Starting phenix.real_space_refine
on Fri Aug 22 14:56:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8byl_16327/08_2025/8byl_16327.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8byl_16327/08_2025/8byl_16327.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8byl_16327/08_2025/8byl_16327.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8byl_16327/08_2025/8byl_16327.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8byl_16327/08_2025/8byl_16327.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8byl_16327/08_2025/8byl_16327.cif"
  }
  resolution = 3.5
  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=  -0.001 sd=   0.028
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: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      24      5.16       5
     C    2775      2.51       5
     N     745      2.21       5
     O     833      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 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: 4378
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1111
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 1111
          Classifications: {'peptide': 155}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 9, 'TRANS': 145}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 135
          Unresolved non-hydrogen angles: 162
          Unresolved non-hydrogen dihedrals: 111
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'HIS:plan': 1, 'ASP:plan': 4, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 67
    Chain: "B"
      Number of atoms: 2585
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 332, 2585
          Classifications: {'peptide': 332}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 14, 'TRANS': 317}
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 31
          Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 20
    Chain: "C"
      Number of atoms: 584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 584
          Classifications: {'peptide': 69}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 63}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "D"
      Number of atoms: 98
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 98
          Classifications: {'peptide': 15}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 2, 'TRANS': 12}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ASP:plan': 1, 'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 1.24, per 1000 atoms: 0.28
  Number of scatterers: 4378
  At special positions: 0
  Unit cell: (80.25, 113.42, 74.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      24     16.00
     P       1     15.00
     O     833      8.00
     N     745      7.00
     C    2775      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.34
  Conformation dependent library (CDL) restraints added in 184.7 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1092

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 6 sheets defined
      41.2% alpha, 7.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1024 through 1032
      removed outlier: 3.899A  pdb=" N   GLU A1032 " --> pdb=" O   LYS A1028 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1045 through 1057
    Processing helix  chain 'A' and resid 1069 through 1074
    Processing helix  chain 'A' and resid 1074 through 1080
    Processing helix  chain 'A' and resid 1089 through 1094
      removed outlier: 4.073A  pdb=" N   LYS A1094 " --> pdb=" O   GLN A1090 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1096 through 1111
    Processing helix  chain 'A' and resid 1112 through 1127
      removed outlier: 3.903A  pdb=" N   CYS A1120 " --> pdb=" O   LEU A1116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1131 through 1140
      removed outlier: 3.589A  pdb=" N   ILE A1135 " --> pdb=" O   THR A1131 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ARG A1136 " --> pdb=" O   PRO A1132 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   LYS A1137 " --> pdb=" O   GLU A1133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1148 through 1157
      removed outlier: 3.624A  pdb=" N   VAL A1153 " --> pdb=" O   GLU A1149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2101 through 2111
      removed outlier: 3.500A  pdb=" N   GLY B2107 " --> pdb=" O   GLU B2103 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   CYS B2111 " --> pdb=" O   GLY B2107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2113 through 2118
      removed outlier: 3.747A  pdb=" N   LEU B2118 " --> pdb=" O   LEU B2114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2119 through 2123
      removed outlier: 3.647A  pdb=" N   VAL B2123 " --> pdb=" O   VAL B2120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2124 through 2132
      removed outlier: 3.632A  pdb=" N   SER B2132 " --> pdb=" O   TYR B2128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2148 through 2158
    Processing helix  chain 'B' and resid 2194 through 2203
    Processing helix  chain 'B' and resid 2219 through 2226
      removed outlier: 3.509A  pdb=" N   VAL B2223 " --> pdb=" O   SER B2219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2227 through 2229
      No H-bonds generated for 'chain 'B' and resid 2227 through 2229'
    Processing helix  chain 'B' and resid 2244 through 2255
    Processing helix  chain 'B' and resid 2270 through 2281
    Processing helix  chain 'B' and resid 2293 through 2297
    Processing helix  chain 'B' and resid 2298 through 2309
    Processing helix  chain 'B' and resid 2324 through 2326
      No H-bonds generated for 'chain 'B' and resid 2324 through 2326'
    Processing helix  chain 'B' and resid 2327 through 2334
      removed outlier: 3.722A  pdb=" N   PHE B2331 " --> pdb=" O   CYS B2327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2352 through 2357
      removed outlier: 4.003A  pdb=" N   LEU B2356 " --> pdb=" O   THR B2352 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLY B2357 " --> pdb=" O   LEU B2353 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 2352 through 2357'
    Processing helix  chain 'B' and resid 2374 through 2382
      removed outlier: 3.651A  pdb=" N   LEU B2378 " --> pdb=" O   GLY B2374 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 3025 through 3030
      removed outlier: 4.156A  pdb=" N   LYS C3030 " --> pdb=" O   LYS C3026 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 3039 through 3044
      removed outlier: 3.581A  pdb=" N   ARG C3044 " --> pdb=" O   GLU C3040 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1008 through 1009
      removed outlier: 4.317A  pdb=" N   PHE A1014 " --> pdb=" O   SER A1008 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 2185 through 2187
      removed outlier: 3.798A  pdb=" N   ASP B2141 " --> pdb=" O   LEU B2416 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 2210 through 2212
      removed outlier: 8.026A  pdb=" N   LEU B2235 " --> pdb=" O   ASN B2262 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU B2261 " --> pdb=" O   GLN B2287 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 2317 through 2318
      removed outlier: 7.304A  pdb=" N   LEU B2317 " --> pdb=" O   SER B2343 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 3007 through 3008
      removed outlier: 3.896A  pdb=" N   TYR C3007 " --> pdb=" O   MET C3023 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 3007 through 3008
      removed outlier: 3.896A  pdb=" N   TYR C3007 " --> pdb=" O   MET C3023 " (cutoff:3.500A)
      removed outlier: 8.736A  pdb=" N   ILE C3066 " --> pdb=" O   ILE C3059 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   ILE C3059 " --> pdb=" O   ILE C3066 " (cutoff:3.500A)
      removed outlier: 8.055A  pdb=" N   LEU C3068 " --> pdb=" O   TYR C3057 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   TYR C3057 " --> pdb=" O   LEU C3068 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   VAL C3055 " --> pdb=" O   ARG C3070 " (cutoff:3.500A)

    133 hydrogen bonds defined for protein.
    378 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: 0.44

  Time building geometry restraints manager: 0.45 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: 921
        1.33 -     1.45: 962
        1.45 -     1.57: 2555
        1.57 -     1.69: 1
        1.69 -     1.81: 31
  Bond restraints: 4470
  Sorted by residual:
  bond pdb=" OG1 TPO D4187 "
       pdb=" P   TPO D4187 "
    ideal  model  delta    sigma   weight residual
    1.717  1.604  0.113 2.00e-02 2.50e+03 3.19e+01
  bond pdb=" CB  TPO D4187 "
       pdb=" OG1 TPO D4187 "
    ideal  model  delta    sigma   weight residual
    1.406  1.464 -0.058 2.00e-02 2.50e+03 8.35e+00
  bond pdb=" C   PRO A1070 "
       pdb=" N   PRO A1071 "
    ideal  model  delta    sigma   weight residual
    1.329  1.363 -0.034 1.18e-02 7.18e+03 8.23e+00
  bond pdb=" N   LEU B2130 "
       pdb=" CA  LEU B2130 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.032 1.31e-02 5.83e+03 6.03e+00
  bond pdb=" C   PRO A1132 "
       pdb=" O   PRO A1132 "
    ideal  model  delta    sigma   weight residual
    1.238  1.209  0.029 1.37e-02 5.33e+03 4.47e+00
  ... (remaining 4465 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 5924
        1.72 -     3.44: 135
        3.44 -     5.16: 26
        5.16 -     6.87: 4
        6.87 -     8.59: 3
  Bond angle restraints: 6092
  Sorted by residual:
  angle pdb=" N   PRO A1072 "
        pdb=" CA  PRO A1072 "
        pdb=" CB  PRO A1072 "
      ideal   model   delta    sigma   weight residual
     103.33  109.89   -6.56 1.10e+00 8.26e-01 3.56e+01
  angle pdb=" C   PRO A1132 "
        pdb=" CA  PRO A1132 "
        pdb=" CB  PRO A1132 "
      ideal   model   delta    sigma   weight residual
     111.44  103.18    8.26 1.51e+00 4.39e-01 3.00e+01
  angle pdb=" C   TYR C3012 "
        pdb=" N   ASP C3013 "
        pdb=" CA  ASP C3013 "
      ideal   model   delta    sigma   weight residual
     122.82  114.23    8.59 1.68e+00 3.54e-01 2.62e+01
  angle pdb=" C   ARG B2294 "
        pdb=" CA  ARG B2294 "
        pdb=" CB  ARG B2294 "
      ideal   model   delta    sigma   weight residual
     116.63  111.53    5.10 1.16e+00 7.43e-01 1.94e+01
  angle pdb=" N   ASP A1084 "
        pdb=" CA  ASP A1084 "
        pdb=" C   ASP A1084 "
      ideal   model   delta    sigma   weight residual
     108.31  101.83    6.48 1.52e+00 4.33e-01 1.82e+01
  ... (remaining 6087 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 2323
       17.64 -    35.29: 291
       35.29 -    52.93: 58
       52.93 -    70.58: 15
       70.58 -    88.22: 7
  Dihedral angle restraints: 2694
    sinusoidal: 1026
      harmonic: 1668
  Sorted by residual:
  dihedral pdb=" CA  VAL A1087 "
           pdb=" C   VAL A1087 "
           pdb=" N   TRP A1088 "
           pdb=" CA  TRP A1088 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.98  -22.02     0      5.00e+00 4.00e-02 1.94e+01
  dihedral pdb=" CA  PRO B2384 "
           pdb=" C   PRO B2384 "
           pdb=" N   HIS B2385 "
           pdb=" CA  HIS B2385 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.49   18.51     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" C   PRO A1132 "
           pdb=" N   PRO A1132 "
           pdb=" CA  PRO A1132 "
           pdb=" CB  PRO A1132 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -111.79   -8.91     0      2.50e+00 1.60e-01 1.27e+01
  ... (remaining 2691 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 526
       0.046 -    0.092: 138
       0.092 -    0.138: 40
       0.138 -    0.184: 4
       0.184 -    0.230: 4
  Chirality restraints: 712
  Sorted by residual:
  chirality pdb=" CA  PRO A1072 "
            pdb=" N   PRO A1072 "
            pdb=" C   PRO A1072 "
            pdb=" CB  PRO A1072 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CA  LEU B2416 "
            pdb=" N   LEU B2416 "
            pdb=" C   LEU B2416 "
            pdb=" CB  LEU B2416 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CB  ILE A1112 "
            pdb=" CA  ILE A1112 "
            pdb=" CG1 ILE A1112 "
            pdb=" CG2 ILE A1112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 709 not shown)

  Planarity restraints: 785
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B2169 "   -0.011 2.00e-02 2.50e+03   2.13e-02 4.55e+00
        pdb=" C   PHE B2169 "    0.037 2.00e-02 2.50e+03
        pdb=" O   PHE B2169 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   MET B2170 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A1085 "   -0.032 5.00e-02 4.00e+02   4.93e-02 3.88e+00
        pdb=" N   PRO A1086 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A1086 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A1086 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A1045 "    0.030 5.00e-02 4.00e+02   4.49e-02 3.23e+00
        pdb=" N   PRO A1046 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A1046 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A1046 "    0.025 5.00e-02 4.00e+02
  ... (remaining 782 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1342
        2.82 -     3.34: 4074
        3.34 -     3.86: 6796
        3.86 -     4.38: 7721
        4.38 -     4.90: 13382
  Nonbonded interactions: 33315
  Sorted by model distance:
  nonbonded pdb=" N   GLU A1019 "
            pdb=" OE1 GLU A1019 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" OD1 ASP B2316 "
            pdb=" OG  SER B2318 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   LEU B2118 "
            pdb=" OG  SER B2121 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" O   THR B2139 "
            pdb=" OG1 THR B2139 "
     model   vdw
     2.354 3.040
  nonbonded pdb=" NE1 TRP B2265 "
            pdb=" OG  SER C3041 "
     model   vdw
     2.355 3.120
  ... (remaining 33310 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:             2.070
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.670
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.113   4470  Z= 0.194
  Angle     :  0.657   8.592   6092  Z= 0.385
  Chirality :  0.047   0.230    712
  Planarity :  0.004   0.049    785
  Dihedral  : 16.827  88.221   1602
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 23.16 %
    Favored  : 75.79 %
  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: -1.39 (0.36), residues: 558
  helix: -0.13 (0.40), residues: 185
  sheet: -1.76 (0.77), residues: 48
  loop : -1.26 (0.35), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B2294 
 TYR   0.008   0.001   TYR A1109 
 PHE   0.010   0.001   PHE B2267 
 TRP   0.020   0.001   TRP A1088 
 HIS   0.003   0.001   HIS B2339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 4470)
  covalent geometry    : angle       0.65677 ( 6092)
  hydrogen bonds       : bond        0.20836 (  132)
  hydrogen bonds       : angle       6.42630 (  378)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
REVERT: B 2332 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7916 (m-80)
  outliers start: 5
  outliers final: 1
  residues processed: 77
  average time/residue: 0.0722
  time to fit residues: 7.1565
Evaluate side-chains
  77 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 75
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 2147 LEU
Chi-restraints excluded: chain B residue 2332 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    0.2980
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0970
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    0.3980
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** C3021 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 = 0.4306 r_free = 0.4306 target = 0.202331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.152253 restraints weight = 5296.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.156268 restraints weight = 3473.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.159300 restraints weight = 2601.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.161245 restraints weight = 2139.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.162482 restraints weight = 1862.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.1027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4470  Z= 0.145
  Angle     :  0.590   6.546   6092  Z= 0.308
  Chirality :  0.045   0.204    712
  Planarity :  0.004   0.054    785
  Dihedral  :  5.042  43.994    601
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 22.11 %
    Favored  : 74.95 %
  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: -1.43 (0.36), residues: 558
  helix: -0.23 (0.38), residues: 203
  sheet: -1.75 (0.74), residues: 53
  loop : -1.28 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B2308 
 TYR   0.012   0.001   TYR C3012 
 PHE   0.007   0.001   PHE B2246 
 TRP   0.016   0.001   TRP C3043 
 HIS   0.003   0.001   HIS B2339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 4470)
  covalent geometry    : angle       0.58955 ( 6092)
  hydrogen bonds       : bond        0.03977 (  132)
  hydrogen bonds       : angle       5.14572 (  378)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
REVERT: A 1014 PHE cc_start: 0.7769 (t80) cc_final: 0.7518 (t80)
REVERT: B 2289 ASN cc_start: 0.8539 (t0) cc_final: 0.8280 (t0)
REVERT: C 3012 TYR cc_start: 0.7348 (OUTLIER) cc_final: 0.5446 (p90)
REVERT: C 3021 HIS cc_start: 0.7917 (p90) cc_final: 0.7592 (p90)
  outliers start: 14
  outliers final: 9
  residues processed: 87
  average time/residue: 0.0544
  time to fit residues: 6.1990
Evaluate side-chains
  84 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1059 ILE
Chi-restraints excluded: chain A residue 1088 TRP
Chi-restraints excluded: chain A residue 1141 ILE
Chi-restraints excluded: chain A residue 1144 ASP
Chi-restraints excluded: chain B residue 2168 SER
Chi-restraints excluded: chain B residue 2216 LEU
Chi-restraints excluded: chain B residue 2394 THR
Chi-restraints excluded: chain C residue 3012 TYR
Chi-restraints excluded: chain C residue 3050 GLN
Chi-restraints excluded: chain C residue 3059 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0870
   chunk 1 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0470
   chunk 11 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 46 optimal weight:    0.0970
   chunk 43 optimal weight:    5.9990
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
C3021 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.202572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.152636 restraints weight = 5205.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.156687 restraints weight = 3429.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.159745 restraints weight = 2584.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.161615 restraints weight = 2112.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.163418 restraints weight = 1850.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.1251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4470  Z= 0.128
  Angle     :  0.586   7.822   6092  Z= 0.302
  Chirality :  0.044   0.188    712
  Planarity :  0.004   0.054    785
  Dihedral  :  4.459  17.535    597
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 21.89 %
    Favored  : 73.89 %
  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: -1.35 (0.36), residues: 558
  helix: -0.08 (0.38), residues: 202
  sheet: -2.21 (0.67), residues: 65
  loop : -1.11 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B2308 
 TYR   0.012   0.001   TYR A1109 
 PHE   0.007   0.001   PHE B2393 
 TRP   0.017   0.001   TRP C3043 
 HIS   0.003   0.001   HIS B2339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 4470)
  covalent geometry    : angle       0.58575 ( 6092)
  hydrogen bonds       : bond        0.03392 (  132)
  hydrogen bonds       : angle       4.89039 (  378)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
REVERT: A 1014 PHE cc_start: 0.7775 (t80) cc_final: 0.7430 (t80)
REVERT: B 2269 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.8079 (m-10)
REVERT: B 2289 ASN cc_start: 0.8535 (t0) cc_final: 0.8277 (t0)
REVERT: C 3012 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.5686 (p90)
  outliers start: 20
  outliers final: 11
  residues processed: 91
  average time/residue: 0.0633
  time to fit residues: 7.5614
Evaluate side-chains
  88 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1059 ILE
Chi-restraints excluded: chain A residue 1088 TRP
Chi-restraints excluded: chain A residue 1102 GLU
Chi-restraints excluded: chain A residue 1116 LEU
Chi-restraints excluded: chain A residue 1141 ILE
Chi-restraints excluded: chain A residue 1144 ASP
Chi-restraints excluded: chain B residue 2168 SER
Chi-restraints excluded: chain B residue 2216 LEU
Chi-restraints excluded: chain B residue 2269 PHE
Chi-restraints excluded: chain C residue 3012 TYR
Chi-restraints excluded: chain C residue 3050 GLN
Chi-restraints excluded: chain C residue 3059 ILE
Chi-restraints excluded: chain C residue 3066 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 13 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 6 optimal weight:    0.5980
   chunk 2 optimal weight:    7.9990
   chunk 46 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
B2289 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.199923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.149559 restraints weight = 5202.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.153601 restraints weight = 3457.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.156476 restraints weight = 2620.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.158586 restraints weight = 2160.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.160156 restraints weight = 1886.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.1511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4470  Z= 0.167
  Angle     :  0.621   6.534   6092  Z= 0.322
  Chirality :  0.046   0.173    712
  Planarity :  0.004   0.052    785
  Dihedral  :  4.614  17.670    597
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 22.32 %
    Favored  : 73.26 %
  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: -1.30 (0.36), residues: 558
  helix: -0.12 (0.39), residues: 197
  sheet: -1.88 (0.74), residues: 55
  loop : -1.13 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C3020 
 TYR   0.020   0.002   TYR A1109 
 PHE   0.009   0.001   PHE B2246 
 TRP   0.018   0.001   TRP C3043 
 HIS   0.003   0.001   HIS B2339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 4470)
  covalent geometry    : angle       0.62119 ( 6092)
  hydrogen bonds       : bond        0.03508 (  132)
  hydrogen bonds       : angle       4.97231 (  378)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
REVERT: B 2269 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.8000 (m-10)
REVERT: C 3012 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.5638 (p90)
  outliers start: 21
  outliers final: 14
  residues processed: 96
  average time/residue: 0.0574
  time to fit residues: 7.2492
Evaluate side-chains
  93 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1059 ILE
Chi-restraints excluded: chain A residue 1088 TRP
Chi-restraints excluded: chain A residue 1102 GLU
Chi-restraints excluded: chain A residue 1141 ILE
Chi-restraints excluded: chain A residue 1144 ASP
Chi-restraints excluded: chain B residue 2161 ILE
Chi-restraints excluded: chain B residue 2168 SER
Chi-restraints excluded: chain B residue 2202 LEU
Chi-restraints excluded: chain B residue 2216 LEU
Chi-restraints excluded: chain B residue 2269 PHE
Chi-restraints excluded: chain B residue 2345 CYS
Chi-restraints excluded: chain B residue 2394 THR
Chi-restraints excluded: chain C residue 3012 TYR
Chi-restraints excluded: chain C residue 3050 GLN
Chi-restraints excluded: chain C residue 3059 ILE
Chi-restraints excluded: chain C residue 3066 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 2 optimal weight:    7.9990
   chunk 52 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 1 optimal weight:    5.9990
   chunk 45 optimal weight:    0.4980
   chunk 13 optimal weight:    0.6980
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.4274 r_free = 0.4274 target = 0.198722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.148503 restraints weight = 5195.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.152405 restraints weight = 3484.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.155344 restraints weight = 2646.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.157148 restraints weight = 2188.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.158749 restraints weight = 1918.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.1649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   4470  Z= 0.170
  Angle     :  0.632   8.324   6092  Z= 0.325
  Chirality :  0.046   0.171    712
  Planarity :  0.004   0.052    785
  Dihedral  :  4.687  18.533    597
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 22.53 %
    Favored  : 72.21 %
  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: -1.51 (0.36), residues: 558
  helix: -0.31 (0.37), residues: 208
  sheet: -1.71 (0.75), residues: 53
  loop : -1.35 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C3020 
 TYR   0.020   0.002   TYR A1109 
 PHE   0.009   0.001   PHE B2246 
 TRP   0.019   0.001   TRP C3043 
 HIS   0.004   0.001   HIS B2339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 4470)
  covalent geometry    : angle       0.63157 ( 6092)
  hydrogen bonds       : bond        0.03464 (  132)
  hydrogen bonds       : angle       4.96388 (  378)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 75
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
REVERT: B 2269 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.7985 (m-10)
REVERT: C 3012 TYR cc_start: 0.7762 (OUTLIER) cc_final: 0.5765 (p90)
  outliers start: 25
  outliers final: 15
  residues processed: 93
  average time/residue: 0.0566
  time to fit residues: 6.9468
Evaluate side-chains
  91 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1059 ILE
Chi-restraints excluded: chain A residue 1063 THR
Chi-restraints excluded: chain A residue 1088 TRP
Chi-restraints excluded: chain A residue 1102 GLU
Chi-restraints excluded: chain A residue 1141 ILE
Chi-restraints excluded: chain A residue 1144 ASP
Chi-restraints excluded: chain B residue 2168 SER
Chi-restraints excluded: chain B residue 2202 LEU
Chi-restraints excluded: chain B residue 2216 LEU
Chi-restraints excluded: chain B residue 2269 PHE
Chi-restraints excluded: chain B residue 2297 LEU
Chi-restraints excluded: chain B residue 2323 LEU
Chi-restraints excluded: chain B residue 2345 CYS
Chi-restraints excluded: chain B residue 2394 THR
Chi-restraints excluded: chain C residue 3012 TYR
Chi-restraints excluded: chain C residue 3050 GLN
Chi-restraints excluded: chain C residue 3066 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 44 optimal weight:    0.6980
   chunk 47 optimal weight:    0.6980
   chunk 54 optimal weight:    0.0030
   chunk 15 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0970
   chunk 21 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   overall best weight:    0.4188

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

Flipped N/Q/H residues before XYZ refinement:
B2224 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.203678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.154523 restraints weight = 5188.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.159517 restraints weight = 3160.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.163133 restraints weight = 2253.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.165610 restraints weight = 1783.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.167119 restraints weight = 1519.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4470  Z= 0.111
  Angle     :  0.577   6.361   6092  Z= 0.301
  Chirality :  0.044   0.145    712
  Planarity :  0.004   0.051    785
  Dihedral  :  4.384  17.901    597
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 24.00 %
    Favored  : 71.79 %
  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: -1.32 (0.36), residues: 558
  helix: -0.10 (0.38), residues: 206
  sheet: -2.03 (0.72), residues: 60
  loop : -1.13 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B2308 
 TYR   0.019   0.002   TYR A1109 
 PHE   0.007   0.001   PHE B2393 
 TRP   0.018   0.001   TRP C3043 
 HIS   0.004   0.001   HIS B2339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 4470)
  covalent geometry    : angle       0.57736 ( 6092)
  hydrogen bonds       : bond        0.02904 (  132)
  hydrogen bonds       : angle       4.72941 (  378)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 83
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: A 1150 GLU cc_start: 0.6517 (tt0) cc_final: 0.5658 (tp30)
REVERT: B 2269 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.7957 (m-10)
REVERT: B 2289 ASN cc_start: 0.8471 (t0) cc_final: 0.8197 (t0)
REVERT: C 3012 TYR cc_start: 0.7688 (OUTLIER) cc_final: 0.6075 (p90)
  outliers start: 20
  outliers final: 15
  residues processed: 95
  average time/residue: 0.0583
  time to fit residues: 7.1488
Evaluate side-chains
  91 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1059 ILE
Chi-restraints excluded: chain A residue 1088 TRP
Chi-restraints excluded: chain A residue 1102 GLU
Chi-restraints excluded: chain A residue 1116 LEU
Chi-restraints excluded: chain A residue 1141 ILE
Chi-restraints excluded: chain A residue 1144 ASP
Chi-restraints excluded: chain B residue 2147 LEU
Chi-restraints excluded: chain B residue 2168 SER
Chi-restraints excluded: chain B residue 2197 THR
Chi-restraints excluded: chain B residue 2202 LEU
Chi-restraints excluded: chain B residue 2269 PHE
Chi-restraints excluded: chain B residue 2323 LEU
Chi-restraints excluded: chain B residue 2345 CYS
Chi-restraints excluded: chain B residue 2394 THR
Chi-restraints excluded: chain C residue 3012 TYR
Chi-restraints excluded: chain C residue 3050 GLN
Chi-restraints excluded: chain C residue 3059 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 39 optimal weight:    0.0050
   chunk 3 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 14 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    0.5996

-------------------------------------------------------------------------------
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 = 0.4296 r_free = 0.4296 target = 0.203099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.154000 restraints weight = 5127.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.158866 restraints weight = 3137.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.162342 restraints weight = 2258.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.164846 restraints weight = 1798.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.166254 restraints weight = 1530.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7323
moved from start:          0.1741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4470  Z= 0.126
  Angle     :  0.598   6.362   6092  Z= 0.312
  Chirality :  0.044   0.145    712
  Planarity :  0.004   0.051    785
  Dihedral  :  4.341  17.750    597
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 23.37 %
    Favored  : 71.37 %
  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: -1.32 (0.36), residues: 558
  helix: -0.07 (0.38), residues: 206
  sheet: -2.04 (0.71), residues: 60
  loop : -1.16 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C3020 
 TYR   0.021   0.002   TYR A1109 
 PHE   0.008   0.001   PHE A1014 
 TRP   0.018   0.001   TRP C3043 
 HIS   0.004   0.001   HIS B2339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4470)
  covalent geometry    : angle       0.59825 ( 6092)
  hydrogen bonds       : bond        0.02995 (  132)
  hydrogen bonds       : angle       4.74398 (  378)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 75
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
REVERT: A 1150 GLU cc_start: 0.6559 (tt0) cc_final: 0.5698 (tp30)
REVERT: B 2169 PHE cc_start: 0.8014 (t80) cc_final: 0.7725 (t80)
REVERT: B 2269 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7908 (m-10)
REVERT: B 2289 ASN cc_start: 0.8552 (t0) cc_final: 0.8282 (t0)
REVERT: C 3012 TYR cc_start: 0.7722 (OUTLIER) cc_final: 0.5981 (p90)
  outliers start: 25
  outliers final: 18
  residues processed: 92
  average time/residue: 0.0561
  time to fit residues: 6.8013
Evaluate side-chains
  94 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1059 ILE
Chi-restraints excluded: chain A residue 1088 TRP
Chi-restraints excluded: chain A residue 1102 GLU
Chi-restraints excluded: chain A residue 1116 LEU
Chi-restraints excluded: chain A residue 1141 ILE
Chi-restraints excluded: chain A residue 1144 ASP
Chi-restraints excluded: chain B residue 2147 LEU
Chi-restraints excluded: chain B residue 2168 SER
Chi-restraints excluded: chain B residue 2197 THR
Chi-restraints excluded: chain B residue 2202 LEU
Chi-restraints excluded: chain B residue 2269 PHE
Chi-restraints excluded: chain B residue 2297 LEU
Chi-restraints excluded: chain B residue 2323 LEU
Chi-restraints excluded: chain B residue 2345 CYS
Chi-restraints excluded: chain B residue 2394 THR
Chi-restraints excluded: chain C residue 3012 TYR
Chi-restraints excluded: chain C residue 3048 VAL
Chi-restraints excluded: chain C residue 3050 GLN
Chi-restraints excluded: chain C residue 3059 ILE
Chi-restraints excluded: chain C residue 3066 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 43 optimal weight:    0.0980
   chunk 15 optimal weight:    0.0470
   chunk 8 optimal weight:    0.0570
   chunk 22 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 54 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 17 optimal weight:    0.1980
   overall best weight:    0.2596

-------------------------------------------------------------------------------
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 = 0.4329 r_free = 0.4329 target = 0.206937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.157832 restraints weight = 5125.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.162870 restraints weight = 3109.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.166498 restraints weight = 2219.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.169046 restraints weight = 1758.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.170286 restraints weight = 1491.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   4470  Z= 0.104
  Angle     :  0.574   6.319   6092  Z= 0.299
  Chirality :  0.043   0.143    712
  Planarity :  0.004   0.050    785
  Dihedral  :  4.162  18.112    597
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 23.58 %
    Favored  : 72.00 %
  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: -1.23 (0.36), residues: 558
  helix:  0.02 (0.38), residues: 205
  sheet: -1.61 (0.87), residues: 43
  loop : -1.27 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B2308 
 TYR   0.019   0.002   TYR A1109 
 PHE   0.006   0.001   PHE B2393 
 TRP   0.018   0.001   TRP C3043 
 HIS   0.004   0.001   HIS B2339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 4470)
  covalent geometry    : angle       0.57391 ( 6092)
  hydrogen bonds       : bond        0.02663 (  132)
  hydrogen bonds       : angle       4.59166 (  378)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: A 1150 GLU cc_start: 0.6409 (tt0) cc_final: 0.5557 (tp30)
REVERT: B 2231 ASN cc_start: 0.7469 (m110) cc_final: 0.7126 (m-40)
REVERT: B 2269 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.7934 (m-10)
REVERT: B 2289 ASN cc_start: 0.8433 (t0) cc_final: 0.8174 (t0)
REVERT: C 3012 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.6246 (p90)
  outliers start: 21
  outliers final: 16
  residues processed: 89
  average time/residue: 0.0607
  time to fit residues: 6.9294
Evaluate side-chains
  93 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1059 ILE
Chi-restraints excluded: chain A residue 1088 TRP
Chi-restraints excluded: chain A residue 1102 GLU
Chi-restraints excluded: chain A residue 1116 LEU
Chi-restraints excluded: chain A residue 1141 ILE
Chi-restraints excluded: chain A residue 1144 ASP
Chi-restraints excluded: chain B residue 2147 LEU
Chi-restraints excluded: chain B residue 2168 SER
Chi-restraints excluded: chain B residue 2197 THR
Chi-restraints excluded: chain B residue 2202 LEU
Chi-restraints excluded: chain B residue 2269 PHE
Chi-restraints excluded: chain B residue 2323 LEU
Chi-restraints excluded: chain B residue 2345 CYS
Chi-restraints excluded: chain C residue 3012 TYR
Chi-restraints excluded: chain C residue 3048 VAL
Chi-restraints excluded: chain C residue 3050 GLN
Chi-restraints excluded: chain C residue 3059 ILE
Chi-restraints excluded: chain C residue 3066 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 15 optimal weight:    0.0470
   chunk 5 optimal weight:    8.9990
   chunk 54 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 2 optimal weight:    7.9990
   chunk 25 optimal weight:    0.5980
   chunk 44 optimal weight:    0.0270
   chunk 46 optimal weight:    0.0030
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.3348

-------------------------------------------------------------------------------
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 = 0.4337 r_free = 0.4337 target = 0.205754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.156275 restraints weight = 5249.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.160584 restraints weight = 3363.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.163823 restraints weight = 2484.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.165662 restraints weight = 2008.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.167603 restraints weight = 1742.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4470  Z= 0.110
  Angle     :  0.586   6.313   6092  Z= 0.305
  Chirality :  0.043   0.141    712
  Planarity :  0.004   0.051    785
  Dihedral  :  4.080  17.759    597
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 23.58 %
    Favored  : 71.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.16 (0.37), residues: 558
  helix:  0.08 (0.38), residues: 208
  sheet: -1.69 (0.80), residues: 48
  loop : -1.20 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B2257 
 TYR   0.020   0.001   TYR A1109 
 PHE   0.008   0.001   PHE A1014 
 TRP   0.018   0.001   TRP C3043 
 HIS   0.004   0.001   HIS B2339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 4470)
  covalent geometry    : angle       0.58570 ( 6092)
  hydrogen bonds       : bond        0.02720 (  132)
  hydrogen bonds       : angle       4.57339 (  378)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 79
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: A 1133 GLU cc_start: 0.8412 (tp30) cc_final: 0.8143 (tp30)
REVERT: A 1150 GLU cc_start: 0.6457 (tt0) cc_final: 0.5592 (tp30)
REVERT: B 2129 ARG cc_start: 0.7794 (tmm-80) cc_final: 0.7278 (mtt180)
REVERT: B 2231 ASN cc_start: 0.7500 (m110) cc_final: 0.7166 (m-40)
REVERT: B 2269 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.7980 (m-10)
REVERT: B 2289 ASN cc_start: 0.8464 (t0) cc_final: 0.8192 (t0)
REVERT: C 3012 TYR cc_start: 0.7537 (OUTLIER) cc_final: 0.6231 (p90)
REVERT: C 3021 HIS cc_start: 0.8049 (p-80) cc_final: 0.7777 (p-80)
  outliers start: 23
  outliers final: 17
  residues processed: 91
  average time/residue: 0.0740
  time to fit residues: 8.5961
Evaluate side-chains
  94 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1059 ILE
Chi-restraints excluded: chain A residue 1088 TRP
Chi-restraints excluded: chain A residue 1102 GLU
Chi-restraints excluded: chain A residue 1116 LEU
Chi-restraints excluded: chain A residue 1141 ILE
Chi-restraints excluded: chain A residue 1144 ASP
Chi-restraints excluded: chain B residue 2147 LEU
Chi-restraints excluded: chain B residue 2168 SER
Chi-restraints excluded: chain B residue 2197 THR
Chi-restraints excluded: chain B residue 2202 LEU
Chi-restraints excluded: chain B residue 2269 PHE
Chi-restraints excluded: chain B residue 2323 LEU
Chi-restraints excluded: chain B residue 2345 CYS
Chi-restraints excluded: chain B residue 2354 LEU
Chi-restraints excluded: chain C residue 3012 TYR
Chi-restraints excluded: chain C residue 3048 VAL
Chi-restraints excluded: chain C residue 3050 GLN
Chi-restraints excluded: chain C residue 3059 ILE
Chi-restraints excluded: chain C residue 3066 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 5 optimal weight:    7.9990
   chunk 54 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 51 optimal weight:    0.1980
   chunk 53 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
B2325 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.202756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.153359 restraints weight = 5098.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.157975 restraints weight = 3197.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.161337 restraints weight = 2343.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.163487 restraints weight = 1890.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.165297 restraints weight = 1629.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   4470  Z= 0.165
  Angle     :  0.641   6.658   6092  Z= 0.332
  Chirality :  0.045   0.143    712
  Planarity :  0.005   0.052    785
  Dihedral  :  4.414  17.607    597
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 24.00 %
    Favored  : 71.79 %
  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: -1.31 (0.37), residues: 558
  helix: -0.03 (0.38), residues: 206
  sheet: -2.12 (0.67), residues: 65
  loop : -1.12 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B2257 
 TYR   0.023   0.002   TYR A1109 
 PHE   0.009   0.001   PHE A1014 
 TRP   0.016   0.001   TRP C3043 
 HIS   0.003   0.001   HIS B2339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 4470)
  covalent geometry    : angle       0.64141 ( 6092)
  hydrogen bonds       : bond        0.03274 (  132)
  hydrogen bonds       : angle       4.85924 (  378)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 76
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
REVERT: A 1150 GLU cc_start: 0.6626 (tt0) cc_final: 0.5769 (tp30)
REVERT: B 2289 ASN cc_start: 0.8630 (t0) cc_final: 0.8377 (t0)
REVERT: C 3012 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.5982 (p90)
REVERT: C 3021 HIS cc_start: 0.8098 (p-80) cc_final: 0.7800 (p-80)
  outliers start: 20
  outliers final: 18
  residues processed: 87
  average time/residue: 0.0595
  time to fit residues: 6.7093
Evaluate side-chains
  91 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1059 ILE
Chi-restraints excluded: chain A residue 1087 VAL
Chi-restraints excluded: chain A residue 1088 TRP
Chi-restraints excluded: chain A residue 1102 GLU
Chi-restraints excluded: chain A residue 1141 ILE
Chi-restraints excluded: chain A residue 1144 ASP
Chi-restraints excluded: chain B residue 2147 LEU
Chi-restraints excluded: chain B residue 2161 ILE
Chi-restraints excluded: chain B residue 2168 SER
Chi-restraints excluded: chain B residue 2197 THR
Chi-restraints excluded: chain B residue 2202 LEU
Chi-restraints excluded: chain B residue 2323 LEU
Chi-restraints excluded: chain B residue 2345 CYS
Chi-restraints excluded: chain B residue 2354 LEU
Chi-restraints excluded: chain C residue 3012 TYR
Chi-restraints excluded: chain C residue 3048 VAL
Chi-restraints excluded: chain C residue 3050 GLN
Chi-restraints excluded: chain C residue 3059 ILE
Chi-restraints excluded: chain C residue 3066 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 42 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 1 optimal weight:    7.9990
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.4294 r_free = 0.4294 target = 0.201208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.150252 restraints weight = 5254.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.154345 restraints weight = 3473.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.157312 restraints weight = 2611.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.159376 restraints weight = 2145.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.160317 restraints weight = 1874.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.2030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4470  Z= 0.157
  Angle     :  0.641   6.529   6092  Z= 0.333
  Chirality :  0.045   0.148    712
  Planarity :  0.005   0.052    785
  Dihedral  :  4.480  17.833    597
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 24.42 %
    Favored  : 71.79 %
  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: -1.43 (0.36), residues: 558
  helix: -0.09 (0.38), residues: 205
  sheet: -2.09 (0.70), residues: 60
  loop : -1.29 (0.36), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B2257 
 TYR   0.023   0.002   TYR A1109 
 PHE   0.022   0.002   PHE B2169 
 TRP   0.017   0.001   TRP C3043 
 HIS   0.004   0.001   HIS B2339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 4470)
  covalent geometry    : angle       0.64124 ( 6092)
  hydrogen bonds       : bond        0.03193 (  132)
  hydrogen bonds       : angle       4.87026 (  378)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 974.02 seconds
wall clock time: 17 minutes 20.25 seconds (1040.25 seconds total)