Starting phenix.real_space_refine
on Fri Aug 22 18:12:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pq5_17820/08_2025/8pq5_17820.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pq5_17820/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pq5_17820/08_2025/8pq5_17820.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pq5_17820/08_2025/8pq5_17820.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pq5_17820/08_2025/8pq5_17820.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pq5_17820/08_2025/8pq5_17820.map"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.48, per 1000 atoms: 0.23
  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: 0.55
  Conformation dependent library (CDL) restraints added in 289.7 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 0.21
  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: 0.95

  Time building geometry restraints manager: 0.74 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:             0.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.060
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.540
-------------------------------------------------------------------------------
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= 0.137
  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 : 25.42
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.84 (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
 ARG   0.008   0.001   ARG B1154 
 TYR   0.013   0.002   TYR B1140 
 PHE   0.023   0.002   PHE A  12 
 HIS   0.006   0.001   HIS A1145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6409)
  covalent geometry    : angle       0.68967 ( 8622)
  hydrogen bonds       : bond        0.19143 (  258)
  hydrogen bonds       : angle       7.32558 (  723)

*********************** 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  : 0.276 
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: 0.8852 (t80)
REVERT: B  169 ASP cc_start: 0.8874 (p0) cc_final: 0.8592 (p0)
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: 0.8062 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1218
  time to fit residues: 16.1500
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  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    2.3588

-------------------------------------------------------------------------------
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
B1030 GLN
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.103646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.081830 restraints weight = 31533.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.083234 restraints weight = 25799.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.085023 restraints weight = 22403.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.086310 restraints weight = 19610.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.087235 restraints weight = 17491.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7162
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6409  Z= 0.191
  Angle     :  0.728  13.439   8622  Z= 0.371
  Chirality :  0.047   0.161    946
  Planarity :  0.005   0.081   1108
  Dihedral  : 10.310  86.419    912
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 25.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.51 %
    Favored  : 90.49 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  6.36 %
    Favored  : 93.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.26 (0.30), residues: 768
  helix: -1.10 (0.28), residues: 295
  sheet: -1.50 (0.41), residues: 138
  loop : -1.74 (0.36), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 155 
 TYR   0.025   0.003   TYR B  43 
 PHE   0.023   0.002   PHE A  12 
 HIS   0.005   0.001   HIS A1145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 6409)
  covalent geometry    : angle       0.72757 ( 8622)
  hydrogen bonds       : bond        0.04790 (  258)
  hydrogen bonds       : angle       6.56549 (  723)

*********************** 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
  120 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 116
  time to evaluate  : 0.301 
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   27 PHE cc_start: 0.8665 (t80) cc_final: 0.8166 (m-10)
REVERT: A  174 GLU cc_start: 0.8290 (mp0) cc_final: 0.7959 (mp0)
REVERT: A  175 MET cc_start: 0.8262 (mtt) cc_final: 0.7939 (mtt)
REVERT: A 1185 ILE cc_start: 0.9451 (mm) cc_final: 0.9105 (pt)
REVERT: A 1194 TYR cc_start: 0.7353 (p90) cc_final: 0.6999 (p90)
REVERT: B    1 MET cc_start: 0.7364 (tmm) cc_final: 0.6983 (tmm)
REVERT: B   11 PHE cc_start: 0.8235 (t80) cc_final: 0.7971 (t80)
REVERT: B   47 PHE cc_start: 0.9129 (t80) cc_final: 0.8582 (t80)
REVERT: B  160 ARG cc_start: 0.8918 (tmt170) cc_final: 0.8421 (tmt170)
REVERT: B 1100 VAL cc_start: 0.8721 (p) cc_final: 0.8047 (p)
REVERT: B 1102 PHE cc_start: 0.8728 (p90) cc_final: 0.8102 (p90)
REVERT: B 1193 ASN cc_start: 0.8893 (t0) cc_final: 0.8219 (p0)
REVERT: C  592 GLN cc_start: 0.8369 (tp-100) cc_final: 0.8011 (tp-100)
  outliers start: 4
  outliers final: 1
  residues processed: 118
  average time/residue: 0.1091
  time to fit residues: 16.1407
Evaluate side-chains
  91 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 90
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 67 optimal weight:    8.9990
   chunk 12 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   chunk 69 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 75 optimal weight:    5.9990
   chunk 74 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 35 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A1080 ASN
** A1145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  46 GLN
B1114 GLN
** B1132 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.099781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.077952 restraints weight = 30771.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.079926 restraints weight = 24989.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.081447 restraints weight = 21115.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.082641 restraints weight = 18425.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.083433 restraints weight = 16480.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.2639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   6409  Z= 0.225
  Angle     :  0.772  14.159   8622  Z= 0.397
  Chirality :  0.049   0.166    946
  Planarity :  0.005   0.041   1108
  Dihedral  :  9.919  87.118    912
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 30.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.90 %
    Favored  : 90.10 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  9.02 %
    Favored  : 90.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.65 (0.29), residues: 768
  helix: -1.38 (0.27), residues: 294
  sheet: -1.76 (0.42), residues: 138
  loop : -1.97 (0.35), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  88 
 TYR   0.025   0.003   TYR B 137 
 PHE   0.028   0.003   PHE A  12 
 HIS   0.012   0.002   HIS A1145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 ( 6409)
  covalent geometry    : angle       0.77193 ( 8622)
  hydrogen bonds       : bond        0.04770 (  258)
  hydrogen bonds       : angle       6.76117 (  723)

*********************** 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
  119 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 117
  time to evaluate  : 0.304 
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 1194 TYR cc_start: 0.7525 (p90) cc_final: 0.7243 (p90)
REVERT: B    1 MET cc_start: 0.7617 (tmm) cc_final: 0.7357 (tmm)
REVERT: B   11 PHE cc_start: 0.8465 (t80) cc_final: 0.8072 (t80)
REVERT: B   47 PHE cc_start: 0.9176 (t80) cc_final: 0.8650 (t80)
REVERT: B 1100 VAL cc_start: 0.8722 (p) cc_final: 0.8082 (p)
REVERT: B 1102 PHE cc_start: 0.8670 (p90) cc_final: 0.8058 (p90)
  outliers start: 2
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1232
  time to fit residues: 18.0101
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  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 61 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9980
   chunk 23 optimal weight:    8.9990
   chunk 59 optimal weight:    9.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 137 GLN
** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  46 GLN
B1114 GLN
** B1144 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 = 0.4111 r_free = 0.4111 target = 0.100896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.079089 restraints weight = 33318.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.080856 restraints weight = 27776.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.082379 restraints weight = 23898.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.083233 restraints weight = 20999.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.084393 restraints weight = 19150.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7185
moved from start:          0.2837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6409  Z= 0.182
  Angle     :  0.735  12.534   8622  Z= 0.376
  Chirality :  0.048   0.176    946
  Planarity :  0.004   0.031   1108
  Dihedral  :  9.911  88.045    912
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 27.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.29 %
    Favored  : 89.71 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  6.51 %
    Favored  : 93.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.63 (0.29), residues: 768
  helix: -1.38 (0.27), residues: 297
  sheet: -1.77 (0.41), residues: 133
  loop : -1.95 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 160 
 TYR   0.023   0.002   TYR A1194 
 PHE   0.023   0.002   PHE A  79 
 HIS   0.011   0.002   HIS B  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 6409)
  covalent geometry    : angle       0.73506 ( 8622)
  hydrogen bonds       : bond        0.04408 (  258)
  hydrogen bonds       : angle       6.58860 (  723)

*********************** 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
  120 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 118
  time to evaluate  : 0.273 
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: 0.8977 (tmm) cc_final: 0.8714 (tmm)
REVERT: A  131 ARG cc_start: 0.7936 (mmp80) cc_final: 0.7733 (mmp80)
REVERT: A  174 GLU cc_start: 0.8454 (mp0) cc_final: 0.8161 (mp0)
REVERT: A  175 MET cc_start: 0.8389 (mtt) cc_final: 0.8113 (mtt)
REVERT: A 1056 LYS cc_start: 0.9232 (tptp) cc_final: 0.8850 (tptp)
REVERT: B    1 MET cc_start: 0.7477 (tmm) cc_final: 0.7253 (tmm)
REVERT: B   47 PHE cc_start: 0.9114 (t80) cc_final: 0.8852 (t80)
REVERT: B  160 ARG cc_start: 0.8854 (tmt170) cc_final: 0.8465 (tmt170)
REVERT: B 1100 VAL cc_start: 0.8733 (p) cc_final: 0.8048 (p)
REVERT: B 1102 PHE cc_start: 0.8603 (p90) cc_final: 0.7979 (p90)
REVERT: C  592 GLN cc_start: 0.8436 (tp-100) cc_final: 0.8061 (tp-100)
  outliers start: 2
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1124
  time to fit residues: 16.4419
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  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 29 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 43 optimal weight:    9.9990
   chunk 11 optimal weight:    6.9990
   chunk 42 optimal weight:   10.0000
   chunk 62 optimal weight:    0.9980
   chunk 66 optimal weight:    7.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  46 GLN
B1114 GLN
** B1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.098765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.077172 restraints weight = 34609.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.079116 restraints weight = 28362.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.080611 restraints weight = 24044.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.081876 restraints weight = 20951.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.082592 restraints weight = 18678.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7225
moved from start:          0.3212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   6409  Z= 0.214
  Angle     :  0.772  13.434   8622  Z= 0.399
  Chirality :  0.049   0.171    946
  Planarity :  0.005   0.051   1108
  Dihedral  :  9.970  87.243    912
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 31.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.20 %
    Favored  : 88.80 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  5.92 %
    Favored  : 93.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.73 (0.29), residues: 768
  helix: -1.41 (0.28), residues: 291
  sheet: -1.86 (0.42), residues: 133
  loop : -2.04 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 160 
 TYR   0.021   0.003   TYR B1011 
 PHE   0.025   0.003   PHE A  12 
 HIS   0.008   0.001   HIS A1145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 ( 6409)
  covalent geometry    : angle       0.77194 ( 8622)
  hydrogen bonds       : bond        0.04617 (  258)
  hydrogen bonds       : angle       6.81291 (  723)

*********************** 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
  124 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.247 
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: 0.9016 (tmm) cc_final: 0.8740 (tmm)
REVERT: A 1056 LYS cc_start: 0.9245 (tptp) cc_final: 0.8794 (tptp)
REVERT: B    1 MET cc_start: 0.7599 (tmm) cc_final: 0.7268 (tmm)
REVERT: B   47 PHE cc_start: 0.9103 (t80) cc_final: 0.8903 (t80)
REVERT: B 1100 VAL cc_start: 0.8715 (p) cc_final: 0.8026 (p)
REVERT: B 1102 PHE cc_start: 0.8650 (p90) cc_final: 0.8065 (p90)
REVERT: C  592 GLN cc_start: 0.8409 (tp-100) cc_final: 0.7865 (tp-100)
  outliers start: 1
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1064
  time to fit residues: 16.4833
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  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 22 optimal weight:    9.9990
   chunk 67 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 58 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 54 optimal weight:    8.9990
   chunk 43 optimal weight:    9.9990
   chunk 51 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
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**
** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.101901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.079464 restraints weight = 33446.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.081559 restraints weight = 26831.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.083286 restraints weight = 22568.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.084288 restraints weight = 19459.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.085546 restraints weight = 17477.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7144
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6409  Z= 0.165
  Angle     :  0.725  12.113   8622  Z= 0.372
  Chirality :  0.048   0.180    946
  Planarity :  0.004   0.041   1108
  Dihedral  :  9.931  87.155    912
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 27.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.55 %
    Favored  : 89.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.50 (0.30), residues: 768
  helix: -1.20 (0.29), residues: 293
  sheet: -1.62 (0.41), residues: 136
  loop : -1.99 (0.35), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 160 
 TYR   0.015   0.002   TYR B1140 
 PHE   0.018   0.002   PHE A1218 
 HIS   0.017   0.002   HIS A1145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 6409)
  covalent geometry    : angle       0.72494 ( 8622)
  hydrogen bonds       : bond        0.04220 (  258)
  hydrogen bonds       : angle       6.49292 (  723)

*********************** 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
  122 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.248 
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: 0.8972 (tmm) cc_final: 0.8713 (tmm)
REVERT: B    1 MET cc_start: 0.7439 (tmm) cc_final: 0.6998 (tmm)
REVERT: B 1100 VAL cc_start: 0.8725 (p) cc_final: 0.7980 (p)
REVERT: B 1102 PHE cc_start: 0.8538 (p90) cc_final: 0.7930 (p90)
REVERT: C  592 GLN cc_start: 0.8371 (tp-100) cc_final: 0.7971 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1120
  time to fit residues: 17.3334
Evaluate side-chains
  89 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 41 optimal weight:   10.0000
   chunk 67 optimal weight:   10.0000
   chunk 64 optimal weight:    1.9990
   chunk 52 optimal weight:    0.3980
   chunk 24 optimal weight:    9.9990
   chunk 50 optimal weight:    0.8980
   chunk 72 optimal weight:    8.9990
   chunk 47 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0370
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  46 GLN
B 145 ASN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.108497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.085128 restraints weight = 31380.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.087323 restraints weight = 25283.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.089097 restraints weight = 21250.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.090522 restraints weight = 18423.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.091723 restraints weight = 16381.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7021
moved from start:          0.3170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6409  Z= 0.135
  Angle     :  0.691  10.207   8622  Z= 0.356
  Chirality :  0.048   0.189    946
  Planarity :  0.004   0.040   1108
  Dihedral  :  9.825  87.751    912
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 19.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.59 %
    Favored  : 91.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.25 (0.30), residues: 768
  helix: -0.97 (0.29), residues: 295
  sheet: -1.41 (0.42), residues: 126
  loop : -1.91 (0.35), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 160 
 TYR   0.013   0.002   TYR B1011 
 PHE   0.019   0.002   PHE B  53 
 HIS   0.006   0.001   HIS B  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6409)
  covalent geometry    : angle       0.69114 ( 8622)
  hydrogen bonds       : bond        0.03899 (  258)
  hydrogen bonds       : angle       6.06607 (  723)

*********************** 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
  120 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.252 
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: 0.8858 (tmm) cc_final: 0.8642 (tmm)
REVERT: A  174 GLU cc_start: 0.8555 (mp0) cc_final: 0.8306 (mp0)
REVERT: A  175 MET cc_start: 0.8392 (mtt) cc_final: 0.8137 (mtt)
REVERT: A 1064 LYS cc_start: 0.9229 (ptpp) cc_final: 0.8775 (mmmt)
REVERT: A 1085 TYR cc_start: 0.8891 (t80) cc_final: 0.8636 (t80)
REVERT: A 1097 PHE cc_start: 0.8895 (t80) cc_final: 0.8664 (t80)
REVERT: B   43 TYR cc_start: 0.7873 (m-80) cc_final: 0.7626 (m-80)
REVERT: B   47 PHE cc_start: 0.9080 (t80) cc_final: 0.8867 (t80)
REVERT: B 1026 TYR cc_start: 0.8986 (t80) cc_final: 0.8734 (t80)
REVERT: B 1100 VAL cc_start: 0.8775 (p) cc_final: 0.8073 (p)
REVERT: B 1102 PHE cc_start: 0.8549 (p90) cc_final: 0.7959 (p90)
REVERT: B 1112 MET cc_start: 0.7851 (ppp) cc_final: 0.7573 (ppp)
REVERT: C  592 GLN cc_start: 0.8138 (tp-100) cc_final: 0.7695 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1131
  time to fit residues: 17.0299
Evaluate side-chains
  98 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 56 optimal weight:    5.9990
   chunk 71 optimal weight:    9.9990
   chunk 30 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 40 optimal weight:    9.9990
   chunk 61 optimal weight:    0.5980
   chunk 68 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0980
   chunk 15 optimal weight:    6.9990
   chunk 67 optimal weight:    4.9990
   overall best weight:    3.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 137 GLN
** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  46 GLN
B1114 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 = 0.4103 r_free = 0.4103 target = 0.099699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.078701 restraints weight = 34200.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.080734 restraints weight = 27373.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.082440 restraints weight = 22933.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.083744 restraints weight = 19710.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.084812 restraints weight = 17402.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.3587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   6409  Z= 0.228
  Angle     :  0.801  13.561   8622  Z= 0.416
  Chirality :  0.050   0.171    946
  Planarity :  0.005   0.040   1108
  Dihedral  : 10.096  87.180    912
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 32.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.20 %
    Favored  : 88.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.71 (0.29), residues: 768
  helix: -1.37 (0.28), residues: 300
  sheet: -1.69 (0.45), residues: 119
  loop : -2.14 (0.34), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 131 
 TYR   0.019   0.003   TYR A 105 
 PHE   0.029   0.003   PHE A  12 
 HIS   0.008   0.001   HIS B  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 6409)
  covalent geometry    : angle       0.80098 ( 8622)
  hydrogen bonds       : bond        0.04625 (  258)
  hydrogen bonds       : angle       6.72912 (  723)

*********************** 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
  113 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 MET cc_start: 0.9002 (tmm) cc_final: 0.8733 (tmm)
REVERT: A 1097 PHE cc_start: 0.8900 (t80) cc_final: 0.8684 (t80)
REVERT: B    1 MET cc_start: 0.7801 (tmm) cc_final: 0.7490 (tmm)
REVERT: B  169 ASP cc_start: 0.8867 (p0) cc_final: 0.8570 (p0)
REVERT: B 1100 VAL cc_start: 0.8795 (p) cc_final: 0.8063 (p)
REVERT: B 1102 PHE cc_start: 0.8577 (p90) cc_final: 0.7986 (p90)
REVERT: C  592 GLN cc_start: 0.8333 (tp-100) cc_final: 0.7781 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1099
  time to fit residues: 15.6030
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  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 42 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0980
   chunk 55 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 41 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9980
   chunk 32 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  46 GLN
** B1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1153 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.104576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.082511 restraints weight = 33555.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.084698 restraints weight = 27059.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.086413 restraints weight = 22606.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.087755 restraints weight = 19453.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.088830 restraints weight = 17261.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7091
moved from start:          0.3553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6409  Z= 0.148
  Angle     :  0.720   9.684   8622  Z= 0.373
  Chirality :  0.049   0.188    946
  Planarity :  0.005   0.088   1108
  Dihedral  : 10.108  88.890    912
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 24.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.98 %
    Favored  : 91.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.40 (0.30), residues: 768
  helix: -1.15 (0.29), residues: 295
  sheet: -1.57 (0.41), residues: 133
  loop : -1.89 (0.35), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 160 
 TYR   0.018   0.002   TYR B1011 
 PHE   0.022   0.002   PHE A  12 
 HIS   0.006   0.001   HIS B  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 6409)
  covalent geometry    : angle       0.72017 ( 8622)
  hydrogen bonds       : bond        0.04076 (  258)
  hydrogen bonds       : angle       6.35802 (  723)

*********************** 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
  122 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.263 
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: symmetry clash
REVERT: A   42 MET cc_start: 0.8940 (tmm) cc_final: 0.8722 (tmm)
REVERT: A  174 GLU cc_start: 0.8470 (mp0) cc_final: 0.8171 (mp0)
REVERT: A  175 MET cc_start: 0.8427 (mtt) cc_final: 0.8172 (mtt)
REVERT: A 1097 PHE cc_start: 0.8909 (t80) cc_final: 0.8682 (t80)
REVERT: A 1194 TYR cc_start: 0.7338 (p90) cc_final: 0.6934 (p90)
REVERT: B    1 MET cc_start: 0.7638 (tmm) cc_final: 0.7312 (tmm)
REVERT: B   43 TYR cc_start: 0.7801 (m-80) cc_final: 0.7587 (m-80)
REVERT: B   47 PHE cc_start: 0.9138 (t80) cc_final: 0.8930 (t80)
REVERT: B 1100 VAL cc_start: 0.8731 (p) cc_final: 0.7995 (p)
REVERT: B 1102 PHE cc_start: 0.8512 (p90) cc_final: 0.7888 (p90)
REVERT: B 1112 MET cc_start: 0.7936 (ppp) cc_final: 0.7649 (ppp)
REVERT: C  592 GLN cc_start: 0.8261 (tp-100) cc_final: 0.7872 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.0979
  time to fit residues: 15.0271
Evaluate side-chains
  99 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0970
   chunk 38 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 36 optimal weight:    0.6980
   chunk 67 optimal weight:    9.9990
   chunk 48 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
A1183 GLN
B  46 GLN
B1144 GLN
B1153 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.107487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.084783 restraints weight = 33053.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.087009 restraints weight = 26693.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.088632 restraints weight = 22459.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.090018 restraints weight = 19578.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.091105 restraints weight = 17404.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7041
moved from start:          0.3625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6409  Z= 0.138
  Angle     :  0.714   9.569   8622  Z= 0.369
  Chirality :  0.048   0.195    946
  Planarity :  0.005   0.071   1108
  Dihedral  :  9.905  89.096    912
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 20.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.72 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  0.59 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.22 (0.30), residues: 768
  helix: -1.00 (0.29), residues: 294
  sheet: -1.29 (0.42), residues: 127
  loop : -1.87 (0.35), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 160 
 TYR   0.033   0.002   TYR B1026 
 PHE   0.019   0.002   PHE C 600 
 HIS   0.005   0.001   HIS B  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 6409)
  covalent geometry    : angle       0.71404 ( 8622)
  hydrogen bonds       : bond        0.04012 (  258)
  hydrogen bonds       : angle       6.16244 (  723)

********************** 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
  125 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 123
  time to evaluate  : 0.228 
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: 0.8861 (tmm) cc_final: 0.8644 (tmm)
REVERT: A  173 LYS cc_start: 0.7136 (pttm) cc_final: 0.6865 (pttm)
REVERT: A  174 GLU cc_start: 0.8446 (mp0) cc_final: 0.8131 (mp0)
REVERT: A  175 MET cc_start: 0.8296 (mtt) cc_final: 0.8048 (mtt)
REVERT: A 1097 PHE cc_start: 0.8935 (t80) cc_final: 0.8686 (t80)
REVERT: A 1194 TYR cc_start: 0.7096 (p90) cc_final: 0.6723 (p90)
REVERT: B    1 MET cc_start: 0.7482 (tmm) cc_final: 0.7031 (tmm)
REVERT: B   43 TYR cc_start: 0.7759 (m-80) cc_final: 0.7532 (m-80)
REVERT: B   47 PHE cc_start: 0.9069 (t80) cc_final: 0.8851 (t80)
REVERT: B  130 PHE cc_start: 0.7973 (m-80) cc_final: 0.7737 (m-80)
REVERT: B  160 ARG cc_start: 0.8873 (tmt170) cc_final: 0.8482 (tmt170)
REVERT: B 1099 ARG cc_start: 0.7654 (mmt90) cc_final: 0.7399 (ttm-80)
REVERT: B 1100 VAL cc_start: 0.8740 (p) cc_final: 0.7727 (p)
REVERT: B 1102 PHE cc_start: 0.8529 (p90) cc_final: 0.7951 (p90)
REVERT: B 1112 MET cc_start: 0.7938 (ppp) cc_final: 0.7692 (ppp)
REVERT: C  592 GLN cc_start: 0.8217 (tp-100) cc_final: 0.7819 (tp-100)
  outliers start: 2
  outliers final: 0
  residues processed: 125
  average time/residue: 0.0881
  time to fit residues: 13.9729
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  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 59 optimal weight:    8.9990
   chunk 70 optimal weight:    6.9990
   chunk 43 optimal weight:    9.9990
   chunk 50 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0870
   chunk 44 optimal weight:    8.9990
   chunk 12 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    1.7562

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

Flipped N/Q/H residues before XYZ refinement:
** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  46 GLN
** 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 = 0.4180 r_free = 0.4180 target = 0.104829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.082975 restraints weight = 32984.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.085039 restraints weight = 26637.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.086634 restraints weight = 22449.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.087957 restraints weight = 19491.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.089088 restraints weight = 17296.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
moved from start:          0.3655

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= 0.165
  Angle     :  0.746  11.394   8622  Z= 0.385
  Chirality :  0.048   0.190    946
  Planarity :  0.005   0.063   1108
  Dihedral  :  9.804  88.574    912
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 25.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.37 (0.30), residues: 768
  helix: -1.11 (0.29), residues: 293
  sheet: -1.40 (0.43), residues: 119
  loop : -1.96 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 160 
 TYR   0.019   0.002   TYR B1011 
 PHE   0.021   0.002   PHE B  53 
 HIS   0.005   0.001   HIS B  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 6409)
  covalent geometry    : angle       0.74560 ( 8622)
  hydrogen bonds       : bond        0.04139 (  258)
  hydrogen bonds       : angle       6.35472 (  723)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1176.04 seconds
wall clock time: 21 minutes 15.75 seconds (1275.75 seconds total)