OUTLIER) cc_final: 0.5875 (tm-30)
REVERT: A 2470 MET cc_start: 0.7814 (tpp) cc_final: 0.7253 (tpp)
  outliers start: 30
  outliers final: 16
  residues processed: 107
  average time/residue: 0.0713
  time to fit residues: 9.8277
Evaluate side-chains
  95 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 76
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1955 LEU
Chi-restraints excluded: chain A residue 1959 LEU
Chi-restraints excluded: chain A residue 2006 TYR
Chi-restraints excluded: chain A residue 2117 GLU
Chi-restraints excluded: chain A residue 2140 LEU
Chi-restraints excluded: chain A residue 2189 TYR
Chi-restraints excluded: chain A residue 2201 CYS
Chi-restraints excluded: chain A residue 2209 VAL
Chi-restraints excluded: chain A residue 2211 LYS
Chi-restraints excluded: chain A residue 2276 GLU
Chi-restraints excluded: chain A residue 2280 VAL
Chi-restraints excluded: chain A residue 2335 LEU
Chi-restraints excluded: chain A residue 2359 VAL
Chi-restraints excluded: chain A residue 2390 VAL
Chi-restraints excluded: chain A residue 2506 ASN
Chi-restraints excluded: chain A residue 2521 MET
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   81 TYR
Chi-restraints excluded: chain C residue  124 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 12 optimal weight:    0.4980
   chunk 32 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 45 optimal weight:    0.3980
   chunk 57 optimal weight:    0.6980
   chunk 40 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A1977 HIS ** 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 = 0.3950 r_free = 0.3950 target = 0.151521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.131130 restraints weight = 7630.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.134278 restraints weight = 4903.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.136535 restraints weight = 3529.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.138122 restraints weight = 2736.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.139329 restraints weight = 2250.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7262
moved from start:          0.1479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4657  Z= 0.140
  Angle     :  0.636   9.551   6336  Z= 0.317
  Chirality :  0.043   0.140    782
  Planarity :  0.004   0.036    789
  Dihedral  :  4.878  19.920    629
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  7.89 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  7.07 %
    Allowed  : 33.26 %
    Favored  : 59.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.47 (0.35), residues: 583
  helix: -0.35 (0.37), residues: 205
  sheet: -0.87 (0.52), residues: 84
  loop : -1.42 (0.38), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2514 
 TYR   0.010   0.001   TYR A2006 
 PHE   0.010   0.001   PHE A2181 
 TRP   0.016   0.001   TRP A2214 
 HIS   0.004   0.001   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 4656)
  covalent geometry    : angle       0.63569 ( 6334)
  SS BOND              : bond        0.00072 (    1)
  SS BOND              : angle       0.10461 (    2)
  hydrogen bonds       : bond        0.03266 (  169)
  hydrogen bonds       : angle       5.72682 (  438)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 80
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A 1955 LEU cc_start: 0.5969 (OUTLIER) cc_final: 0.5579 (tt)
REVERT: A 2117 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7952 (tp30)
REVERT: A 2315 MET cc_start: 0.6934 (tpp) cc_final: 0.6723 (tpp)
  outliers start: 34
  outliers final: 18
  residues processed: 105
  average time/residue: 0.0574
  time to fit residues: 8.0275
Evaluate side-chains
  96 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 76
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1955 LEU
Chi-restraints excluded: chain A residue 2006 TYR
Chi-restraints excluded: chain A residue 2058 SER
Chi-restraints excluded: chain A residue 2117 GLU
Chi-restraints excluded: chain A residue 2140 LEU
Chi-restraints excluded: chain A residue 2189 TYR
Chi-restraints excluded: chain A residue 2201 CYS
Chi-restraints excluded: chain A residue 2209 VAL
Chi-restraints excluded: chain A residue 2211 LYS
Chi-restraints excluded: chain A residue 2237 THR
Chi-restraints excluded: chain A residue 2280 VAL
Chi-restraints excluded: chain A residue 2281 LYS
Chi-restraints excluded: chain A residue 2359 VAL
Chi-restraints excluded: chain A residue 2390 VAL
Chi-restraints excluded: chain A residue 2506 ASN
Chi-restraints excluded: chain A residue 2521 MET
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   81 TYR
Chi-restraints excluded: chain C residue  150 THR
Chi-restraints excluded: chain C residue  163 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 47 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 60 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A1977 HIS ** 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 = 0.3925 r_free = 0.3925 target = 0.149830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.129749 restraints weight = 7706.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.132823 restraints weight = 4954.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.135017 restraints weight = 3551.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.136581 restraints weight = 2748.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.137610 restraints weight = 2255.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.1626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4657  Z= 0.178
  Angle     :  0.684  12.084   6336  Z= 0.342
  Chirality :  0.045   0.255    782
  Planarity :  0.004   0.037    789
  Dihedral  :  5.069  20.758    629
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  8.75 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  6.24 %
    Allowed  : 35.34 %
    Favored  : 58.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.59 (0.35), residues: 583
  helix: -0.35 (0.38), residues: 197
  sheet: -0.89 (0.51), residues: 95
  loop : -1.57 (0.38), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2514 
 TYR   0.008   0.001   TYR A2006 
 PHE   0.017   0.002   PHE C  83 
 TRP   0.022   0.001   TRP A2214 
 HIS   0.004   0.001   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 4656)
  covalent geometry    : angle       0.68384 ( 6334)
  SS BOND              : bond        0.00119 (    1)
  SS BOND              : angle       0.09903 (    2)
  hydrogen bonds       : bond        0.03413 (  169)
  hydrogen bonds       : angle       5.68373 (  438)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 79
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A 1955 LEU cc_start: 0.6158 (OUTLIER) cc_final: 0.5786 (tt)
REVERT: A 2117 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7985 (tp30)
REVERT: A 2276 GLU cc_start: 0.6191 (OUTLIER) cc_final: 0.5891 (tm-30)
REVERT: A 2315 MET cc_start: 0.6987 (tpp) cc_final: 0.6767 (tpp)
  outliers start: 30
  outliers final: 19
  residues processed: 104
  average time/residue: 0.0595
  time to fit residues: 8.1527
Evaluate side-chains
  99 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1955 LEU
Chi-restraints excluded: chain A residue 2006 TYR
Chi-restraints excluded: chain A residue 2058 SER
Chi-restraints excluded: chain A residue 2117 GLU
Chi-restraints excluded: chain A residue 2140 LEU
Chi-restraints excluded: chain A residue 2189 TYR
Chi-restraints excluded: chain A residue 2201 CYS
Chi-restraints excluded: chain A residue 2209 VAL
Chi-restraints excluded: chain A residue 2211 LYS
Chi-restraints excluded: chain A residue 2237 THR
Chi-restraints excluded: chain A residue 2276 GLU
Chi-restraints excluded: chain A residue 2280 VAL
Chi-restraints excluded: chain A residue 2281 LYS
Chi-restraints excluded: chain A residue 2321 THR
Chi-restraints excluded: chain A residue 2359 VAL
Chi-restraints excluded: chain A residue 2390 VAL
Chi-restraints excluded: chain A residue 2455 VAL
Chi-restraints excluded: chain A residue 2506 ASN
Chi-restraints excluded: chain A residue 2521 MET
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   81 TYR
Chi-restraints excluded: chain C residue  150 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0050
   chunk 4 optimal weight:    0.4980
   chunk 55 optimal weight:    0.0060
   chunk 5 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 15 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.3810

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

Flipped N/Q/H residues before XYZ refinement:
A1977 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.150596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.129411 restraints weight = 8023.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.132712 restraints weight = 5236.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.135013 restraints weight = 3799.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.136525 restraints weight = 2962.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.137902 restraints weight = 2460.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4657  Z= 0.122
  Angle     :  0.642  11.634   6336  Z= 0.320
  Chirality :  0.043   0.238    782
  Planarity :  0.004   0.037    789
  Dihedral  :  4.842  19.293    629
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  7.89 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 36.59 %
    Favored  : 58.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.56 (0.35), residues: 583
  helix: -0.36 (0.37), residues: 197
  sheet: -0.90 (0.53), residues: 89
  loop : -1.52 (0.37), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2122 
 TYR   0.011   0.001   TYR A2006 
 PHE   0.007   0.001   PHE A2181 
 TRP   0.022   0.001   TRP A2214 
 HIS   0.003   0.001   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 4656)
  covalent geometry    : angle       0.64235 ( 6334)
  SS BOND              : bond        0.00050 (    1)
  SS BOND              : angle       0.20526 (    2)
  hydrogen bonds       : bond        0.03123 (  169)
  hydrogen bonds       : angle       5.50448 (  438)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 80
  time to evaluate  : 0.170 
Fit side-chains
REVERT: A 1955 LEU cc_start: 0.6402 (OUTLIER) cc_final: 0.6034 (tt)
REVERT: A 2117 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7955 (tp30)
REVERT: A 2276 GLU cc_start: 0.6084 (OUTLIER) cc_final: 0.5789 (tm-30)
REVERT: A 2315 MET cc_start: 0.6911 (tpp) cc_final: 0.6702 (tpp)
REVERT: A 2470 MET cc_start: 0.7636 (tpp) cc_final: 0.7222 (tpp)
  outliers start: 25
  outliers final: 17
  residues processed: 100
  average time/residue: 0.0601
  time to fit residues: 7.9155
Evaluate side-chains
  94 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1955 LEU
Chi-restraints excluded: chain A residue 1959 LEU
Chi-restraints excluded: chain A residue 2006 TYR
Chi-restraints excluded: chain A residue 2117 GLU
Chi-restraints excluded: chain A residue 2140 LEU
Chi-restraints excluded: chain A residue 2189 TYR
Chi-restraints excluded: chain A residue 2201 CYS
Chi-restraints excluded: chain A residue 2209 VAL
Chi-restraints excluded: chain A residue 2211 LYS
Chi-restraints excluded: chain A residue 2226 VAL
Chi-restraints excluded: chain A residue 2276 GLU
Chi-restraints excluded: chain A residue 2280 VAL
Chi-restraints excluded: chain A residue 2281 LYS
Chi-restraints excluded: chain A residue 2335 LEU
Chi-restraints excluded: chain A residue 2359 VAL
Chi-restraints excluded: chain A residue 2455 VAL
Chi-restraints excluded: chain A residue 2506 ASN
Chi-restraints excluded: chain A residue 2521 MET
Chi-restraints excluded: chain C residue   81 TYR
Chi-restraints excluded: chain C residue  150 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 50 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 43 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.150243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.130459 restraints weight = 7741.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.133367 restraints weight = 5148.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.135467 restraints weight = 3783.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.136858 restraints weight = 2978.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.138048 restraints weight = 2476.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4657  Z= 0.150
  Angle     :  0.651  11.540   6336  Z= 0.326
  Chirality :  0.044   0.231    782
  Planarity :  0.004   0.036    789
  Dihedral  :  4.898  20.224    629
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  8.58 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  6.65 %
    Allowed  : 34.93 %
    Favored  : 58.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.51 (0.35), residues: 583
  helix: -0.36 (0.37), residues: 198
  sheet: -0.84 (0.54), residues: 91
  loop : -1.47 (0.38), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2122 
 TYR   0.009   0.001   TYR A2006 
 PHE   0.016   0.002   PHE C  83 
 TRP   0.026   0.001   TRP A2214 
 HIS   0.004   0.001   HIS A2206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 4656)
  covalent geometry    : angle       0.65122 ( 6334)
  SS BOND              : bond        0.00087 (    1)
  SS BOND              : angle       0.15585 (    2)
  hydrogen bonds       : bond        0.03203 (  169)
  hydrogen bonds       : angle       5.50314 (  438)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 79
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A 1955 LEU cc_start: 0.6385 (OUTLIER) cc_final: 0.6021 (tt)
REVERT: A 2117 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7891 (tp30)
REVERT: A 2276 GLU cc_start: 0.5970 (OUTLIER) cc_final: 0.5544 (tm-30)
REVERT: A 2470 MET cc_start: 0.7527 (tpp) cc_final: 0.7087 (tpp)
  outliers start: 32
  outliers final: 24
  residues processed: 104
  average time/residue: 0.0572
  time to fit residues: 7.8155
Evaluate side-chains
  100 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 73
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1955 LEU
Chi-restraints excluded: chain A residue 1959 LEU
Chi-restraints excluded: chain A residue 2006 TYR
Chi-restraints excluded: chain A residue 2058 SER
Chi-restraints excluded: chain A residue 2117 GLU
Chi-restraints excluded: chain A residue 2140 LEU
Chi-restraints excluded: chain A residue 2189 TYR
Chi-restraints excluded: chain A residue 2201 CYS
Chi-restraints excluded: chain A residue 2209 VAL
Chi-restraints excluded: chain A residue 2211 LYS
Chi-restraints excluded: chain A residue 2226 VAL
Chi-restraints excluded: chain A residue 2237 THR
Chi-restraints excluded: chain A residue 2276 GLU
Chi-restraints excluded: chain A residue 2280 VAL
Chi-restraints excluded: chain A residue 2281 LYS
Chi-restraints excluded: chain A residue 2321 THR
Chi-restraints excluded: chain A residue 2335 LEU
Chi-restraints excluded: chain A residue 2359 VAL
Chi-restraints excluded: chain A residue 2390 VAL
Chi-restraints excluded: chain A residue 2455 VAL
Chi-restraints excluded: chain A residue 2506 ASN
Chi-restraints excluded: chain A residue 2521 MET
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   81 TYR
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  150 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.149193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.129387 restraints weight = 7809.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.132282 restraints weight = 5208.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.134389 restraints weight = 3831.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.135946 restraints weight = 3014.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.136902 restraints weight = 2495.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4657  Z= 0.166
  Angle     :  0.675  11.384   6336  Z= 0.336
  Chirality :  0.044   0.225    782
  Planarity :  0.004   0.038    789
  Dihedral  :  5.034  20.564    629
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  8.40 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  6.24 %
    Allowed  : 36.17 %
    Favored  : 57.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.52 (0.35), residues: 583
  helix: -0.33 (0.38), residues: 198
  sheet: -0.78 (0.55), residues: 89
  loop : -1.53 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2122 
 TYR   0.008   0.001   TYR C 125 
 PHE   0.012   0.002   PHE A2181 
 TRP   0.025   0.001   TRP A2214 
 HIS   0.005   0.001   HIS A1977 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 4656)
  covalent geometry    : angle       0.67472 ( 6334)
  SS BOND              : bond        0.00101 (    1)
  SS BOND              : angle       0.13506 (    2)
  hydrogen bonds       : bond        0.03234 (  169)
  hydrogen bonds       : angle       5.60321 (  438)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 75
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A 1955 LEU cc_start: 0.6336 (OUTLIER) cc_final: 0.5980 (tt)
REVERT: A 2117 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7889 (tp30)
REVERT: A 2276 GLU cc_start: 0.5972 (OUTLIER) cc_final: 0.5605 (tm-30)
REVERT: A 2315 MET cc_start: 0.7111 (tpp) cc_final: 0.6838 (tpp)
REVERT: A 2470 MET cc_start: 0.7696 (tpp) cc_final: 0.7297 (tpp)
  outliers start: 30
  outliers final: 24
  residues processed: 101
  average time/residue: 0.0668
  time to fit residues: 8.8388
Evaluate side-chains
  100 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 73
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1955 LEU
Chi-restraints excluded: chain A residue 1959 LEU
Chi-restraints excluded: chain A residue 2006 TYR
Chi-restraints excluded: chain A residue 2058 SER
Chi-restraints excluded: chain A residue 2117 GLU
Chi-restraints excluded: chain A residue 2140 LEU
Chi-restraints excluded: chain A residue 2189 TYR
Chi-restraints excluded: chain A residue 2201 CYS
Chi-restraints excluded: chain A residue 2209 VAL
Chi-restraints excluded: chain A residue 2211 LYS
Chi-restraints excluded: chain A residue 2237 THR
Chi-restraints excluded: chain A residue 2276 GLU
Chi-restraints excluded: chain A residue 2280 VAL
Chi-restraints excluded: chain A residue 2281 LYS
Chi-restraints excluded: chain A residue 2321 THR
Chi-restraints excluded: chain A residue 2359 VAL
Chi-restraints excluded: chain A residue 2390 VAL
Chi-restraints excluded: chain A residue 2455 VAL
Chi-restraints excluded: chain A residue 2457 VAL
Chi-restraints excluded: chain A residue 2506 ASN
Chi-restraints excluded: chain A residue 2521 MET
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   81 TYR
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue   99 GLU
Chi-restraints excluded: chain C residue  150 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 3 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 22 optimal weight:    4.9990
   chunk 31 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0770
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.5938

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.150593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.130963 restraints weight = 7670.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.133854 restraints weight = 5076.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.135957 restraints weight = 3732.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.137364 restraints weight = 2934.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.138528 restraints weight = 2450.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4657  Z= 0.144
  Angle     :  0.654  11.948   6336  Z= 0.327
  Chirality :  0.043   0.211    782
  Planarity :  0.004   0.037    789
  Dihedral  :  4.966  22.253    629
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  8.06 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  6.24 %
    Allowed  : 35.76 %
    Favored  : 58.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.50 (0.35), residues: 583
  helix: -0.34 (0.38), residues: 198
  sheet: -0.78 (0.55), residues: 89
  loop : -1.49 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2122 
 TYR   0.009   0.001   TYR A2006 
 PHE   0.017   0.002   PHE C  83 
 TRP   0.024   0.001   TRP A2214 
 HIS   0.003   0.001   HIS C 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 4656)
  covalent geometry    : angle       0.65449 ( 6334)
  SS BOND              : bond        0.00064 (    1)
  SS BOND              : angle       0.20310 (    2)
  hydrogen bonds       : bond        0.03189 (  169)
  hydrogen bonds       : angle       5.52640 (  438)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 74
  time to evaluate  : 0.188 
Fit side-chains
REVERT: A 1955 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.6030 (tt)
REVERT: A 2117 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7896 (tp30)
REVERT: A 2276 GLU cc_start: 0.5924 (OUTLIER) cc_final: 0.5599 (tm-30)
REVERT: A 2315 MET cc_start: 0.7071 (tpp) cc_final: 0.6785 (tpp)
REVERT: A 2354 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7871 (mm)
REVERT: A 2470 MET cc_start: 0.7643 (tpp) cc_final: 0.7254 (tpp)
  outliers start: 30
  outliers final: 24
  residues processed: 99
  average time/residue: 0.0577
  time to fit residues: 7.7422
Evaluate side-chains
  100 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 72
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1955 LEU
Chi-restraints excluded: chain A residue 1959 LEU
Chi-restraints excluded: chain A residue 2006 TYR
Chi-restraints excluded: chain A residue 2058 SER
Chi-restraints excluded: chain A residue 2117 GLU
Chi-restraints excluded: chain A residue 2140 LEU
Chi-restraints excluded: chain A residue 2189 TYR
Chi-restraints excluded: chain A residue 2201 CYS
Chi-restraints excluded: chain A residue 2209 VAL
Chi-restraints excluded: chain A residue 2211 LYS
Chi-restraints excluded: chain A residue 2237 THR
Chi-restraints excluded: chain A residue 2276 GLU
Chi-restraints excluded: chain A residue 2280 VAL
Chi-restraints excluded: chain A residue 2281 LYS
Chi-restraints excluded: chain A residue 2321 THR
Chi-restraints excluded: chain A residue 2354 ILE
Chi-restraints excluded: chain A residue 2359 VAL
Chi-restraints excluded: chain A residue 2390 VAL
Chi-restraints excluded: chain A residue 2455 VAL
Chi-restraints excluded: chain A residue 2457 VAL
Chi-restraints excluded: chain A residue 2506 ASN
Chi-restraints excluded: chain A residue 2521 MET
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   81 TYR
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  150 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 6 optimal weight:    0.0000
   chunk 29 optimal weight:    0.2980
   chunk 1 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.5184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.150235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.129202 restraints weight = 7924.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.132446 restraints weight = 5198.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.134770 restraints weight = 3775.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.136428 restraints weight = 2949.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.137572 restraints weight = 2434.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4657  Z= 0.135
  Angle     :  0.653  11.809   6336  Z= 0.324
  Chirality :  0.043   0.206    782
  Planarity :  0.004   0.037    789
  Dihedral  :  4.910  22.830    629
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  7.72 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 36.80 %
    Favored  : 57.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.54 (0.35), residues: 583
  helix: -0.49 (0.37), residues: 204
  sheet: -0.75 (0.56), residues: 92
  loop : -1.46 (0.38), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2122 
 TYR   0.009   0.001   TYR A2006 
 PHE   0.010   0.001   PHE A2181 
 TRP   0.023   0.001   TRP A2214 
 HIS   0.003   0.001   HIS A2206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 4656)
  covalent geometry    : angle       0.65312 ( 6334)
  SS BOND              : bond        0.00063 (    1)
  SS BOND              : angle       0.19823 (    2)
  hydrogen bonds       : bond        0.03106 (  169)
  hydrogen bonds       : angle       5.46733 (  438)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 75
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A 1955 LEU cc_start: 0.6267 (OUTLIER) cc_final: 0.5959 (tt)
REVERT: A 2117 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8014 (tp30)
REVERT: A 2211 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7410 (pptt)
REVERT: A 2276 GLU cc_start: 0.5971 (OUTLIER) cc_final: 0.5613 (tm-30)
REVERT: A 2315 MET cc_start: 0.6992 (tpp) cc_final: 0.6711 (tpp)
REVERT: A 2354 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7697 (mm)
REVERT: C   33 ARG cc_start: 0.6780 (ttt180) cc_final: 0.6551 (ttt180)
  outliers start: 26
  outliers final: 20
  residues processed: 97
  average time/residue: 0.0616
  time to fit residues: 7.8205
Evaluate side-chains
  97 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 72
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1955 LEU
Chi-restraints excluded: chain A residue 1959 LEU
Chi-restraints excluded: chain A residue 2006 TYR
Chi-restraints excluded: chain A residue 2058 SER
Chi-restraints excluded: chain A residue 2117 GLU
Chi-restraints excluded: chain A residue 2140 LEU
Chi-restraints excluded: chain A residue 2189 TYR
Chi-restraints excluded: chain A residue 2201 CYS
Chi-restraints excluded: chain A residue 2209 VAL
Chi-restraints excluded: chain A residue 2211 LYS
Chi-restraints excluded: chain A residue 2237 THR
Chi-restraints excluded: chain A residue 2276 GLU
Chi-restraints excluded: chain A residue 2280 VAL
Chi-restraints excluded: chain A residue 2281 LYS
Chi-restraints excluded: chain A residue 2321 THR
Chi-restraints excluded: chain A residue 2354 ILE
Chi-restraints excluded: chain A residue 2359 VAL
Chi-restraints excluded: chain A residue 2390 VAL
Chi-restraints excluded: chain A residue 2455 VAL
Chi-restraints excluded: chain A residue 2506 ASN
Chi-restraints excluded: chain A residue 2521 MET
Chi-restraints excluded: chain C residue   81 TYR
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  150 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0970
   chunk 0 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 5 optimal weight:    0.3980
   chunk 37 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.5578

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.151049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.131314 restraints weight = 7736.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.134261 restraints weight = 5131.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.136364 restraints weight = 3754.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.137890 restraints weight = 2950.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.139042 restraints weight = 2439.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7299
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4657  Z= 0.139
  Angle     :  0.651  11.776   6336  Z= 0.324
  Chirality :  0.043   0.199    782
  Planarity :  0.004   0.045    789
  Dihedral  :  4.910  22.896    629
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  7.89 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 36.59 %
    Favored  : 57.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.51 (0.36), residues: 583
  helix: -0.47 (0.37), residues: 204
  sheet: -0.67 (0.56), residues: 92
  loop : -1.46 (0.38), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2514 
 TYR   0.009   0.001   TYR A2006 
 PHE   0.017   0.002   PHE C  83 
 TRP   0.023   0.001   TRP A2214 
 HIS   0.003   0.001   HIS C 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 4656)
  covalent geometry    : angle       0.65153 ( 6334)
  SS BOND              : bond        0.00064 (    1)
  SS BOND              : angle       0.16473 (    2)
  hydrogen bonds       : bond        0.03126 (  169)
  hydrogen bonds       : angle       5.42454 (  438)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 969.19 seconds
wall clock time: 17 minutes 24.12 seconds (1044.12 seconds total)