Starting phenix.real_space_refine
on Wed Jun  4 23:53:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8byl_16327/06_2025/8byl_16327.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8byl_16327/06_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_16327/06_2025/8byl_16327.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8byl_16327/06_2025/8byl_16327.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8byl_16327/06_2025/8byl_16327.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8byl_16327/06_2025/8byl_16327.cif"
  }
  resolution = 3.5
  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=  -0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'ASP:plan': 4, 'ARG:plan': 2, 'HIS:plan': 1}
          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: {'GLU:plan': 3, 'HIS:plan': 1, 'ASP:plan': 1}
          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: {'GLU:plan': 1, 'ASP:plan': 2}
          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: {'TPO:plan-1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 3.40, per 1000 atoms: 0.78
  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: 1.08
  Conformation dependent library (CDL) restraints added in 536.5 milliseconds
  

  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: 0.51
  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: 1.03

  Time building geometry restraints manager: 1.29 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:             1.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.850
  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:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.480
-------------------------------------------------------------------------------
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 (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: -1.39 (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
 TRP   0.020   0.001   TRP A1088 
 HIS   0.003   0.001   HIS B2339 
 PHE   0.010   0.001   PHE B2267 
 TYR   0.008   0.001   TYR A1109 
 ARG   0.002   0.000   ARG B2294 

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

*********************** 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  : 0.473 
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: 0.1672
  time to fit residues: 16.4427
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  : 0.476 
-------------------------------------------------------------------------------
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 46 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0070
   chunk 22 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0970
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.4996

-------------------------------------------------------------------------------
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 = 0.4322 r_free = 0.4322 target = 0.204188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.154316 restraints weight = 5200.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.158593 restraints weight = 3399.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.161101 restraints weight = 2539.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          0.1031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4470  Z= 0.118
  Angle     :  0.568   6.467   6092  Z= 0.297
  Chirality :  0.044   0.199    712
  Planarity :  0.004   0.055    785
  Dihedral  :  4.937  43.276    601
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 21.68 %
    Favored  : 75.16 %
  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: -1.37 (0.36), residues: 558
  helix: -0.19 (0.38), residues: 203
  sheet: -1.70 (0.75), residues: 53
  loop : -1.24 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C3043 
 HIS   0.003   0.001   HIS B2339 
 PHE   0.006   0.001   PHE B2267 
 TYR   0.012   0.001   TYR C3012 
 ARG   0.003   0.000   ARG B2308 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03498 (  132)
  hydrogen bonds       : angle       5.04004 (  378)
  covalent geometry    : bond        0.00279 ( 4470)
  covalent geometry    : angle       0.56773 ( 6092)

*********************** 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: 15
    poor density    : 78
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
REVERT: A 1014 PHE cc_start: 0.7718 (t80) cc_final: 0.7447 (t80)
REVERT: B 2289 ASN cc_start: 0.8442 (t0) cc_final: 0.8199 (t0)
REVERT: C 3012 TYR cc_start: 0.7135 (OUTLIER) cc_final: 0.5682 (p90)
REVERT: C 3021 HIS cc_start: 0.7865 (p90) cc_final: 0.7604 (p90)
  outliers start: 15
  outliers final: 9
  residues processed: 87
  average time/residue: 0.1588
  time to fit residues: 17.8395
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  : 0.509 
-------------------------------------------------------------------------------
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 9 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 50 optimal weight:    0.3980
   chunk 47 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 2 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
B2289 ASN
** C3021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.198472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.153382 restraints weight = 5216.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.153342 restraints weight = 3534.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.155158 restraints weight = 2816.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.1376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   4470  Z= 0.201
  Angle     :  0.653   7.577   6092  Z= 0.337
  Chirality :  0.047   0.200    712
  Planarity :  0.005   0.054    785
  Dihedral  :  4.760  19.115    597
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 22.11 %
    Favored  : 73.47 %
  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: -1.33 (0.36), residues: 558
  helix: -0.15 (0.39), residues: 191
  sheet: -1.92 (0.72), residues: 55
  loop : -1.13 (0.35), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C3043 
 HIS   0.003   0.001   HIS B2185 
 PHE   0.013   0.002   PHE C3069 
 TYR   0.013   0.002   TYR C3012 
 ARG   0.003   0.000   ARG C3020 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04028 (  132)
  hydrogen bonds       : angle       5.16816 (  378)
  covalent geometry    : bond        0.00485 ( 4470)
  covalent geometry    : angle       0.65281 ( 6092)

*********************** 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
  98 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
REVERT: A 1014 PHE cc_start: 0.7817 (t80) cc_final: 0.7446 (t80)
REVERT: B 2269 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8097 (m-10)
REVERT: C 3012 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.5622 (p90)
REVERT: C 3021 HIS cc_start: 0.8004 (p90) cc_final: 0.7542 (p90)
  outliers start: 21
  outliers final: 12
  residues processed: 91
  average time/residue: 0.1479
  time to fit residues: 17.5674
Evaluate side-chains
  86 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
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 2216 LEU
Chi-restraints excluded: chain B residue 2223 VAL
Chi-restraints excluded: chain B residue 2269 PHE
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 2 optimal weight:    7.9990
   chunk 27 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
B2273 HIS
** C3021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.199061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.148646 restraints weight = 5216.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.152583 restraints weight = 3496.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.155484 restraints weight = 2648.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.1564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4470  Z= 0.169
  Angle     :  0.622   7.949   6092  Z= 0.321
  Chirality :  0.046   0.169    712
  Planarity :  0.004   0.054    785
  Dihedral  :  4.748  18.861    597
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 21.68 %
    Favored  : 72.84 %
  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: -1.39 (0.36), residues: 558
  helix: -0.22 (0.38), residues: 198
  sheet: -2.01 (0.71), residues: 55
  loop : -1.15 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C3043 
 HIS   0.004   0.001   HIS B2339 
 PHE   0.011   0.001   PHE B2169 
 TYR   0.020   0.002   TYR A1109 
 ARG   0.002   0.000   ARG C3020 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03543 (  132)
  hydrogen bonds       : angle       5.03577 (  378)
  covalent geometry    : bond        0.00409 ( 4470)
  covalent geometry    : angle       0.62222 ( 6092)

*********************** 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
  101 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 75
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
REVERT: B 2169 PHE cc_start: 0.8228 (t80) cc_final: 0.8026 (t80)
REVERT: B 2269 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.7980 (m-10)
REVERT: C 3012 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.5807 (p90)
REVERT: C 3021 HIS cc_start: 0.8032 (p90) cc_final: 0.7574 (p90)
  outliers start: 26
  outliers final: 16
  residues processed: 92
  average time/residue: 0.1622
  time to fit residues: 19.3419
Evaluate side-chains
  90 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
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 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 2202 LEU
Chi-restraints excluded: chain B residue 2216 LEU
Chi-restraints excluded: chain B residue 2223 VAL
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 19 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 48 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 1 optimal weight:    7.9990
   chunk 25 optimal weight:    0.6980
   chunk 34 optimal weight:    0.0980
   chunk 52 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0470
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
B2273 HIS
C3021 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.201699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.151688 restraints weight = 5281.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.155721 restraints weight = 3448.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.158873 restraints weight = 2584.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.1608

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= 0.115
  Angle     :  0.579   6.416   6092  Z= 0.303
  Chirality :  0.045   0.162    712
  Planarity :  0.004   0.052    785
  Dihedral  :  4.494  17.709    597
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 23.16 %
    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 (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: -1.33 (0.36), residues: 558
  helix: -0.03 (0.38), residues: 200
  sheet: -2.26 (0.65), residues: 65
  loop : -1.10 (0.37), residues: 293

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03027 (  132)
  hydrogen bonds       : angle       4.80966 (  378)
  covalent geometry    : bond        0.00276 ( 4470)
  covalent geometry    : angle       0.57938 ( 6092)

*********************** 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
  99 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
REVERT: A 1150 GLU cc_start: 0.6695 (tt0) cc_final: 0.5767 (tp30)
REVERT: B 2169 PHE cc_start: 0.8092 (t80) cc_final: 0.7879 (t80)
REVERT: B 2269 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.7937 (m-10)
REVERT: B 2289 ASN cc_start: 0.8472 (t0) cc_final: 0.8213 (t0)
REVERT: C 3012 TYR cc_start: 0.7767 (OUTLIER) cc_final: 0.6047 (p90)
  outliers start: 22
  outliers final: 13
  residues processed: 92
  average time/residue: 0.1491
  time to fit residues: 17.8653
Evaluate side-chains
  97 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
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 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 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
B2273 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.203024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.153527 restraints weight = 5085.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.158272 restraints weight = 3183.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.161585 restraints weight = 2326.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4470  Z= 0.138
  Angle     :  0.592   6.434   6092  Z= 0.310
  Chirality :  0.045   0.152    712
  Planarity :  0.004   0.051    785
  Dihedral  :  4.494  17.962    597
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 22.74 %
    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 (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: -1.35 (0.36), residues: 558
  helix: -0.14 (0.38), residues: 205
  sheet: -1.74 (0.73), residues: 53
  loop : -1.25 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C3043 
 HIS   0.003   0.001   HIS B2339 
 PHE   0.007   0.001   PHE B2246 
 TYR   0.021   0.002   TYR A1109 
 ARG   0.001   0.000   ARG C3020 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03150 (  132)
  hydrogen bonds       : angle       4.83978 (  378)
  covalent geometry    : bond        0.00335 ( 4470)
  covalent geometry    : angle       0.59208 ( 6092)

*********************** 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
  110 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 84
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
REVERT: A 1150 GLU cc_start: 0.6712 (tt0) cc_final: 0.5777 (tp30)
REVERT: B 2169 PHE cc_start: 0.8132 (t80) cc_final: 0.7879 (t80)
REVERT: B 2269 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.7926 (m-10)
REVERT: B 2289 ASN cc_start: 0.8530 (t0) cc_final: 0.8268 (t0)
REVERT: C 3012 TYR cc_start: 0.7860 (OUTLIER) cc_final: 0.5941 (p90)
  outliers start: 26
  outliers final: 17
  residues processed: 103
  average time/residue: 0.1424
  time to fit residues: 19.0626
Evaluate side-chains
  95 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 76
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
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 2197 THR
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 3059 ILE
Chi-restraints excluded: chain C residue 3066 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 47 optimal weight:    0.0770
   chunk 20 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 48 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 46 optimal weight:    0.4980
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   overall best weight:    1.0342

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

Flipped N/Q/H residues before XYZ refinement:
B2185 HIS
B2273 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.200837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.151637 restraints weight = 5138.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.156199 restraints weight = 3227.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.159312 restraints weight = 2366.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4470  Z= 0.173
  Angle     :  0.637   6.938   6092  Z= 0.331
  Chirality :  0.046   0.150    712
  Planarity :  0.005   0.052    785
  Dihedral  :  4.632  18.558    597
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 23.58 %
    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 (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: -1.47 (0.36), residues: 558
  helix: -0.21 (0.38), residues: 204
  sheet: -1.80 (0.72), residues: 53
  loop : -1.34 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C3043 
 HIS   0.004   0.001   HIS B2339 
 PHE   0.008   0.001   PHE B2246 
 TYR   0.022   0.002   TYR A1109 
 ARG   0.002   0.000   ARG C3020 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03435 (  132)
  hydrogen bonds       : angle       4.98059 (  378)
  covalent geometry    : bond        0.00421 ( 4470)
  covalent geometry    : angle       0.63723 ( 6092)

*********************** 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
  99 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 75
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
REVERT: A 1150 GLU cc_start: 0.6727 (tt0) cc_final: 0.5767 (tp30)
REVERT: B 2269 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7894 (m-10)
REVERT: B 2289 ASN cc_start: 0.8590 (t0) cc_final: 0.8337 (t0)
REVERT: C 3012 TYR cc_start: 0.7870 (OUTLIER) cc_final: 0.5762 (p90)
  outliers start: 24
  outliers final: 17
  residues processed: 91
  average time/residue: 0.1442
  time to fit residues: 17.0127
Evaluate side-chains
  93 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
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 2197 THR
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 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 36 optimal weight:    1.9990
   chunk 19 optimal weight:    0.4980
   chunk 6 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0670
   chunk 5 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 8 optimal weight:    0.3980
   chunk 54 optimal weight:    5.9990
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
B2224 ASN
B2273 HIS
B2325 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.202575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.153449 restraints weight = 5058.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.158102 restraints weight = 3105.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.161240 restraints weight = 2248.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.1895

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= 0.127
  Angle     :  0.598   6.371   6092  Z= 0.312
  Chirality :  0.045   0.245    712
  Planarity :  0.004   0.051    785
  Dihedral  :  4.408  17.988    597
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 23.79 %
    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 (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: -1.46 (0.36), residues: 558
  helix: -0.11 (0.38), residues: 205
  sheet: -2.26 (0.64), residues: 65
  loop : -1.24 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C3043 
 HIS   0.004   0.001   HIS B2339 
 PHE   0.007   0.001   PHE B2393 
 TYR   0.020   0.002   TYR A1109 
 ARG   0.002   0.000   ARG B2129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02912 (  132)
  hydrogen bonds       : angle       4.81795 (  378)
  covalent geometry    : bond        0.00310 ( 4470)
  covalent geometry    : angle       0.59848 ( 6092)

*********************** 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
  101 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
REVERT: A 1150 GLU cc_start: 0.6606 (tt0) cc_final: 0.5653 (tp30)
REVERT: B 2169 PHE cc_start: 0.8094 (t80) cc_final: 0.7853 (t80)
REVERT: B 2269 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.7904 (m-10)
REVERT: B 2289 ASN cc_start: 0.8508 (t0) cc_final: 0.8269 (t0)
REVERT: C 3012 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.6146 (p90)
REVERT: C 3021 HIS cc_start: 0.7887 (p90) cc_final: 0.7668 (p90)
  outliers start: 23
  outliers final: 17
  residues processed: 94
  average time/residue: 0.1510
  time to fit residues: 18.4599
Evaluate side-chains
  95 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 76
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
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 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0980
   chunk 6 optimal weight:    4.9990
   chunk 43 optimal weight:    6.9990
   chunk 52 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 10 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B2273 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.201307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.151735 restraints weight = 5102.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.156400 restraints weight = 3187.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.159906 restraints weight = 2305.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4470  Z= 0.148
  Angle     :  0.622   6.499   6092  Z= 0.325
  Chirality :  0.046   0.233    712
  Planarity :  0.005   0.052    785
  Dihedral  :  4.458  17.966    597
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 23.79 %
    Favored  : 71.16 %
  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: -1.43 (0.36), residues: 558
  helix: -0.10 (0.38), residues: 204
  sheet: -1.83 (0.72), residues: 53
  loop : -1.36 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C3043 
 HIS   0.003   0.001   HIS B2339 
 PHE   0.008   0.001   PHE B2393 
 TYR   0.023   0.002   TYR A1109 
 ARG   0.002   0.000   ARG C3020 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03144 (  132)
  hydrogen bonds       : angle       4.88354 (  378)
  covalent geometry    : bond        0.00360 ( 4470)
  covalent geometry    : angle       0.62155 ( 6092)

*********************** 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
  99 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 75
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
REVERT: A 1133 GLU cc_start: 0.8436 (tp30) cc_final: 0.8184 (tp30)
REVERT: A 1150 GLU cc_start: 0.6671 (tt0) cc_final: 0.5733 (tp30)
REVERT: B 2169 PHE cc_start: 0.8100 (t80) cc_final: 0.7773 (t80)
REVERT: B 2269 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.7931 (m-10)
REVERT: B 2289 ASN cc_start: 0.8568 (t0) cc_final: 0.8295 (t0)
REVERT: C 3012 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.5965 (p90)
  outliers start: 24
  outliers final: 19
  residues processed: 90
  average time/residue: 0.1530
  time to fit residues: 17.9129
Evaluate side-chains
  94 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
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 1112 ILE
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 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 51 optimal weight:    0.5980
   chunk 2 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   chunk 15 optimal weight:    0.1980
   chunk 9 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B2273 HIS
B2325 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.200018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.150530 restraints weight = 5089.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.154496 restraints weight = 3356.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.157278 restraints weight = 2531.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4470  Z= 0.139
  Angle     :  0.620   6.376   6092  Z= 0.324
  Chirality :  0.045   0.229    712
  Planarity :  0.004   0.051    785
  Dihedral  :  4.438  18.060    597
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 23.79 %
    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 (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: 558
  helix: -0.10 (0.38), residues: 205
  sheet: -2.29 (0.64), residues: 65
  loop : -1.32 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C3043 
 HIS   0.004   0.001   HIS B2339 
 PHE   0.008   0.001   PHE B2393 
 TYR   0.022   0.002   TYR A1109 
 ARG   0.001   0.000   ARG C3020 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03042 (  132)
  hydrogen bonds       : angle       4.83990 (  378)
  covalent geometry    : bond        0.00339 ( 4470)
  covalent geometry    : angle       0.62028 ( 6092)

********************** 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
  98 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
REVERT: A 1133 GLU cc_start: 0.8478 (tp30) cc_final: 0.8192 (tp30)
REVERT: A 1150 GLU cc_start: 0.6632 (tt0) cc_final: 0.5682 (tp30)
REVERT: B 2269 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7940 (m-10)
REVERT: B 2289 ASN cc_start: 0.8538 (t0) cc_final: 0.8302 (t0)
REVERT: C 3012 TYR cc_start: 0.7872 (OUTLIER) cc_final: 0.6081 (p90)
REVERT: C 3021 HIS cc_start: 0.7899 (p90) cc_final: 0.7640 (p90)
  outliers start: 23
  outliers final: 19
  residues processed: 89
  average time/residue: 0.1482
  time to fit residues: 17.1791
Evaluate side-chains
  96 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
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 1112 ILE
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 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 2354 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 6 optimal weight:    8.9990
   chunk 5 optimal weight:    0.0060
   chunk 15 optimal weight:    0.4980
   chunk 19 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0980
   chunk 49 optimal weight:    0.7980
   chunk 46 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0050
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.2810

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

Flipped N/Q/H residues before XYZ refinement:
B2273 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.205713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.156788 restraints weight = 5145.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.161669 restraints weight = 3113.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.165221 restraints weight = 2232.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
moved from start:          0.1993

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= 0.105
  Angle     :  0.581   6.392   6092  Z= 0.303
  Chirality :  0.044   0.213    712
  Planarity :  0.004   0.051    785
  Dihedral  :  4.163  18.040    597
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 23.79 %
    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 (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: -1.39 (0.36), residues: 558
  helix:  0.02 (0.38), residues: 208
  sheet: -1.90 (0.78), residues: 48
  loop : -1.43 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C3043 
 HIS   0.004   0.001   HIS B2339 
 PHE   0.008   0.001   PHE A1014 
 TYR   0.020   0.001   TYR A1109 
 ARG   0.001   0.000   ARG B2308 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02639 (  132)
  hydrogen bonds       : angle       4.62251 (  378)
  covalent geometry    : bond        0.00251 ( 4470)
  covalent geometry    : angle       0.58091 ( 6092)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1948.14 seconds
wall clock time: 34 minutes 14.56 seconds (2054.56 seconds total)