Starting phenix.real_space_refine
on Tue Mar 11 21:42:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pq5_17820/03_2025/8pq5_17820.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pq5_17820/03_2025/8pq5_17820.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pq5_17820/03_2025/8pq5_17820.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pq5_17820/03_2025/8pq5_17820.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pq5_17820/03_2025/8pq5_17820.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pq5_17820/03_2025/8pq5_17820.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 413 atoms to isotropic.
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       6      5.49       5
     S      25      5.16       5
     C    3991      2.51       5
     N    1082      2.21       5
     O    1196      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6300
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2781
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 353, 2781
          Classifications: {'peptide': 353}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 338}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2990
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 372, 2990
          Classifications: {'peptide': 372}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 361}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 467
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 467
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 3, 'TRANS': 53}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.47, per 1000 atoms: 0.71
  Number of scatterers: 6300
  At special positions: 0
  Unit cell: (109.021, 81.991, 97.308, 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      25     16.00
     P       6     15.00
     O    1196      8.00
     N    1082      7.00
     C    3991      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: 1.60
  Conformation dependent library (CDL) restraints added in 932.4 milliseconds
  

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1472

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 6 sheets defined
      44.2% alpha, 12.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 49
      removed outlier: 3.672A  pdb=" N   MET A  42 " --> pdb=" O   LYS A  38 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU A  49 " --> pdb=" O   ILE A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 71
      removed outlier: 4.019A  pdb=" N   VAL A  70 " --> pdb=" O   GLY A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 122
    Processing helix  chain 'A' and resid 123 through 125
      No H-bonds generated for 'chain 'A' and resid 123 through 125'
    Processing helix  chain 'A' and resid 138 through 142
    Processing helix  chain 'A' and resid 147 through 158
      removed outlier: 3.867A  pdb=" N   ARG A 151 " --> pdb=" O   ASN A 147 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ILE A 158 " --> pdb=" O   LEU A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 160
      No H-bonds generated for 'chain 'A' and resid 159 through 160'
    Processing helix  chain 'A' and resid 161 through 163
      No H-bonds generated for 'chain 'A' and resid 161 through 163'
    Processing helix  chain 'A' and resid 164 through 169
    Processing helix  chain 'A' and resid 171 through 181
      removed outlier: 3.560A  pdb=" N   MET A 175 " --> pdb=" O   ARG A 171 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   VAL A 176 " --> pdb=" O   LYS A 172 " (cutoff:3.500A)
      removed outlier: 5.248A  pdb=" N   LYS A 177 " --> pdb=" O   LYS A 173 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ALA A 178 " --> pdb=" O   GLU A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1053 through 1090
      removed outlier: 4.968A  pdb=" N   GLN A1061 " --> pdb=" O   GLN A1057 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   ILE A1062 " --> pdb=" O   ALA A1058 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   ARG A1069 " --> pdb=" O   GLU A1065 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   ALA A1072 " --> pdb=" O   ASP A1068 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   CYS A1073 " --> pdb=" O   ARG A1069 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   ASP A1082 " --> pdb=" O   ALA A1078 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   GLU A1083 " --> pdb=" O   THR A1079 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1129 through 1131
      No H-bonds generated for 'chain 'A' and resid 1129 through 1131'
    Processing helix  chain 'A' and resid 1132 through 1147
    Processing helix  chain 'A' and resid 1163 through 1176
      removed outlier: 3.937A  pdb=" N   GLY A1168 " --> pdb=" O   ASN A1164 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   LYS A1169 " --> pdb=" O   THR A1165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 50
      removed outlier: 3.521A  pdb=" N   PHE B  42 " --> pdb=" O   LYS B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 54
    Processing helix  chain 'B' and resid 59 through 64
      removed outlier: 3.703A  pdb=" N   ALA B  63 " --> pdb=" O   GLU B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 128
      removed outlier: 4.512A  pdb=" N   LEU B 124 " --> pdb=" O   ASP B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 147
    Processing helix  chain 'B' and resid 151 through 164
      removed outlier: 3.887A  pdb=" N   ARG B 155 " --> pdb=" O   PRO B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 182
      removed outlier: 4.399A  pdb=" N   GLU B 173 " --> pdb=" O   ASP B 169 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   GLU B 174 " --> pdb=" O   GLU B 170 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   MET B 179 " --> pdb=" O   SER B 175 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   GLU B 181 " --> pdb=" O   SER B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 193
      removed outlier: 3.584A  pdb=" N   ARG B 186 " --> pdb=" O   THR B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1006 through 1048
      removed outlier: 4.382A  pdb=" N   ARG B1024 " --> pdb=" O   VAL B1020 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   LYS B1025 " --> pdb=" O   LEU B1021 " (cutoff:3.500A)
      removed outlier: 5.242A  pdb=" N   GLN B1035 " --> pdb=" O   LEU B1031 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   PHE B1040 " --> pdb=" O   VAL B1036 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1111 through 1115
    Processing helix  chain 'B' and resid 1119 through 1135
    Processing helix  chain 'B' and resid 1150 through 1165
      removed outlier: 3.629A  pdb=" N   ALA B1156 " --> pdb=" O   GLN B1152 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   GLU B1163 " --> pdb=" O   ASP B1159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1176 through 1181
      removed outlier: 3.592A  pdb=" N   LEU B1180 " --> pdb=" O   ARG B1176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1202 through 1210
      removed outlier: 4.196A  pdb=" N   ASP B1208 " --> pdb=" O   GLU B1204 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   VAL B1210 " --> pdb=" O   ALA B1206 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 559 through 563
    Processing helix  chain 'C' and resid 589 through 603
    Processing helix  chain 'C' and resid 604 through 607
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21
      removed outlier: 4.552A  pdb=" N   LEU A   6 " --> pdb=" O   VAL A  83 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1152 through 1154
      removed outlier: 6.047A  pdb=" N   PHE A1153 " --> pdb=" O   ILE A1185 " (cutoff:3.500A)
      removed outlier: 8.221A  pdb=" N   ILE A1187 " --> pdb=" O   PHE A1153 " (cutoff:3.500A)
      removed outlier: 8.182A  pdb=" N   ILE A1201 " --> pdb=" O   PHE A  27 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   ALA A  29 " --> pdb=" O   ILE A1201 " (cutoff:3.500A)
      removed outlier: 8.327A  pdb=" N   VAL A1203 " --> pdb=" O   ALA A  29 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1095 through 1099
    Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 9
    Processing sheet with id=AA5, first strand: chain 'B' and resid 1139 through 1141
      removed outlier: 6.415A  pdb=" N   TYR B1140 " --> pdb=" O   ILE B1171 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ASN B  28 " --> pdb=" O   PHE B1170 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   HIS B  27 " --> pdb=" O   LYS B1185 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   TYR B1187 " --> pdb=" O   HIS B  27 " (cutoff:3.500A)
      removed outlier: 5.595A  pdb=" N   VAL B  29 " --> pdb=" O   TYR B1187 " (cutoff:3.500A)
      removed outlier: 7.459A  pdb=" N   VAL B1189 " --> pdb=" O   VAL B  29 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   VAL B  31 " --> pdb=" O   VAL B1189 " (cutoff:3.500A)
      removed outlier: 8.625A  pdb=" N   PHE B1191 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 1054 through 1057

    258 hydrogen bonds defined for protein.
    723 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: 1.81

  Time building geometry restraints manager: 1.88 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2066
        1.35 -     1.46: 1357
        1.46 -     1.58: 2932
        1.58 -     1.69: 10
        1.69 -     1.81: 44
  Bond restraints: 6409
  Sorted by residual:
  bond pdb=" CA  MET B1109 "
       pdb=" CB  MET B1109 "
    ideal  model  delta    sigma   weight residual
    1.528  1.588 -0.059 2.61e-02 1.47e+03 5.15e+00
  bond pdb=" CA  GLU B1108 "
       pdb=" CB  GLU B1108 "
    ideal  model  delta    sigma   weight residual
    1.524  1.540 -0.016 1.31e-02 5.83e+03 1.52e+00
  bond pdb=" CG1 ILE A1174 "
       pdb=" CD1 ILE A1174 "
    ideal  model  delta    sigma   weight residual
    1.513  1.470  0.043 3.90e-02 6.57e+02 1.20e+00
  bond pdb=" CG  LEU C 581 "
       pdb=" CD1 LEU C 581 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.05e+00
  bond pdb=" CG1 ILE B1128 "
       pdb=" CD1 ILE B1128 "
    ideal  model  delta    sigma   weight residual
    1.513  1.473  0.040 3.90e-02 6.57e+02 1.04e+00
  ... (remaining 6404 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 8337
        1.69 -     3.39: 235
        3.39 -     5.08: 38
        5.08 -     6.77: 8
        6.77 -     8.47: 4
  Bond angle restraints: 8622
  Sorted by residual:
  angle pdb=" C   ALA A  78 "
        pdb=" N   PHE A  79 "
        pdb=" CA  PHE A  79 "
      ideal   model   delta    sigma   weight residual
     121.75  116.65    5.10 1.73e+00 3.34e-01 8.68e+00
  angle pdb=" N   ALA B 163 "
        pdb=" CA  ALA B 163 "
        pdb=" C   ALA B 163 "
      ideal   model   delta    sigma   weight residual
     110.97  107.76    3.21 1.09e+00 8.42e-01 8.67e+00
  angle pdb=" N   ASN A  11 "
        pdb=" CA  ASN A  11 "
        pdb=" C   ASN A  11 "
      ideal   model   delta    sigma   weight residual
     111.28  115.20   -3.92 1.35e+00 5.49e-01 8.43e+00
  angle pdb=" N   THR B1214 "
        pdb=" CA  THR B1214 "
        pdb=" C   THR B1214 "
      ideal   model   delta    sigma   weight residual
     111.30  107.28    4.02 1.43e+00 4.89e-01 7.92e+00
  angle pdb=" CB  ARG A 131 "
        pdb=" CG  ARG A 131 "
        pdb=" CD  ARG A 131 "
      ideal   model   delta    sigma   weight residual
     111.30  117.24   -5.94 2.30e+00 1.89e-01 6.68e+00
  ... (remaining 8617 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.10: 3484
       17.10 -    34.21: 389
       34.21 -    51.31: 71
       51.31 -    68.41: 13
       68.41 -    85.51: 10
  Dihedral angle restraints: 3967
    sinusoidal: 1694
      harmonic: 2273
  Sorted by residual:
  dihedral pdb=" CA  GLU B 161 "
           pdb=" C   GLU B 161 "
           pdb=" N   VAL B 162 "
           pdb=" CA  VAL B 162 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.32   23.68     0      5.00e+00 4.00e-02 2.24e+01
  dihedral pdb=" CA  LYS A1175 "
           pdb=" C   LYS A1175 "
           pdb=" N   GLU A1176 "
           pdb=" CA  GLU A1176 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.61   21.39     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  TYR A1194 "
           pdb=" C   TYR A1194 "
           pdb=" N   THR A1195 "
           pdb=" CA  THR A1195 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.12   20.88     0      5.00e+00 4.00e-02 1.74e+01
  ... (remaining 3964 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 595
       0.036 -    0.072: 223
       0.072 -    0.108: 94
       0.108 -    0.143: 26
       0.143 -    0.179: 8
  Chirality restraints: 946
  Sorted by residual:
  chirality pdb=" CB  ILE B 138 "
            pdb=" CA  ILE B 138 "
            pdb=" CG1 ILE B 138 "
            pdb=" CG2 ILE B 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.82   -0.18 2.00e-01 2.50e+01 8.04e-01
  chirality pdb=" CA  GLU B 161 "
            pdb=" N   GLU B 161 "
            pdb=" C   GLU B 161 "
            pdb=" CB  GLU B 161 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.31e-01
  chirality pdb=" CA  TYR A1194 "
            pdb=" N   TYR A1194 "
            pdb=" C   TYR A1194 "
            pdb=" CB  TYR A1194 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.16 2.00e-01 2.50e+01 6.02e-01
  ... (remaining 943 not shown)

  Planarity restraints: 1108
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B1154 "   -0.231 9.50e-02 1.11e+02   1.04e-01 6.83e+00
        pdb=" NE  ARG B1154 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG B1154 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG B1154 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG B1154 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 151 "    0.008 2.00e-02 2.50e+03   1.59e-02 2.54e+00
        pdb=" C   PRO B 151 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   PRO B 151 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ASP B 152 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A1204 "   -0.026 5.00e-02 4.00e+02   3.87e-02 2.40e+00
        pdb=" N   PRO A1205 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A1205 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A1205 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1105 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 220
        2.69 -     3.24: 6940
        3.24 -     3.79: 10805
        3.79 -     4.35: 14142
        4.35 -     4.90: 21206
  Nonbonded interactions: 53313
  Sorted by model distance:
  nonbonded pdb=" O   GLU A 156 "
            pdb=" OG  SER A 161 "
     model   vdw
     2.133 3.040
  nonbonded pdb=" OD1 ASP B  51 "
            pdb=" OG  SER B  54 "
     model   vdw
     2.154 3.040
  nonbonded pdb=" OG  SER A1178 "
            pdb=" O   PHE A1182 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" OD2 ASP B1150 "
            pdb=" OH  TYR C 598 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" OG1 THR A1217 "
            pdb=" O   PRO C 616 "
     model   vdw
     2.235 3.040
  ... (remaining 53308 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:             1.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     18.730
  Find NCS groups from input model:        0.080
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7021
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6409  Z= 0.192
  Angle     :  0.690   8.465   8622  Z= 0.366
  Chirality :  0.047   0.179    946
  Planarity :  0.005   0.104   1108
  Dihedral  : 14.875  85.513   2495
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 25.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.24 %
    Favored  : 90.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -1.84 (0.31), residues: 768
  helix: -0.74 (0.31), residues: 275
  sheet: -1.61 (0.40), residues: 140
  loop : -1.32 (0.36), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS A1145 
 PHE   0.023   0.002   PHE A  12 
 TYR   0.013   0.002   TYR B1140 
 ARG   0.008   0.001   ARG B1154 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.739 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 PHE cc_start: 0.8863 (t80) cc_final: 0.8255 (m-80)
REVERT: A   42 MET cc_start: 0.8925 (tmm) cc_final: 0.8617 (tmm)
REVERT: A 1084 ILE cc_start: 0.9431 (mm) cc_final: 0.9171 (pt)
REVERT: A 1174 ILE cc_start: 0.8999 (mp) cc_final: 0.8726 (mp)
REVERT: B    1 MET cc_start: 0.7335 (tmm) cc_final: 0.6939 (tmm)
REVERT: B   47 PHE cc_start: 0.9293 (t80) cc_final: 0.8841 (t80)
REVERT: B  169 ASP cc_start: 0.8874 (p0) cc_final: 0.8592 (p0)
REVERT: B 1057 MET cc_start: 0.5718 (ppp) cc_final: 0.5321 (tmm)
REVERT: B 1100 VAL cc_start: 0.8519 (p) cc_final: 0.7819 (p)
REVERT: B 1102 PHE cc_start: 0.8853 (p90) cc_final: 0.8198 (p90)
REVERT: B 1153 HIS cc_start: 0.8207 (m90) cc_final: 0.7909 (m90)
REVERT: B 1193 ASN cc_start: 0.8995 (t0) cc_final: 0.8417 (p0)
REVERT: C  592 GLN cc_start: 0.8427 (tp-100) cc_final: 0.8063 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.2586
  time to fit residues: 34.4088
Evaluate side-chains
  90 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 58 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 19 optimal weight:    8.9990
   chunk 39 optimal weight:    6.9990
   chunk 31 optimal weight:    8.9990
   chunk 60 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 69 optimal weight:    5.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  40 ASN
** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1153 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 = 0.4035 r_free = 0.4035 target = 0.095328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.074212 restraints weight = 34299.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.075898 restraints weight = 28446.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.077158 restraints weight = 24440.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.2905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.085   6409  Z= 0.471
  Angle     :  0.941  17.623   8622  Z= 0.480
  Chirality :  0.052   0.200    946
  Planarity :  0.007   0.076   1108
  Dihedral  : 10.779  89.478    912
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 41.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.94 %
    Favored  : 89.06 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 10.21 %
    Favored  : 88.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -3.01 (0.29), residues: 768
  helix: -1.71 (0.27), residues: 287
  sheet: -2.04 (0.42), residues: 135
  loop : -2.11 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS A1145 
 PHE   0.032   0.003   PHE A  12 
 TYR   0.030   0.004   TYR A1194 
 ARG   0.008   0.001   ARG A1090 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 0.687 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 PHE cc_start: 0.8697 (t80) cc_final: 0.8103 (m-10)
REVERT: A  174 GLU cc_start: 0.8382 (mp0) cc_final: 0.8082 (mp0)
REVERT: A 1185 ILE cc_start: 0.9482 (mm) cc_final: 0.9175 (pt)
REVERT: A 1194 TYR cc_start: 0.7532 (p90) cc_final: 0.7201 (p90)
REVERT: B    1 MET cc_start: 0.7588 (tmm) cc_final: 0.7318 (tmm)
REVERT: B   11 PHE cc_start: 0.8394 (t80) cc_final: 0.8128 (t80)
REVERT: B   47 PHE cc_start: 0.9154 (t80) cc_final: 0.8754 (t80)
REVERT: B  160 ARG cc_start: 0.8912 (tmt170) cc_final: 0.8466 (tmt170)
REVERT: B 1100 VAL cc_start: 0.8695 (p) cc_final: 0.8088 (p)
REVERT: B 1102 PHE cc_start: 0.8708 (p90) cc_final: 0.8098 (p90)
  outliers start: 9
  outliers final: 5
  residues processed: 127
  average time/residue: 0.2435
  time to fit residues: 38.3690
Evaluate side-chains
  100 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 95
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 20 optimal weight:    8.9990
   chunk 8 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   chunk 61 optimal weight:    5.9990
   chunk 42 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 63 optimal weight:    0.6980
   chunk 37 optimal weight:    0.3980
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1080 ASN
A1145 HIS
** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  46 GLN
** B1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.106842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.083119 restraints weight = 30609.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.085144 restraints weight = 24936.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.086808 restraints weight = 21233.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7109
moved from start:          0.2616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6409  Z= 0.207
  Angle     :  0.698   9.034   8622  Z= 0.361
  Chirality :  0.048   0.173    946
  Planarity :  0.004   0.042   1108
  Dihedral  : 10.159  88.476    912
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 21.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  5.92 %
    Favored  : 93.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -2.56 (0.29), residues: 768
  helix: -1.27 (0.28), residues: 297
  sheet: -1.65 (0.41), residues: 136
  loop : -2.00 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.011   0.002   HIS A1145 
 PHE   0.024   0.002   PHE A  12 
 TYR   0.023   0.002   TYR A1194 
 ARG   0.010   0.001   ARG B 160 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 130
  time to evaluate  : 0.665 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 MET cc_start: 0.8941 (tmm) cc_final: 0.8675 (tmm)
REVERT: A  175 MET cc_start: 0.8095 (mtt) cc_final: 0.7339 (mtt)
REVERT: A 1194 TYR cc_start: 0.7299 (p90) cc_final: 0.7050 (p90)
REVERT: B    1 MET cc_start: 0.7405 (tmm) cc_final: 0.6948 (tmm)
REVERT: B 1100 VAL cc_start: 0.8699 (p) cc_final: 0.8112 (p)
REVERT: B 1102 PHE cc_start: 0.8665 (p90) cc_final: 0.8083 (p90)
REVERT: C  592 GLN cc_start: 0.8325 (tp-100) cc_final: 0.8003 (tp-100)
  outliers start: 3
  outliers final: 0
  residues processed: 131
  average time/residue: 0.2497
  time to fit residues: 40.4684
Evaluate side-chains
  97 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    7.9990
   chunk 73 optimal weight:    2.9990
   chunk 28 optimal weight:    7.9990
   chunk 36 optimal weight:    4.9990
   chunk 17 optimal weight:    0.0470
   chunk 47 optimal weight:    0.8980
   chunk 16 optimal weight:   10.0000
   chunk 72 optimal weight:    9.9990
   chunk 22 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   overall best weight:    1.7682

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1030 GLN
** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1153 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 = 0.4158 r_free = 0.4158 target = 0.104718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.081808 restraints weight = 31603.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.083727 restraints weight = 26137.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.084834 restraints weight = 22346.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6409  Z= 0.243
  Angle     :  0.710  12.888   8622  Z= 0.364
  Chirality :  0.047   0.175    946
  Planarity :  0.004   0.028   1108
  Dihedral  :  9.909  88.446    912
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 26.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.16 %
    Favored  : 89.84 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  5.62 %
    Favored  : 94.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -2.54 (0.29), residues: 768
  helix: -1.29 (0.27), residues: 299
  sheet: -1.59 (0.43), residues: 130
  loop : -1.97 (0.35), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  66 
 PHE   0.032   0.002   PHE A  12 
 TYR   0.018   0.002   TYR A1194 
 ARG   0.011   0.001   ARG B 160 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 122
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 MET cc_start: 0.8968 (tmm) cc_final: 0.8705 (tmm)
REVERT: A  174 GLU cc_start: 0.8545 (mp0) cc_final: 0.8230 (mp0)
REVERT: A  175 MET cc_start: 0.7971 (mtt) cc_final: 0.7624 (mtt)
REVERT: B    1 MET cc_start: 0.7425 (tmm) cc_final: 0.7117 (tmm)
REVERT: B   47 PHE cc_start: 0.9177 (t80) cc_final: 0.8942 (t80)
REVERT: B 1100 VAL cc_start: 0.8698 (p) cc_final: 0.8036 (p)
REVERT: B 1102 PHE cc_start: 0.8602 (p90) cc_final: 0.7966 (p90)
REVERT: C  592 GLN cc_start: 0.8384 (tp-100) cc_final: 0.8009 (tp-100)
  outliers start: 2
  outliers final: 0
  residues processed: 122
  average time/residue: 0.2340
  time to fit residues: 35.6792
Evaluate side-chains
  94 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 74 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 75 optimal weight:    0.3980
   chunk 38 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 52 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0870
   chunk 8 optimal weight:    6.9990
   overall best weight:    0.5760

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  34 ASN
** B1144 GLN ** 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 = 0.4242 r_free = 0.4242 target = 0.109867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.087473 restraints weight = 32606.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.089394 restraints weight = 27023.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.090897 restraints weight = 23223.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7060
moved from start:          0.2889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6409  Z= 0.187
  Angle     :  0.668   9.802   8622  Z= 0.343
  Chirality :  0.048   0.177    946
  Planarity :  0.004   0.032   1108
  Dihedral  :  9.959  87.006    912
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 19.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.07 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  2.22 %
    Favored  : 97.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -2.21 (0.30), residues: 768
  helix: -0.98 (0.29), residues: 295
  sheet: -1.24 (0.43), residues: 130
  loop : -1.91 (0.34), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  66 
 PHE   0.025   0.002   PHE A  12 
 TYR   0.016   0.002   TYR A1085 
 ARG   0.006   0.001   ARG B 160 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 121
  time to evaluate  : 0.704 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 MET cc_start: 0.8858 (tmm) cc_final: 0.8594 (tmm)
REVERT: A  175 MET cc_start: 0.7774 (mtt) cc_final: 0.7475 (mtt)
REVERT: A 1064 LYS cc_start: 0.9291 (ptpp) cc_final: 0.8831 (mmmt)
REVERT: A 1097 PHE cc_start: 0.8881 (t80) cc_final: 0.8678 (t80)
REVERT: A 1194 TYR cc_start: 0.7079 (p90) cc_final: 0.6862 (p90)
REVERT: B   47 PHE cc_start: 0.9105 (t80) cc_final: 0.8878 (t80)
REVERT: B 1100 VAL cc_start: 0.8769 (p) cc_final: 0.8152 (p)
REVERT: B 1102 PHE cc_start: 0.8620 (p90) cc_final: 0.8017 (p90)
REVERT: B 1112 MET cc_start: 0.7824 (ppp) cc_final: 0.7623 (ppp)
REVERT: C  592 GLN cc_start: 0.8251 (tp-100) cc_final: 0.7871 (tp-100)
  outliers start: 2
  outliers final: 0
  residues processed: 122
  average time/residue: 0.2608
  time to fit residues: 39.6743
Evaluate side-chains
  94 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 51 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 36 optimal weight:    0.3980
   chunk 33 optimal weight:   10.0000
   overall best weight:    2.4788

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.102158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.079829 restraints weight = 31579.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 17)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.081298 restraints weight = 25671.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.082988 restraints weight = 22251.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
moved from start:          0.3301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6409  Z= 0.286
  Angle     :  0.759  14.214   8622  Z= 0.388
  Chirality :  0.049   0.162    946
  Planarity :  0.005   0.037   1108
  Dihedral  :  9.668  89.970    912
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 28.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.55 %
    Favored  : 89.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -2.46 (0.30), residues: 768
  helix: -1.19 (0.28), residues: 292
  sheet: -1.69 (0.45), residues: 125
  loop : -1.91 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  66 
 PHE   0.037   0.003   PHE A  12 
 TYR   0.020   0.003   TYR B1011 
 ARG   0.006   0.001   ARG B 160 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 MET cc_start: 0.8991 (tmm) cc_final: 0.8714 (tmm)
REVERT: A  175 MET cc_start: 0.7968 (mtt) cc_final: 0.7725 (mtt)
REVERT: B   11 PHE cc_start: 0.8503 (t80) cc_final: 0.8273 (t80)
REVERT: B 1057 MET cc_start: 0.6975 (ptt) cc_final: 0.5745 (ppp)
REVERT: B 1100 VAL cc_start: 0.8694 (p) cc_final: 0.7994 (p)
REVERT: B 1102 PHE cc_start: 0.8550 (p90) cc_final: 0.7937 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.2388
  time to fit residues: 35.7989
Evaluate side-chains
  92 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 0 optimal weight:    9.9990
   chunk 64 optimal weight:    0.0030
   chunk 45 optimal weight:    4.9990
   chunk 18 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9980
   chunk 53 optimal weight:    7.9990
   chunk 49 optimal weight:    0.8980
   chunk 46 optimal weight:    0.4980
   chunk 71 optimal weight:    6.9990
   overall best weight:    0.6590

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  46 GLN
** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1144 GLN ** 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 = 0.4221 r_free = 0.4221 target = 0.108178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.085543 restraints weight = 32871.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.087680 restraints weight = 26621.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.089422 restraints weight = 22443.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
moved from start:          0.3283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6409  Z= 0.190
  Angle     :  0.684   9.619   8622  Z= 0.351
  Chirality :  0.048   0.186    946
  Planarity :  0.004   0.046   1108
  Dihedral  :  9.363  87.401    912
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 19.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.07 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  2.66 %
    Favored  : 97.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -2.26 (0.30), residues: 768
  helix: -1.04 (0.28), residues: 297
  sheet: -1.27 (0.47), residues: 119
  loop : -1.91 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  66 
 PHE   0.022   0.002   PHE A  12 
 TYR   0.013   0.002   TYR B1140 
 ARG   0.008   0.001   ARG B 160 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 MET cc_start: 0.8919 (tmm) cc_final: 0.8681 (tmm)
REVERT: A  175 MET cc_start: 0.7784 (mtt) cc_final: 0.7520 (mtt)
REVERT: A 1064 LYS cc_start: 0.9280 (ptpp) cc_final: 0.8861 (mmmt)
REVERT: A 1097 PHE cc_start: 0.8898 (t80) cc_final: 0.8659 (t80)
REVERT: B   43 TYR cc_start: 0.7951 (m-80) cc_final: 0.7719 (m-80)
REVERT: B 1057 MET cc_start: 0.6455 (ptt) cc_final: 0.5983 (ppp)
REVERT: B 1100 VAL cc_start: 0.8739 (p) cc_final: 0.8085 (p)
REVERT: B 1102 PHE cc_start: 0.8544 (p90) cc_final: 0.7949 (p90)
REVERT: B 1112 MET cc_start: 0.7768 (ppp) cc_final: 0.7553 (ppp)
  outliers start: 1
  outliers final: 0
  residues processed: 127
  average time/residue: 0.2557
  time to fit residues: 40.1119
Evaluate side-chains
  93 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0670
   chunk 62 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 42 optimal weight:   10.0000
   chunk 51 optimal weight:    3.9990
   overall best weight:    0.6920

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  46 GLN
** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1153 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 = 0.4230 r_free = 0.4230 target = 0.109084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.087002 restraints weight = 32914.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.089120 restraints weight = 26672.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.090788 restraints weight = 22385.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7050
moved from start:          0.3350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6409  Z= 0.188
  Angle     :  0.683  10.465   8622  Z= 0.350
  Chirality :  0.048   0.183    946
  Planarity :  0.005   0.067   1108
  Dihedral  :  9.185  87.509    912
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 19.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -2.03 (0.30), residues: 768
  helix: -0.84 (0.29), residues: 293
  sheet: -1.19 (0.44), residues: 130
  loop : -1.76 (0.35), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  66 
 PHE   0.028   0.002   PHE A  12 
 TYR   0.016   0.002   TYR B1011 
 ARG   0.008   0.001   ARG B 160 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 MET cc_start: 0.8902 (tmm) cc_final: 0.8669 (tmm)
REVERT: A  175 MET cc_start: 0.7765 (mtt) cc_final: 0.7537 (mtt)
REVERT: A 1064 LYS cc_start: 0.9287 (ptpp) cc_final: 0.8779 (tptp)
REVERT: A 1097 PHE cc_start: 0.8915 (t80) cc_final: 0.8674 (t80)
REVERT: B    1 MET cc_start: 0.7150 (tmm) cc_final: 0.6917 (tmm)
REVERT: B   47 PHE cc_start: 0.9139 (t80) cc_final: 0.8892 (t80)
REVERT: B  160 ARG cc_start: 0.8996 (tmt170) cc_final: 0.8690 (tmt170)
REVERT: B 1026 TYR cc_start: 0.9201 (m-80) cc_final: 0.8802 (m-80)
REVERT: B 1057 MET cc_start: 0.6361 (ptt) cc_final: 0.5868 (ppp)
REVERT: B 1100 VAL cc_start: 0.8708 (p) cc_final: 0.7810 (p)
REVERT: B 1102 PHE cc_start: 0.8552 (p90) cc_final: 0.7957 (p90)
REVERT: B 1112 MET cc_start: 0.7824 (ppp) cc_final: 0.7588 (ppp)
REVERT: C  592 GLN cc_start: 0.8270 (tp-100) cc_final: 0.7962 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.2375
  time to fit residues: 35.2920
Evaluate side-chains
  96 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0060
   chunk 67 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 66 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   chunk 59 optimal weight:   10.0000
   chunk 44 optimal weight:    4.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    2.1802

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  46 GLN
** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1144 GLN ** 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 = 0.4159 r_free = 0.4159 target = 0.104483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.082559 restraints weight = 33620.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.084611 restraints weight = 27123.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.086181 restraints weight = 22797.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7170
moved from start:          0.3539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6409  Z= 0.261
  Angle     :  0.750  12.022   8622  Z= 0.387
  Chirality :  0.049   0.180    946
  Planarity :  0.006   0.093   1108
  Dihedral  :  9.238  89.163    912
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 27.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -2.29 (0.30), residues: 768
  helix: -1.01 (0.29), residues: 293
  sheet: -1.53 (0.45), residues: 119
  loop : -1.89 (0.35), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  66 
 PHE   0.030   0.003   PHE A  12 
 TYR   0.016   0.002   TYR A1194 
 ARG   0.008   0.001   ARG B 160 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 MET cc_start: 0.8930 (tmm) cc_final: 0.8669 (tmm)
REVERT: A  174 GLU cc_start: 0.8496 (mp0) cc_final: 0.8214 (mp0)
REVERT: A  175 MET cc_start: 0.7861 (mtt) cc_final: 0.7497 (mtt)
REVERT: A 1064 LYS cc_start: 0.9289 (ptpp) cc_final: 0.8812 (mmmt)
REVERT: A 1097 PHE cc_start: 0.8941 (t80) cc_final: 0.8713 (t80)
REVERT: B   43 TYR cc_start: 0.7826 (m-80) cc_final: 0.7586 (m-80)
REVERT: B   47 PHE cc_start: 0.9117 (t80) cc_final: 0.8913 (t80)
REVERT: B 1026 TYR cc_start: 0.9144 (m-80) cc_final: 0.8748 (m-80)
REVERT: B 1100 VAL cc_start: 0.8659 (p) cc_final: 0.8040 (p)
REVERT: B 1102 PHE cc_start: 0.8526 (p90) cc_final: 0.7910 (p90)
REVERT: C  592 GLN cc_start: 0.8340 (tp-100) cc_final: 0.8041 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.2408
  time to fit residues: 35.5205
Evaluate side-chains
  94 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 71 optimal weight:   10.0000
   chunk 68 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1153 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 = 0.4210 r_free = 0.4210 target = 0.107740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.085712 restraints weight = 33984.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.087797 restraints weight = 27516.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.089390 restraints weight = 23229.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7091
moved from start:          0.3560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6409  Z= 0.207
  Angle     :  0.705   9.794   8622  Z= 0.363
  Chirality :  0.048   0.196    946
  Planarity :  0.005   0.085   1108
  Dihedral  :  9.223  88.930    912
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 22.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.24 %
    Favored  : 90.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -2.16 (0.30), residues: 768
  helix: -0.86 (0.29), residues: 292
  sheet: -1.57 (0.44), residues: 119
  loop : -1.80 (0.35), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  66 
 PHE   0.029   0.002   PHE B 110 
 TYR   0.017   0.002   TYR A1194 
 ARG   0.007   0.001   ARG B  88 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.874 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 MET cc_start: 0.8897 (tmm) cc_final: 0.8645 (tmm)
REVERT: A  175 MET cc_start: 0.7658 (mtt) cc_final: 0.7416 (mtt)
REVERT: A 1064 LYS cc_start: 0.9265 (ptpp) cc_final: 0.8804 (mmmt)
REVERT: A 1097 PHE cc_start: 0.8980 (t80) cc_final: 0.8726 (t80)
REVERT: B    1 MET cc_start: 0.7286 (tmm) cc_final: 0.6929 (tmm)
REVERT: B   47 PHE cc_start: 0.9186 (t80) cc_final: 0.8961 (t80)
REVERT: B 1026 TYR cc_start: 0.9223 (m-80) cc_final: 0.8830 (m-80)
REVERT: B 1057 MET cc_start: 0.6198 (ptm) cc_final: 0.5306 (tmm)
REVERT: B 1099 ARG cc_start: 0.8418 (ttt90) cc_final: 0.7929 (ttm-80)
REVERT: B 1100 VAL cc_start: 0.8569 (p) cc_final: 0.7566 (p)
REVERT: B 1102 PHE cc_start: 0.8606 (p90) cc_final: 0.8025 (p90)
REVERT: B 1112 MET cc_start: 0.8032 (ppp) cc_final: 0.7783 (ppp)
REVERT: C  592 GLN cc_start: 0.8157 (tp-100) cc_final: 0.7860 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.2395
  time to fit residues: 36.3362
Evaluate side-chains
  97 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 41 optimal weight:    8.9990
   chunk 29 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 68 optimal weight:    7.9990
   chunk 19 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 22 optimal weight:   10.0000
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1153 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 = 0.4167 r_free = 0.4167 target = 0.105311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.083904 restraints weight = 34264.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.085876 restraints weight = 27556.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.087568 restraints weight = 23201.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
moved from start:          0.3672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6409  Z= 0.239
  Angle     :  0.738  12.006   8622  Z= 0.379
  Chirality :  0.049   0.190    946
  Planarity :  0.006   0.071   1108
  Dihedral  :  9.237  89.808    912
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 26.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.51 %
    Favored  : 90.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -2.29 (0.30), residues: 768
  helix: -0.94 (0.29), residues: 291
  sheet: -1.46 (0.44), residues: 121
  loop : -1.97 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  66 
 PHE   0.033   0.002   PHE B 110 
 TYR   0.019   0.002   TYR A1194 
 ARG   0.017   0.001   ARG B 160 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2201.37 seconds
wall clock time: 39 minutes 17.18 seconds (2357.18 seconds total)