Starting phenix.real_space_refine
on Tue Feb 11 07:36:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u1b_41806/02_2025/8u1b_41806.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u1b_41806/02_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_41806/02_2025/8u1b_41806.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u1b_41806/02_2025/8u1b_41806.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u1b_41806/02_2025/8u1b_41806.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u1b_41806/02_2025/8u1b_41806.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 4, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5}
          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, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 25
  Time building chain proxies: 3.36, per 1000 atoms: 0.73
  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: 1.06
  Conformation dependent library (CDL) restraints added in 462.6 milliseconds
  

  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: 0.66
  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: 1.29

  Time building geometry restraints manager: 1.25 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:             2.680
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.720
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.240
-------------------------------------------------------------------------------
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   4656  Z= 0.214
  Angle     :  0.753  12.139   6334  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 : 14.05
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.037   0.002   TRP A2214 
 HIS   0.002   0.001   HIS C  61 
 PHE   0.008   0.001   PHE A2181 
 TYR   0.013   0.001   TYR A2189 
 ARG   0.005   0.000   ARG A2122 

*********************** 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  : 0.503 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1454
  time to fit residues: 15.1173
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  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 46 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:    0.2980
   chunk 31 optimal weight:    0.3980
   chunk 24 optimal weight:    0.7980
   chunk 47 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3886 r_free = 0.3886 target = 0.145667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.124225 restraints weight = 8009.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.127278 restraints weight = 5380.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.129454 restraints weight = 3991.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.1099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   4656  Z= 0.320
  Angle     :  0.718  10.186   6334  Z= 0.363
  Chirality :  0.045   0.145    782
  Planarity :  0.005   0.055    789
  Dihedral  :  5.417  24.553    629
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  9.26 %
    Favored  : 90.22 %
  Rotamer:
    Outliers :  6.24 %
    Allowed  : 31.19 %
    Favored  : 62.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.35), residues: 583
  helix: -0.52 (0.38), residues: 194
  sheet: -0.94 (0.52), residues: 84
  loop : -1.59 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A2214 
 HIS   0.006   0.001   HIS C  54 
 PHE   0.016   0.002   PHE A2181 
 TYR   0.008   0.001   TYR A1984 
 ARG   0.001   0.000   ARG C  25 

*********************** 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
  113 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 83
  time to evaluate  : 0.525 
Fit side-chains
REVERT: A 1955 LEU cc_start: 0.5822 (OUTLIER) cc_final: 0.5387 (tt)
REVERT: A 2155 MET cc_start: 0.8018 (ptm) cc_final: 0.7740 (ptm)
REVERT: A 2211 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7365 (pptt)
REVERT: A 2459 MET cc_start: 0.8126 (pmm) cc_final: 0.7703 (pmm)
REVERT: C  103 LYS cc_start: 0.8524 (ttmt) cc_final: 0.8157 (ptmt)
  outliers start: 30
  outliers final: 10
  residues processed: 107
  average time/residue: 0.1667
  time to fit residues: 22.6692
Evaluate side-chains
  83 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
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 2211 LYS
Chi-restraints excluded: chain A residue 2340 THR
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  150 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 57 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 8 optimal weight:    4.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3933 r_free = 0.3933 target = 0.150485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.130076 restraints weight = 7671.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.133228 restraints weight = 4877.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.135469 restraints weight = 3474.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
moved from start:          0.1331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4656  Z= 0.233
  Angle     :  0.681  11.970   6334  Z= 0.338
  Chirality :  0.044   0.143    782
  Planarity :  0.004   0.047    789
  Dihedral  :  5.221  22.197    629
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  8.75 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  6.44 %
    Allowed  : 33.68 %
    Favored  : 59.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.35), residues: 583
  helix: -0.46 (0.38), residues: 197
  sheet: -1.06 (0.52), residues: 84
  loop : -1.58 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A2214 
 HIS   0.006   0.001   HIS A1977 
 PHE   0.017   0.002   PHE C  83 
 TYR   0.010   0.001   TYR A2006 
 ARG   0.007   0.000   ARG A2514 

*********************** 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
  112 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 81
  time to evaluate  : 0.459 
Fit side-chains
REVERT: A 1955 LEU cc_start: 0.5848 (OUTLIER) cc_final: 0.5395 (tt)
REVERT: A 2117 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8062 (tp30)
REVERT: A 2276 GLU cc_start: 0.6203 (OUTLIER) cc_final: 0.5924 (tm-30)
REVERT: C  103 LYS cc_start: 0.8483 (ttmt) cc_final: 0.8169 (ptmt)
  outliers start: 31
  outliers final: 13
  residues processed: 106
  average time/residue: 0.1583
  time to fit residues: 21.5707
Evaluate side-chains
  90 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
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 2117 GLU
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 2211 LYS
Chi-restraints excluded: chain A residue 2237 THR
Chi-restraints excluded: chain A residue 2276 GLU
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 2506 ASN
Chi-restraints excluded: chain A residue 2521 MET
Chi-restraints excluded: chain C residue  150 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0570
   chunk 16 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.6098

-------------------------------------------------------------------------------
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 = 0.3915 r_free = 0.3915 target = 0.148105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.126891 restraints weight = 7931.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.130157 restraints weight = 5203.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.132498 restraints weight = 3781.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.1556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4656  Z= 0.216
  Angle     :  0.657  11.632   6334  Z= 0.327
  Chirality :  0.043   0.159    782
  Planarity :  0.004   0.038    789
  Dihedral  :  5.081  20.033    629
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  8.58 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  7.28 %
    Allowed  : 33.68 %
    Favored  : 59.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.74 (0.35), residues: 583
  helix: -0.57 (0.37), residues: 196
  sheet: -1.17 (0.51), residues: 89
  loop : -1.52 (0.37), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A2214 
 HIS   0.005   0.001   HIS C  54 
 PHE   0.017   0.002   PHE C  83 
 TYR   0.010   0.001   TYR A2006 
 ARG   0.005   0.000   ARG A2514 

*********************** 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: 35
    poor density    : 79
  time to evaluate  : 0.478 
Fit side-chains
REVERT: A 1955 LEU cc_start: 0.5884 (OUTLIER) cc_final: 0.5510 (tt)
REVERT: A 2117 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8035 (tp30)
REVERT: A 2276 GLU cc_start: 0.6106 (OUTLIER) cc_final: 0.5682 (tm-30)
REVERT: A 2459 MET cc_start: 0.8217 (pmm) cc_final: 0.7228 (pmm)
  outliers start: 35
  outliers final: 18
  residues processed: 107
  average time/residue: 0.1383
  time to fit residues: 19.5438
Evaluate side-chains
  95 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 74
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
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 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   53 LEU
Chi-restraints excluded: chain C residue   81 TYR
Chi-restraints excluded: chain C residue  150 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 36 optimal weight:    0.3980
   chunk 17 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0980
   chunk 41 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3928 r_free = 0.3928 target = 0.148918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.127989 restraints weight = 7982.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.131232 restraints weight = 5211.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.133516 restraints weight = 3798.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.1706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4656  Z= 0.206
  Angle     :  0.652  11.233   6334  Z= 0.323
  Chirality :  0.043   0.142    782
  Planarity :  0.004   0.037    789
  Dihedral  :  5.000  19.351    629
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  8.40 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  6.44 %
    Allowed  : 35.97 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.35), residues: 583
  helix: -0.50 (0.37), residues: 197
  sheet: -1.08 (0.51), residues: 88
  loop : -1.55 (0.37), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A2214 
 HIS   0.004   0.001   HIS C  54 
 PHE   0.009   0.001   PHE A2181 
 TYR   0.010   0.001   TYR A2006 
 ARG   0.004   0.000   ARG A2514 

*********************** 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: 31
    poor density    : 78
  time to evaluate  : 0.530 
Fit side-chains
REVERT: A 1955 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.5916 (tt)
REVERT: A 2117 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8054 (tp30)
REVERT: A 2276 GLU cc_start: 0.6059 (OUTLIER) cc_final: 0.5785 (tm-30)
REVERT: A 2315 MET cc_start: 0.6844 (tpp) cc_final: 0.6615 (mmt)
REVERT: A 2326 PHE cc_start: 0.7476 (m-10) cc_final: 0.7274 (m-10)
REVERT: A 2459 MET cc_start: 0.8163 (pmm) cc_final: 0.7159 (pmm)
  outliers start: 31
  outliers final: 23
  residues processed: 104
  average time/residue: 0.1482
  time to fit residues: 20.0903
Evaluate side-chains
  100 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 74
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
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 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 2517 LEU
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  150 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 4 optimal weight:    0.2980
   chunk 12 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 44 optimal weight:    0.5980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3920 r_free = 0.3920 target = 0.148431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.127646 restraints weight = 7988.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.130842 restraints weight = 5221.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.133074 restraints weight = 3807.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
moved from start:          0.1791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4656  Z= 0.221
  Angle     :  0.658  11.518   6334  Z= 0.328
  Chirality :  0.043   0.142    782
  Planarity :  0.004   0.037    789
  Dihedral  :  4.984  20.504    629
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  8.40 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  6.65 %
    Allowed  : 35.97 %
    Favored  : 57.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.35), residues: 583
  helix: -0.65 (0.37), residues: 204
  sheet: -1.05 (0.53), residues: 88
  loop : -1.52 (0.37), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A2214 
 HIS   0.004   0.001   HIS A2206 
 PHE   0.019   0.002   PHE C  83 
 TYR   0.009   0.001   TYR A2006 
 ARG   0.004   0.000   ARG A2514 

*********************** 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
  113 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 81
  time to evaluate  : 0.529 
Fit side-chains
REVERT: A 1955 LEU cc_start: 0.6384 (OUTLIER) cc_final: 0.5941 (tt)
REVERT: A 2117 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8059 (tp30)
REVERT: A 2276 GLU cc_start: 0.6059 (OUTLIER) cc_final: 0.5778 (tm-30)
REVERT: A 2459 MET cc_start: 0.8149 (pmm) cc_final: 0.7095 (pmm)
  outliers start: 32
  outliers final: 24
  residues processed: 106
  average time/residue: 0.1483
  time to fit residues: 20.5491
Evaluate side-chains
  102 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 75
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
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 2506 ASN
Chi-restraints excluded: chain A residue 2517 LEU
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   86 LEU
Chi-restraints excluded: chain C residue   98 VAL
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 13 optimal weight:    0.4980
   chunk 48 optimal weight:    0.0870
   chunk 3 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 55 optimal weight:    0.0170
   chunk 31 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0770
   overall best weight:    0.3154

-------------------------------------------------------------------------------
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 = 0.3954 r_free = 0.3954 target = 0.151124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.130372 restraints weight = 7860.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.133682 restraints weight = 5129.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.135972 restraints weight = 3719.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.1955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4656  Z= 0.171
  Angle     :  0.642  11.046   6334  Z= 0.320
  Chirality :  0.043   0.140    782
  Planarity :  0.004   0.037    789
  Dihedral  :  4.791  20.775    629
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  7.38 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  5.61 %
    Allowed  : 37.01 %
    Favored  : 57.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.35), residues: 583
  helix: -0.59 (0.36), residues: 204
  sheet: -0.99 (0.54), residues: 89
  loop : -1.45 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A2214 
 HIS   0.003   0.001   HIS C 127 
 PHE   0.007   0.001   PHE A2181 
 TYR   0.011   0.001   TYR A2006 
 ARG   0.003   0.000   ARG A2514 

*********************** 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
  106 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 79
  time to evaluate  : 0.499 
Fit side-chains
REVERT: A 1955 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.5869 (tt)
REVERT: A 2117 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8040 (tp30)
REVERT: A 2219 THR cc_start: 0.8513 (m) cc_final: 0.8200 (p)
REVERT: A 2276 GLU cc_start: 0.5960 (OUTLIER) cc_final: 0.5722 (tm-30)
REVERT: A 2459 MET cc_start: 0.8103 (pmm) cc_final: 0.6990 (pmm)
  outliers start: 27
  outliers final: 21
  residues processed: 101
  average time/residue: 0.1574
  time to fit residues: 20.7077
Evaluate side-chains
  100 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 76
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
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 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   53 LEU
Chi-restraints excluded: chain C residue   81 TYR
Chi-restraints excluded: chain C residue   86 LEU
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 10 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3917 r_free = 0.3917 target = 0.148144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.127402 restraints weight = 7932.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.130458 restraints weight = 5288.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.132678 restraints weight = 3858.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4656  Z= 0.252
  Angle     :  0.669  10.966   6334  Z= 0.333
  Chirality :  0.044   0.145    782
  Planarity :  0.004   0.036    789
  Dihedral  :  4.987  22.699    629
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  8.58 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 37.21 %
    Favored  : 56.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.35), residues: 583
  helix: -0.56 (0.37), residues: 204
  sheet: -0.93 (0.55), residues: 83
  loop : -1.52 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A2214 
 HIS   0.003   0.001   HIS A2206 
 PHE   0.014   0.002   PHE C  83 
 TYR   0.008   0.001   TYR A2006 
 ARG   0.003   0.000   ARG A2514 

*********************** 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
  106 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 78
  time to evaluate  : 0.488 
Fit side-chains
REVERT: A 1955 LEU cc_start: 0.6220 (OUTLIER) cc_final: 0.5825 (tt)
REVERT: A 2117 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8090 (tp30)
REVERT: A 2276 GLU cc_start: 0.6144 (OUTLIER) cc_final: 0.5681 (tm-30)
REVERT: A 2459 MET cc_start: 0.8168 (pmm) cc_final: 0.7127 (pmm)
  outliers start: 28
  outliers final: 23
  residues processed: 102
  average time/residue: 0.1560
  time to fit residues: 20.6415
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  : 0.549 
-------------------------------------------------------------------------------
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 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 2517 LEU
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   86 LEU
Chi-restraints excluded: chain C residue   98 VAL
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 0 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 59 optimal weight:    0.3980
   chunk 24 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0000
   chunk 23 optimal weight:    0.4980
   chunk 10 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.4584

-------------------------------------------------------------------------------
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 = 0.3946 r_free = 0.3946 target = 0.150459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.129542 restraints weight = 7885.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.132828 restraints weight = 5175.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.135148 restraints weight = 3775.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.2078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4656  Z= 0.194
  Angle     :  0.660  10.903   6334  Z= 0.327
  Chirality :  0.043   0.138    782
  Planarity :  0.004   0.036    789
  Dihedral  :  4.894  21.925    629
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  7.55 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  5.61 %
    Allowed  : 37.21 %
    Favored  : 57.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.35), residues: 583
  helix: -0.54 (0.37), residues: 204
  sheet: -0.95 (0.55), residues: 84
  loop : -1.46 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A2214 
 HIS   0.003   0.001   HIS C 127 
 PHE   0.009   0.001   PHE A2181 
 TYR   0.010   0.001   TYR A2006 
 ARG   0.003   0.000   ARG A2514 

*********************** 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
  103 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 76
  time to evaluate  : 0.524 
Fit side-chains
REVERT: A 1955 LEU cc_start: 0.6189 (OUTLIER) cc_final: 0.5815 (tt)
REVERT: A 2117 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8076 (tp30)
REVERT: A 2276 GLU cc_start: 0.6073 (OUTLIER) cc_final: 0.5716 (tm-30)
REVERT: A 2459 MET cc_start: 0.8127 (pmm) cc_final: 0.7013 (pmm)
  outliers start: 27
  outliers final: 23
  residues processed: 100
  average time/residue: 0.1621
  time to fit residues: 21.1872
Evaluate side-chains
  98 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 72
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
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 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 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 2517 LEU
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   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 20 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   chunk 2 optimal weight:    0.1980
   chunk 3 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3937 r_free = 0.3937 target = 0.150469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.130927 restraints weight = 7570.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.133830 restraints weight = 5052.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.135865 restraints weight = 3718.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4656  Z= 0.216
  Angle     :  0.664  10.857   6334  Z= 0.330
  Chirality :  0.043   0.141    782
  Planarity :  0.004   0.036    789
  Dihedral  :  4.952  22.929    629
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  8.40 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 37.63 %
    Favored  : 56.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.35), residues: 583
  helix: -0.56 (0.37), residues: 204
  sheet: -0.85 (0.56), residues: 84
  loop : -1.45 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A2214 
 HIS   0.004   0.001   HIS A1977 
 PHE   0.016   0.002   PHE C  83 
 TYR   0.009   0.001   TYR A2006 
 ARG   0.003   0.000   ARG A2514 

********************** 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
  98 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 72
  time to evaluate  : 0.518 
Fit side-chains
REVERT: A 1955 LEU cc_start: 0.6272 (OUTLIER) cc_final: 0.5894 (tt)
REVERT: A 2012 ILE cc_start: 0.8478 (mp) cc_final: 0.8263 (mt)
REVERT: A 2117 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8011 (tp30)
REVERT: A 2276 GLU cc_start: 0.5993 (OUTLIER) cc_final: 0.5678 (tm-30)
REVERT: A 2459 MET cc_start: 0.8140 (pmm) cc_final: 0.7169 (pmm)
  outliers start: 26
  outliers final: 22
  residues processed: 95
  average time/residue: 0.1563
  time to fit residues: 19.4292
Evaluate side-chains
  98 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 73
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
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 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 2517 LEU
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   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 19 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 36 optimal weight:    0.6980
   chunk 60 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0980
   chunk 1 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0370
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
A2450 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.151007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.129884 restraints weight = 7827.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.133231 restraints weight = 5102.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.135584 restraints weight = 3704.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4656  Z= 0.186
  Angle     :  0.649  10.695   6334  Z= 0.321
  Chirality :  0.043   0.143    782
  Planarity :  0.003   0.036    789
  Dihedral  :  4.838  21.999    629
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  7.55 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  5.61 %
    Allowed  : 36.59 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.58 (0.35), residues: 583
  helix: -0.54 (0.37), residues: 204
  sheet: -0.87 (0.57), residues: 84
  loop : -1.42 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A2214 
 HIS   0.003   0.001   HIS A1977 
 PHE   0.009   0.001   PHE A2181 
 TYR   0.010   0.001   TYR A2006 
 ARG   0.003   0.000   ARG A2514 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1772.91 seconds
wall clock time: 32 minutes 34.40 seconds (1954.40 seconds total)