Starting phenix.real_space_refine
on Fri Aug 22 21:59:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pd7_17602/08_2025/8pd7_17602.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pd7_17602/08_2025/8pd7_17602.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pd7_17602/08_2025/8pd7_17602.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pd7_17602/08_2025/8pd7_17602.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pd7_17602/08_2025/8pd7_17602.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pd7_17602/08_2025/8pd7_17602.cif"
  }
  resolution = 3.4
  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=   0.002 sd=   0.028
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      41      5.16       5
     C    5304      2.51       5
     N    1347      2.21       5
     O    1429      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8121
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 8121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1028, 8121
          Classifications: {'peptide': 1028}
          Link IDs: {'PTRANS': 31, 'TRANS': 996}
          Chain breaks: 5
  Time building chain proxies: 1.96, per 1000 atoms: 0.24
  Number of scatterers: 8121
  At special positions: 0
  Unit cell: (83.6, 116.204, 126.236, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      41     16.00
     O    1429      8.00
     N    1347      7.00
     C    5304      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: 0.63
  Conformation dependent library (CDL) restraints added in 440.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1938

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 4 sheets defined
      77.1% alpha, 4.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 76 through 95
      removed outlier: 3.667A  pdb=" N   PHE A  80 " --> pdb=" O   LYS A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 118
      removed outlier: 4.005A  pdb=" N   VAL A 105 " --> pdb=" O   PRO A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.521A  pdb=" N   GLU A 124 " --> pdb=" O   VAL A 120 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLU A 125 " --> pdb=" O   PRO A 121 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   HIS A 126 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   ASP A 129 " --> pdb=" O   GLU A 125 " (cutoff:3.500A)
      removed outlier: 5.844A  pdb=" N   VAL A 130 " --> pdb=" O   HIS A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 154
      Proline residue:  A 144  - end of helix
      removed outlier: 3.855A  pdb=" N   MET A 154 " --> pdb=" O   SER A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 162
    Processing helix  chain 'A' and resid 162 through 188
      removed outlier: 3.923A  pdb=" N   LEU A 174 " --> pdb=" O   ALA A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 207
      removed outlier: 3.545A  pdb=" N   ALA A 207 " --> pdb=" O   ALA A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 221
    Processing helix  chain 'A' and resid 223 through 254
      removed outlier: 3.596A  pdb=" N   MET A 251 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 273
    Processing helix  chain 'A' and resid 273 through 291
    Processing helix  chain 'A' and resid 296 through 317
      removed outlier: 3.589A  pdb=" N   GLU A 300 " --> pdb=" O   ASP A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 337
    Processing helix  chain 'A' and resid 338 through 341
    Processing helix  chain 'A' and resid 342 through 376
      removed outlier: 3.593A  pdb=" N   PHE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ARG A 351 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 380
    Processing helix  chain 'A' and resid 381 through 411
      removed outlier: 4.145A  pdb=" N   TRP A 385 " --> pdb=" O   ASP A 381 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   PHE A 386 " --> pdb=" O   LYS A 382 " (cutoff:3.500A)
      Proline residue:  A 408  - end of helix
    Processing helix  chain 'A' and resid 418 through 428
    Processing helix  chain 'A' and resid 432 through 447
      removed outlier: 3.679A  pdb=" N   GLY A 447 " --> pdb=" O   GLU A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 469
      removed outlier: 4.284A  pdb=" N   SER A 453 " --> pdb=" O   ASP A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 481
      removed outlier: 4.890A  pdb=" N   GLN A 475 " --> pdb=" O   ALA A 471 " (cutoff:3.500A)
      removed outlier: 4.802A  pdb=" N   THR A 476 " --> pdb=" O   THR A 472 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ARG A 479 " --> pdb=" O   GLN A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 514
      removed outlier: 3.728A  pdb=" N   SER A 514 " --> pdb=" O   ASN A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 519
      removed outlier: 3.749A  pdb=" N   ALA A 519 " --> pdb=" O   ARG A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 530
    Processing helix  chain 'A' and resid 571 through 600
    Processing helix  chain 'A' and resid 604 through 621
    Processing helix  chain 'A' and resid 627 through 632
    Processing helix  chain 'A' and resid 633 through 635
      No H-bonds generated for 'chain 'A' and resid 633 through 635'
    Processing helix  chain 'A' and resid 639 through 653
    Processing helix  chain 'A' and resid 677 through 706
      removed outlier: 4.406A  pdb=" N   GLU A 681 " --> pdb=" O   HIS A 677 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   VAL A 682 " --> pdb=" O   MET A 678 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   VAL A 693 " --> pdb=" O   VAL A 689 " (cutoff:3.500A)
      Proline residue:  A 694  - end of helix
      removed outlier: 4.073A  pdb=" N   PHE A 699 " --> pdb=" O   ILE A 695 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   VAL A 700 " --> pdb=" O   ILE A 696 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ALA A 706 " --> pdb=" O   GLN A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 755
      removed outlier: 3.837A  pdb=" N   SER A 735 " --> pdb=" O   ALA A 731 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   ASN A 736 " --> pdb=" O   LEU A 732 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   TYR A 737 " --> pdb=" O   ARG A 733 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   VAL A 738 " --> pdb=" O   ILE A 734 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   GLY A 753 " --> pdb=" O   VAL A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 756 through 760
      removed outlier: 3.722A  pdb=" N   ILE A 759 " --> pdb=" O   ARG A 756 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 783
    Processing helix  chain 'A' and resid 797 through 802
    Processing helix  chain 'A' and resid 802 through 812
      removed outlier: 3.865A  pdb=" N   ARG A 806 " --> pdb=" O   PHE A 802 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   GLY A 807 " --> pdb=" O   ARG A 803 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ARG A 809 " --> pdb=" O   LEU A 805 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   MET A 810 " --> pdb=" O   ARG A 806 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 813 through 854
      Proline residue:  A 819  - end of helix
      removed outlier: 3.531A  pdb=" N   GLN A 832 " --> pdb=" O   LYS A 828 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   LEU A 835 " --> pdb=" O   ASN A 831 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LYS A 852 " --> pdb=" O   GLU A 848 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 857
      No H-bonds generated for 'chain 'A' and resid 855 through 857'
    Processing helix  chain 'A' and resid 860 through 889
      removed outlier: 3.783A  pdb=" N   GLN A 877 " --> pdb=" O   THR A 873 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ARG A 887 " --> pdb=" O   GLY A 883 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 919
    Processing helix  chain 'A' and resid 925 through 940
    Processing helix  chain 'A' and resid 941 through 944
    Processing helix  chain 'A' and resid 952 through 959
    Processing helix  chain 'A' and resid 966 through 975
    Processing helix  chain 'A' and resid 1043 through 1050
    Processing helix  chain 'A' and resid 1070 through 1080
    Processing helix  chain 'A' and resid 1085 through 1108
      removed outlier: 3.562A  pdb=" N   ARG A1097 " --> pdb=" O   VAL A1093 " (cutoff:3.500A)
      Proline residue:  A1101  - end of helix
      removed outlier: 3.822A  pdb=" N   GLN A1106 " --> pdb=" O   LEU A1102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1113 through 1123
    Processing helix  chain 'A' and resid 1179 through 1183
    Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982
      removed outlier: 6.251A  pdb=" N   GLN A1064 " --> pdb=" O   VAL A1002 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989
      removed outlier: 6.841A  pdb=" N   VAL A 987 " --> pdb=" O   CYS A1059 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   CYS A1059 " --> pdb=" O   VAL A 987 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   VAL A 989 " --> pdb=" O   VAL A1057 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1126
      removed outlier: 6.550A  pdb=" N   ARG A1185 " --> pdb=" O   ILE A1148 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ASP A1144 " --> pdb=" O   VAL A1189 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1134 through 1136
      removed outlier: 3.604A  pdb=" N   TYR A1153 " --> pdb=" O   THR A1175 " (cutoff:3.500A)

    581 hydrogen bonds defined for protein.
    1701 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.61

  Time building geometry restraints manager: 0.87 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1303
        1.32 -     1.44: 2097
        1.44 -     1.56: 4804
        1.56 -     1.69: 0
        1.69 -     1.81: 76
  Bond restraints: 8280
  Sorted by residual:
  bond pdb=" C   ASN A 237 "
       pdb=" O   ASN A 237 "
    ideal  model  delta    sigma   weight residual
    1.236  1.193  0.044 1.15e-02 7.56e+03 1.44e+01
  bond pdb=" CA  ALA A 241 "
       pdb=" CB  ALA A 241 "
    ideal  model  delta    sigma   weight residual
    1.531  1.484  0.047 1.56e-02 4.11e+03 9.15e+00
  bond pdb=" N   HIS A 981 "
       pdb=" CA  HIS A 981 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.21e-02 6.83e+03 7.67e+00
  bond pdb=" N   LEU A 979 "
       pdb=" CA  LEU A 979 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.032 1.24e-02 6.50e+03 6.50e+00
  bond pdb=" N   VAL A1063 "
       pdb=" CA  VAL A1063 "
    ideal  model  delta    sigma   weight residual
    1.458  1.486 -0.028 1.14e-02 7.69e+03 6.17e+00
  ... (remaining 8275 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 11076
        2.08 -     4.16: 136
        4.16 -     6.23: 16
        6.23 -     8.31: 3
        8.31 -    10.39: 1
  Bond angle restraints: 11232
  Sorted by residual:
  angle pdb=" CA  ASN A 237 "
        pdb=" CB  ASN A 237 "
        pdb=" CG  ASN A 237 "
      ideal   model   delta    sigma   weight residual
     112.60  118.31   -5.71 1.00e+00 1.00e+00 3.26e+01
  angle pdb=" N   ALA A 241 "
        pdb=" CA  ALA A 241 "
        pdb=" C   ALA A 241 "
      ideal   model   delta    sigma   weight residual
     112.90  106.40    6.50 1.31e+00 5.83e-01 2.46e+01
  angle pdb=" CA  ASN A 237 "
        pdb=" C   ASN A 237 "
        pdb=" O   ASN A 237 "
      ideal   model   delta    sigma   weight residual
     120.82  115.81    5.01 1.05e+00 9.07e-01 2.27e+01
  angle pdb=" CA  GLN A1064 "
        pdb=" C   GLN A1064 "
        pdb=" O   GLN A1064 "
      ideal   model   delta    sigma   weight residual
     121.16  116.13    5.03 1.13e+00 7.83e-01 1.98e+01
  angle pdb=" CA  LEU A 236 "
        pdb=" C   LEU A 236 "
        pdb=" O   LEU A 236 "
      ideal   model   delta    sigma   weight residual
     120.42  115.77    4.65 1.06e+00 8.90e-01 1.92e+01
  ... (remaining 11227 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 4557
       17.64 -    35.27: 312
       35.27 -    52.91: 57
       52.91 -    70.55: 10
       70.55 -    88.18: 6
  Dihedral angle restraints: 4942
    sinusoidal: 1953
      harmonic: 2989
  Sorted by residual:
  dihedral pdb=" CA  LEU A 801 "
           pdb=" C   LEU A 801 "
           pdb=" N   PHE A 802 "
           pdb=" CA  PHE A 802 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.16  -21.84     0      5.00e+00 4.00e-02 1.91e+01
  dihedral pdb=" CA  GLN A 624 "
           pdb=" C   GLN A 624 "
           pdb=" N   PHE A 625 "
           pdb=" CA  PHE A 625 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.57   21.43     0      5.00e+00 4.00e-02 1.84e+01
  dihedral pdb=" CA  ILE A1161 "
           pdb=" C   ILE A1161 "
           pdb=" N   ARG A1162 "
           pdb=" CA  ARG A1162 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.88  -20.12     0      5.00e+00 4.00e-02 1.62e+01
  ... (remaining 4939 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1086
       0.047 -    0.094: 218
       0.094 -    0.141: 36
       0.141 -    0.188: 8
       0.188 -    0.236: 1
  Chirality restraints: 1349
  Sorted by residual:
  chirality pdb=" CA  ASN A 237 "
            pdb=" N   ASN A 237 "
            pdb=" C   ASN A 237 "
            pdb=" CB  ASN A 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CA  VAL A1063 "
            pdb=" N   VAL A1063 "
            pdb=" C   VAL A1063 "
            pdb=" CB  VAL A1063 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.47e-01
  chirality pdb=" CA  LEU A 980 "
            pdb=" N   LEU A 980 "
            pdb=" C   LEU A 980 "
            pdb=" CB  LEU A 980 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.42e-01
  ... (remaining 1346 not shown)

  Planarity restraints: 1385
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 237 "    0.011 2.00e-02 2.50e+03   2.35e-02 5.52e+00
        pdb=" C   ASN A 237 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   ASN A 237 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ASP A 238 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 236 "   -0.010 2.00e-02 2.50e+03   2.10e-02 4.39e+00
        pdb=" C   LEU A 236 "    0.036 2.00e-02 2.50e+03
        pdb=" O   LEU A 236 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ASN A 237 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 857 "    0.010 2.00e-02 2.50e+03   1.99e-02 3.96e+00
        pdb=" C   MET A 857 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   MET A 857 "    0.013 2.00e-02 2.50e+03
        pdb=" N   VAL A 858 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1382 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1952
        2.80 -     3.33: 8432
        3.33 -     3.85: 12814
        3.85 -     4.38: 14570
        4.38 -     4.90: 25697
  Nonbonded interactions: 63465
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS A1120 "
            pdb=" OD2 ASP A1144 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" OG  SER A 259 "
            pdb=" OE1 GLN A 263 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" O   PHE A  80 "
            pdb=" OG  SER A  84 "
     model   vdw
     2.435 3.040
  nonbonded pdb=" OH  TYR A 392 "
            pdb=" OD1 ASN A 470 "
     model   vdw
     2.452 3.040
  nonbonded pdb=" O   PRO A  75 "
            pdb=" CD1 ILE A  78 "
     model   vdw
     2.459 3.460
  ... (remaining 63460 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.250
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
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   0.047   8280  Z= 0.174
  Angle     :  0.592  10.387  11232  Z= 0.361
  Chirality :  0.040   0.236   1349
  Planarity :  0.004   0.037   1385
  Dihedral  : 12.691  88.183   3004
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  5.21 %
    Favored  : 94.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.39 (0.26), residues: 1016
  helix:  1.29 (0.19), residues: 722
  sheet:  0.19 (0.78), residues: 36
  loop :  0.21 (0.42), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 899 
 TYR   0.013   0.001   TYR A1153 
 PHE   0.024   0.001   PHE A 802 
 TRP   0.012   0.001   TRP A1112 
 HIS   0.005   0.001   HIS A1120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8280)
  covalent geometry    : angle       0.59189 (11232)
  hydrogen bonds       : bond        0.14128 (  581)
  hydrogen bonds       : angle       5.43145 ( 1701)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 284
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.7403 (mm) cc_final: 0.7200 (mt)
REVERT: A  155 ASP cc_start: 0.7233 (t70) cc_final: 0.6805 (t70)
REVERT: A  187 ASN cc_start: 0.7634 (m-40) cc_final: 0.7415 (m-40)
REVERT: A  218 LYS cc_start: 0.7359 (ttmm) cc_final: 0.7093 (ttmm)
REVERT: A  231 GLU cc_start: 0.7340 (tt0) cc_final: 0.7088 (tt0)
REVERT: A  233 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7274 (tt0)
REVERT: A  234 SER cc_start: 0.8043 (t) cc_final: 0.7837 (p)
REVERT: A  250 LYS cc_start: 0.7208 (mttp) cc_final: 0.6981 (mptt)
REVERT: A  273 VAL cc_start: 0.8169 (t) cc_final: 0.7865 (p)
REVERT: A  295 ASN cc_start: 0.7970 (t0) cc_final: 0.7757 (t0)
REVERT: A  337 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7516 (mm-30)
REVERT: A  354 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6926 (tm-30)
REVERT: A  383 MET cc_start: 0.7845 (mmm) cc_final: 0.7493 (tpp)
REVERT: A  443 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7363 (tm-30)
REVERT: A  475 GLN cc_start: 0.8253 (tp40) cc_final: 0.8039 (tp-100)
REVERT: A  579 MET cc_start: 0.6184 (tpp) cc_final: 0.5951 (tpp)
REVERT: A  580 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6892 (tp30)
REVERT: A  587 LEU cc_start: 0.7887 (mt) cc_final: 0.7497 (mp)
REVERT: A  591 LYS cc_start: 0.7785 (mtpp) cc_final: 0.7471 (mtmm)
REVERT: A  599 GLU cc_start: 0.6528 (mt-10) cc_final: 0.5915 (mm-30)
REVERT: A  646 ARG cc_start: 0.7246 (ttp-170) cc_final: 0.6947 (ttp-110)
REVERT: A  684 ILE cc_start: 0.8067 (mm) cc_final: 0.7861 (mt)
REVERT: A  697 MET cc_start: 0.5853 (tpt) cc_final: 0.5546 (tpt)
REVERT: A  765 LYS cc_start: 0.7587 (mtmt) cc_final: 0.7111 (mttm)
REVERT: A  766 PHE cc_start: 0.6959 (t80) cc_final: 0.6746 (t80)
REVERT: A  828 LYS cc_start: 0.8308 (mmmt) cc_final: 0.7882 (mppt)
REVERT: A  849 GLU cc_start: 0.7288 (mt-10) cc_final: 0.7063 (mt-10)
REVERT: A  857 MET cc_start: 0.6708 (ttm) cc_final: 0.6484 (ttm)
REVERT: A  881 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7462 (mm-30)
REVERT: A  954 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7335 (mt-10)
REVERT: A 1033 GLU cc_start: 0.7506 (tt0) cc_final: 0.7287 (tt0)
REVERT: A 1044 GLU cc_start: 0.7509 (mt-10) cc_final: 0.6531 (mt-10)
REVERT: A 1050 LYS cc_start: 0.8050 (mttt) cc_final: 0.7750 (mttp)
REVERT: A 1051 LYS cc_start: 0.8292 (tttt) cc_final: 0.7981 (mttp)
REVERT: A 1054 ASN cc_start: 0.7848 (t0) cc_final: 0.7391 (t0)
REVERT: A 1060 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7799 (mm-30)
REVERT: A 1105 GLU cc_start: 0.7035 (tm-30) cc_final: 0.6738 (tm-30)
REVERT: A 1122 GLU cc_start: 0.7949 (tp30) cc_final: 0.7215 (tt0)
REVERT: A 1143 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6217 (mt-10)
REVERT: A 1144 ASP cc_start: 0.7472 (p0) cc_final: 0.7058 (p0)
REVERT: A 1183 GLU cc_start: 0.7561 (tt0) cc_final: 0.6905 (mt-10)
REVERT: A 1185 ARG cc_start: 0.7760 (mmt-90) cc_final: 0.7517 (mmm-85)
REVERT: A 1188 VAL cc_start: 0.8301 (m) cc_final: 0.8056 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 285
  average time/residue: 0.1000
  time to fit residues: 37.7244
Evaluate side-chains
  255 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 254
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1195 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    6.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 350 HIS
A 636 GLN
A 877 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.131152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.110964 restraints weight = 11421.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 1.58
r_work: 0.3174 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8280  Z= 0.173
  Angle     :  0.526   6.915  11232  Z= 0.282
  Chirality :  0.040   0.140   1349
  Planarity :  0.004   0.043   1385
  Dihedral  :  4.246  20.730   1099
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  :  9.51 %
    Favored  : 87.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.75 (0.26), residues: 1016
  helix:  1.58 (0.19), residues: 729
  sheet: -0.27 (0.72), residues: 43
  loop :  0.35 (0.43), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 128 
 TYR   0.018   0.001   TYR A1153 
 PHE   0.019   0.002   PHE A 598 
 TRP   0.015   0.002   TRP A 635 
 HIS   0.012   0.002   HIS A 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 8280)
  covalent geometry    : angle       0.52620 (11232)
  hydrogen bonds       : bond        0.04829 (  581)
  hydrogen bonds       : angle       4.15326 ( 1701)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 246
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A  113 LEU cc_start: 0.8767 (tp) cc_final: 0.8506 (tt)
REVERT: A  155 ASP cc_start: 0.7743 (t70) cc_final: 0.7541 (t70)
REVERT: A  205 MET cc_start: 0.7824 (mtp) cc_final: 0.7515 (mmt)
REVERT: A  218 LYS cc_start: 0.7851 (ttmm) cc_final: 0.7573 (ttmm)
REVERT: A  233 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7570 (tt0)
REVERT: A  443 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7804 (tm-30)
REVERT: A  492 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8020 (mm)
REVERT: A  533 SER cc_start: 0.8503 (p) cc_final: 0.7758 (m)
REVERT: A  579 MET cc_start: 0.6620 (tpp) cc_final: 0.6313 (tpp)
REVERT: A  621 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6782 (mt-10)
REVERT: A  646 ARG cc_start: 0.7599 (ttp-170) cc_final: 0.7356 (ttp-170)
REVERT: A  697 MET cc_start: 0.6166 (tpt) cc_final: 0.5848 (tpt)
REVERT: A  847 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6928 (mm-30)
REVERT: A  871 SER cc_start: 0.8090 (t) cc_final: 0.7617 (m)
REVERT: A 1050 LYS cc_start: 0.8389 (mttt) cc_final: 0.8156 (mttp)
REVERT: A 1054 ASN cc_start: 0.7919 (t0) cc_final: 0.7475 (t0)
REVERT: A 1119 LEU cc_start: 0.8542 (mt) cc_final: 0.8089 (mt)
REVERT: A 1143 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6694 (mt-10)
REVERT: A 1144 ASP cc_start: 0.7560 (p0) cc_final: 0.7163 (p0)
REVERT: A 1171 VAL cc_start: 0.8221 (t) cc_final: 0.7720 (m)
REVERT: A 1183 GLU cc_start: 0.7585 (tt0) cc_final: 0.7202 (mt-10)
REVERT: A 1190 ARG cc_start: 0.7532 (mmt90) cc_final: 0.7325 (mmt90)
  outliers start: 23
  outliers final: 10
  residues processed: 250
  average time/residue: 0.0894
  time to fit residues: 29.8040
Evaluate side-chains
  237 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 226
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  742 ILE
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  838 ASP
Chi-restraints excluded: chain A residue 1062 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 58 optimal weight:   10.0000
   chunk 16 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0980
   chunk 4 optimal weight:    3.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 877 GLN
** A1133 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 = 0.3598 r_free = 0.3598 target = 0.130086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.110758 restraints weight = 11409.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 1.48
r_work: 0.3203 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3059 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8280  Z= 0.136
  Angle     :  0.474   6.825  11232  Z= 0.256
  Chirality :  0.038   0.139   1349
  Planarity :  0.004   0.044   1385
  Dihedral  :  3.921  18.517   1097
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 11.66 %
    Favored  : 85.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.00 (0.26), residues: 1016
  helix:  1.78 (0.19), residues: 736
  sheet:  0.15 (0.75), residues: 42
  loop :  0.26 (0.43), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 479 
 TYR   0.015   0.001   TYR A1153 
 PHE   0.015   0.002   PHE A 598 
 TRP   0.015   0.001   TRP A 278 
 HIS   0.010   0.001   HIS A1133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 8280)
  covalent geometry    : angle       0.47424 (11232)
  hydrogen bonds       : bond        0.04193 (  581)
  hydrogen bonds       : angle       3.94748 ( 1701)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 226
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 ASP cc_start: 0.7851 (t70) cc_final: 0.7576 (p0)
REVERT: A  205 MET cc_start: 0.7731 (mtp) cc_final: 0.7409 (mmm)
REVERT: A  218 LYS cc_start: 0.7784 (ttmm) cc_final: 0.7520 (ttmm)
REVERT: A  233 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7435 (tt0)
REVERT: A  492 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8049 (mm)
REVERT: A  531 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6933 (tm-30)
REVERT: A  579 MET cc_start: 0.6628 (tpp) cc_final: 0.6307 (tpp)
REVERT: A  646 ARG cc_start: 0.7473 (ttp-170) cc_final: 0.7242 (ttp-170)
REVERT: A  688 ILE cc_start: 0.8204 (mt) cc_final: 0.7999 (mp)
REVERT: A  697 MET cc_start: 0.6103 (tpt) cc_final: 0.5770 (tpt)
REVERT: A  814 THR cc_start: 0.8510 (p) cc_final: 0.8281 (m)
REVERT: A  847 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6808 (mm-30)
REVERT: A  866 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7248 (tm-30)
REVERT: A  871 SER cc_start: 0.7987 (t) cc_final: 0.7636 (m)
REVERT: A  916 LEU cc_start: 0.8443 (mt) cc_final: 0.8242 (mp)
REVERT: A  932 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7883 (tp)
REVERT: A 1104 MET cc_start: 0.7919 (mmm) cc_final: 0.7652 (mmm)
REVERT: A 1119 LEU cc_start: 0.8500 (mt) cc_final: 0.8069 (mt)
REVERT: A 1143 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6538 (mt-10)
REVERT: A 1144 ASP cc_start: 0.7600 (p0) cc_final: 0.7162 (p0)
REVERT: A 1171 VAL cc_start: 0.8184 (t) cc_final: 0.7702 (m)
REVERT: A 1183 GLU cc_start: 0.7570 (tt0) cc_final: 0.7220 (mt-10)
REVERT: A 1185 ARG cc_start: 0.7712 (mmt-90) cc_final: 0.7390 (mmm-85)
  outliers start: 23
  outliers final: 15
  residues processed: 233
  average time/residue: 0.0898
  time to fit residues: 27.5561
Evaluate side-chains
  243 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 226
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  418 THR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  678 MET
Chi-restraints excluded: chain A residue  742 ILE
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  838 ASP
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1062 THR
Chi-restraints excluded: chain A residue 1126 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 84 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 95 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 90 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0060
   chunk 82 optimal weight:    0.7980
   overall best weight:    0.5796

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

Flipped N/Q/H residues before XYZ refinement:
A 187 ASN
A 636 GLN
A 691 ASN
A 877 GLN
** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.127511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.108863 restraints weight = 11630.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 1.41
r_work: 0.3220 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3079 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8280  Z= 0.125
  Angle     :  0.461   6.549  11232  Z= 0.246
  Chirality :  0.038   0.138   1349
  Planarity :  0.003   0.044   1385
  Dihedral  :  3.791  17.238   1097
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 12.68 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.27 (0.27), residues: 1016
  helix:  1.96 (0.19), residues: 736
  sheet:  0.21 (0.71), residues: 42
  loop :  0.46 (0.43), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 903 
 TYR   0.013   0.001   TYR A1153 
 PHE   0.017   0.001   PHE A 766 
 TRP   0.014   0.001   TRP A 278 
 HIS   0.006   0.001   HIS A 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 8280)
  covalent geometry    : angle       0.46148 (11232)
  hydrogen bonds       : bond        0.03891 (  581)
  hydrogen bonds       : angle       3.82080 ( 1701)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 233
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A  155 ASP cc_start: 0.7809 (t70) cc_final: 0.7530 (p0)
REVERT: A  218 LYS cc_start: 0.7744 (ttmm) cc_final: 0.7483 (ttmm)
REVERT: A  233 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7408 (tt0)
REVERT: A  322 SER cc_start: 0.8119 (t) cc_final: 0.7882 (t)
REVERT: A  492 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8011 (mm)
REVERT: A  531 GLU cc_start: 0.7305 (tm-30) cc_final: 0.6601 (tm-30)
REVERT: A  533 SER cc_start: 0.8217 (p) cc_final: 0.7505 (m)
REVERT: A  579 MET cc_start: 0.6586 (tpp) cc_final: 0.6230 (tpp)
REVERT: A  646 ARG cc_start: 0.7508 (ttp-170) cc_final: 0.7277 (ttp-170)
REVERT: A  697 MET cc_start: 0.6113 (tpt) cc_final: 0.5796 (tpt)
REVERT: A  814 THR cc_start: 0.8372 (p) cc_final: 0.8169 (m)
REVERT: A  866 GLU cc_start: 0.7444 (tm-30) cc_final: 0.7157 (tm-30)
REVERT: A 1062 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8450 (p)
REVERT: A 1063 VAL cc_start: 0.8437 (t) cc_final: 0.8180 (t)
REVERT: A 1104 MET cc_start: 0.7961 (mmm) cc_final: 0.7734 (mmm)
REVERT: A 1119 LEU cc_start: 0.8481 (mt) cc_final: 0.8013 (mt)
REVERT: A 1143 GLU cc_start: 0.6794 (mt-10) cc_final: 0.6463 (mt-10)
REVERT: A 1144 ASP cc_start: 0.7605 (p0) cc_final: 0.7219 (p0)
REVERT: A 1171 VAL cc_start: 0.8208 (t) cc_final: 0.7723 (m)
REVERT: A 1183 GLU cc_start: 0.7572 (tt0) cc_final: 0.7193 (mt-10)
  outliers start: 28
  outliers final: 14
  residues processed: 242
  average time/residue: 0.0840
  time to fit residues: 27.1602
Evaluate side-chains
  244 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 228
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  479 ARG
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  742 ILE
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  838 ASP
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1061 THR
Chi-restraints excluded: chain A residue 1062 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 100 optimal weight:    0.6980
   chunk 65 optimal weight:    6.9990
   chunk 48 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 85 optimal weight:    0.6980
   chunk 97 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 187 ASN
A 636 GLN
A 691 ASN
** A1106 GLN ** 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 = 0.3600 r_free = 0.3600 target = 0.130093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.111157 restraints weight = 11546.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 1.43
r_work: 0.3210 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.2799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8280  Z= 0.141
  Angle     :  0.478   6.645  11232  Z= 0.253
  Chirality :  0.038   0.137   1349
  Planarity :  0.004   0.058   1385
  Dihedral  :  3.787  17.693   1097
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 14.50 %
    Favored  : 81.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.20 (0.26), residues: 1016
  helix:  1.90 (0.19), residues: 738
  sheet:  0.24 (0.70), residues: 42
  loop :  0.41 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 976 
 TYR   0.013   0.001   TYR A1153 
 PHE   0.017   0.001   PHE A 766 
 TRP   0.013   0.001   TRP A 278 
 HIS   0.006   0.001   HIS A1120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 8280)
  covalent geometry    : angle       0.47841 (11232)
  hydrogen bonds       : bond        0.03933 (  581)
  hydrogen bonds       : angle       3.81723 ( 1701)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 229
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A  129 ASP cc_start: 0.7908 (m-30) cc_final: 0.7545 (m-30)
REVERT: A  155 ASP cc_start: 0.7810 (t70) cc_final: 0.7491 (p0)
REVERT: A  205 MET cc_start: 0.7564 (mmm) cc_final: 0.6942 (mmt)
REVERT: A  218 LYS cc_start: 0.7757 (ttmm) cc_final: 0.7465 (ttmm)
REVERT: A  233 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7455 (tt0)
REVERT: A  444 ASN cc_start: 0.8246 (t0) cc_final: 0.7995 (t0)
REVERT: A  492 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8033 (mm)
REVERT: A  533 SER cc_start: 0.8273 (p) cc_final: 0.7744 (m)
REVERT: A  579 MET cc_start: 0.6568 (tpp) cc_final: 0.6205 (tpp)
REVERT: A  646 ARG cc_start: 0.7489 (ttp-170) cc_final: 0.7257 (ttp-170)
REVERT: A  697 MET cc_start: 0.6165 (tpt) cc_final: 0.5846 (tpt)
REVERT: A  746 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7454 (tm-30)
REVERT: A  814 THR cc_start: 0.8393 (p) cc_final: 0.8181 (m)
REVERT: A  866 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7017 (tm-30)
REVERT: A 1062 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8672 (p)
REVERT: A 1104 MET cc_start: 0.8029 (mmm) cc_final: 0.7775 (mmm)
REVERT: A 1119 LEU cc_start: 0.8471 (mt) cc_final: 0.8026 (mt)
REVERT: A 1143 GLU cc_start: 0.6702 (mt-10) cc_final: 0.6326 (mt-10)
REVERT: A 1144 ASP cc_start: 0.7631 (p0) cc_final: 0.7220 (p0)
REVERT: A 1171 VAL cc_start: 0.8217 (t) cc_final: 0.7748 (m)
  outliers start: 31
  outliers final: 21
  residues processed: 237
  average time/residue: 0.0856
  time to fit residues: 27.2253
Evaluate side-chains
  245 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 222
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  161 ARG
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  479 ARG
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  678 MET
Chi-restraints excluded: chain A residue  742 ILE
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  931 GLU
Chi-restraints excluded: chain A residue  956 LEU
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1061 THR
Chi-restraints excluded: chain A residue 1062 THR
Chi-restraints excluded: chain A residue 1126 LEU
Chi-restraints excluded: chain A residue 1166 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 82 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0030
   chunk 91 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0670
   chunk 16 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 78 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.3728

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

Flipped N/Q/H residues before XYZ refinement:
A 187 ASN
A 691 ASN
** A1106 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 = 0.3616 r_free = 0.3616 target = 0.131372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.112330 restraints weight = 11392.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 1.44
r_work: 0.3200 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.3003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8280  Z= 0.106
  Angle     :  0.455   6.234  11232  Z= 0.241
  Chirality :  0.037   0.137   1349
  Planarity :  0.003   0.044   1385
  Dihedral  :  3.656  17.618   1097
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 14.72 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.47 (0.26), residues: 1016
  helix:  2.09 (0.19), residues: 738
  sheet:  0.50 (0.74), residues: 42
  loop :  0.51 (0.43), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 976 
 TYR   0.012   0.001   TYR A1153 
 PHE   0.018   0.001   PHE A 766 
 TRP   0.013   0.001   TRP A 278 
 HIS   0.005   0.001   HIS A 869 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 8280)
  covalent geometry    : angle       0.45517 (11232)
  hydrogen bonds       : bond        0.03554 (  581)
  hydrogen bonds       : angle       3.72688 ( 1701)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 231
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A  155 ASP cc_start: 0.7774 (t70) cc_final: 0.7494 (p0)
REVERT: A  161 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.7104 (mpp-170)
REVERT: A  205 MET cc_start: 0.7490 (mmm) cc_final: 0.7197 (mmm)
REVERT: A  218 LYS cc_start: 0.7705 (ttmm) cc_final: 0.7433 (ttmm)
REVERT: A  231 GLU cc_start: 0.7800 (tt0) cc_final: 0.7459 (mt-10)
REVERT: A  233 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7358 (tt0)
REVERT: A  237 ASN cc_start: 0.8395 (t0) cc_final: 0.8104 (m-40)
REVERT: A  443 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7506 (tp30)
REVERT: A  492 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7967 (mm)
REVERT: A  531 GLU cc_start: 0.7223 (tm-30) cc_final: 0.6965 (tm-30)
REVERT: A  533 SER cc_start: 0.8176 (p) cc_final: 0.7971 (m)
REVERT: A  579 MET cc_start: 0.6558 (tpp) cc_final: 0.6176 (tpp)
REVERT: A  600 HIS cc_start: 0.7861 (m90) cc_final: 0.7648 (m-70)
REVERT: A  646 ARG cc_start: 0.7441 (ttp-170) cc_final: 0.7201 (ttp-170)
REVERT: A  697 MET cc_start: 0.6151 (tpt) cc_final: 0.5823 (tpt)
REVERT: A  746 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7472 (tm-30)
REVERT: A  814 THR cc_start: 0.8341 (p) cc_final: 0.8139 (m)
REVERT: A  863 ILE cc_start: 0.8050 (mm) cc_final: 0.7791 (mt)
REVERT: A  866 GLU cc_start: 0.7350 (tm-30) cc_final: 0.7065 (tm-30)
REVERT: A  870 ILE cc_start: 0.7966 (mt) cc_final: 0.7692 (mt)
REVERT: A 1062 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8634 (p)
REVERT: A 1104 MET cc_start: 0.8009 (mmm) cc_final: 0.7775 (mmm)
REVERT: A 1119 LEU cc_start: 0.8427 (mt) cc_final: 0.7999 (mt)
REVERT: A 1143 GLU cc_start: 0.6695 (mt-10) cc_final: 0.6233 (mt-10)
REVERT: A 1144 ASP cc_start: 0.7580 (p0) cc_final: 0.7162 (p0)
REVERT: A 1171 VAL cc_start: 0.8163 (t) cc_final: 0.7703 (m)
  outliers start: 31
  outliers final: 18
  residues processed: 240
  average time/residue: 0.0932
  time to fit residues: 29.9303
Evaluate side-chains
  249 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 228
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  161 ARG
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  479 ARG
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  678 MET
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  931 GLU
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1062 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 96 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 86 optimal weight:    0.0020
   chunk 39 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.6590

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

Flipped N/Q/H residues before XYZ refinement:
A 444 ASN
** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.126788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.107916 restraints weight = 11688.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 1.41
r_work: 0.3216 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3075 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.3123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8280  Z= 0.136
  Angle     :  0.488   7.096  11232  Z= 0.256
  Chirality :  0.038   0.138   1349
  Planarity :  0.003   0.044   1385
  Dihedral  :  3.650  17.322   1097
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 16.53 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.42 (0.26), residues: 1016
  helix:  2.05 (0.19), residues: 738
  sheet:  0.51 (0.75), residues: 42
  loop :  0.52 (0.43), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 856 
 TYR   0.012   0.001   TYR A1153 
 PHE   0.023   0.001   PHE A1109 
 TRP   0.012   0.001   TRP A 278 
 HIS   0.007   0.001   HIS A 981 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8280)
  covalent geometry    : angle       0.48819 (11232)
  hydrogen bonds       : bond        0.03738 (  581)
  hydrogen bonds       : angle       3.75909 ( 1701)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 227
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A  155 ASP cc_start: 0.7804 (t70) cc_final: 0.7583 (p0)
REVERT: A  161 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7175 (mpp-170)
REVERT: A  205 MET cc_start: 0.7515 (mmm) cc_final: 0.7282 (mmm)
REVERT: A  218 LYS cc_start: 0.7737 (ttmm) cc_final: 0.7460 (ttmm)
REVERT: A  231 GLU cc_start: 0.7796 (tt0) cc_final: 0.7571 (mt-10)
REVERT: A  233 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7416 (tt0)
REVERT: A  237 ASN cc_start: 0.8446 (t0) cc_final: 0.8164 (m-40)
REVERT: A  443 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7549 (tp30)
REVERT: A  492 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8013 (mm)
REVERT: A  579 MET cc_start: 0.6622 (tpp) cc_final: 0.6241 (tpp)
REVERT: A  621 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6897 (mp0)
REVERT: A  646 ARG cc_start: 0.7465 (ttp-170) cc_final: 0.7246 (ttp-170)
REVERT: A  697 MET cc_start: 0.6151 (tpt) cc_final: 0.5836 (tpt)
REVERT: A  814 THR cc_start: 0.8383 (p) cc_final: 0.8176 (m)
REVERT: A  863 ILE cc_start: 0.8154 (mm) cc_final: 0.7922 (mt)
REVERT: A  866 GLU cc_start: 0.7393 (tm-30) cc_final: 0.7105 (tm-30)
REVERT: A 1062 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8666 (p)
REVERT: A 1104 MET cc_start: 0.8008 (mmm) cc_final: 0.7782 (mmm)
REVERT: A 1119 LEU cc_start: 0.8482 (mt) cc_final: 0.8051 (mt)
REVERT: A 1143 GLU cc_start: 0.6633 (mt-10) cc_final: 0.6238 (mt-10)
REVERT: A 1144 ASP cc_start: 0.7563 (p0) cc_final: 0.7181 (p0)
REVERT: A 1171 VAL cc_start: 0.8213 (t) cc_final: 0.7757 (m)
  outliers start: 22
  outliers final: 14
  residues processed: 233
  average time/residue: 0.0970
  time to fit residues: 30.1702
Evaluate side-chains
  243 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 226
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  161 ARG
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  479 ARG
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  838 ASP
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  931 GLU
Chi-restraints excluded: chain A residue 1047 VAL
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1062 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 43 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 87 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 88 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.129659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.110012 restraints weight = 11517.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 1.53
r_work: 0.3190 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.3185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8280  Z= 0.139
  Angle     :  0.493   7.425  11232  Z= 0.257
  Chirality :  0.039   0.139   1349
  Planarity :  0.003   0.044   1385
  Dihedral  :  3.662  17.885   1097
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.21 %
    Favored  : 80.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.41 (0.26), residues: 1016
  helix:  2.05 (0.19), residues: 738
  sheet:  0.59 (0.75), residues: 42
  loop :  0.47 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 903 
 TYR   0.011   0.001   TYR A1153 
 PHE   0.019   0.001   PHE A 972 
 TRP   0.012   0.001   TRP A 278 
 HIS   0.006   0.001   HIS A1120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 8280)
  covalent geometry    : angle       0.49288 (11232)
  hydrogen bonds       : bond        0.03804 (  581)
  hydrogen bonds       : angle       3.76866 ( 1701)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 229
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A  155 ASP cc_start: 0.7862 (t70) cc_final: 0.7593 (p0)
REVERT: A  161 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7234 (mpp-170)
REVERT: A  218 LYS cc_start: 0.7760 (ttmm) cc_final: 0.7481 (ttmm)
REVERT: A  233 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7441 (tt0)
REVERT: A  237 ASN cc_start: 0.8469 (t0) cc_final: 0.8196 (m-40)
REVERT: A  443 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7592 (tp30)
REVERT: A  492 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8018 (mm)
REVERT: A  531 GLU cc_start: 0.7500 (tm-30) cc_final: 0.6881 (tm-30)
REVERT: A  579 MET cc_start: 0.6706 (tpp) cc_final: 0.6340 (tpp)
REVERT: A  621 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7145 (mt-10)
REVERT: A  646 ARG cc_start: 0.7549 (ttp-170) cc_final: 0.7318 (ttp-170)
REVERT: A  697 MET cc_start: 0.6186 (tpt) cc_final: 0.5865 (tpt)
REVERT: A  863 ILE cc_start: 0.8189 (mm) cc_final: 0.7984 (mt)
REVERT: A  866 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7045 (tm-30)
REVERT: A  870 ILE cc_start: 0.8168 (mt) cc_final: 0.7821 (mt)
REVERT: A 1069 THR cc_start: 0.8440 (m) cc_final: 0.8181 (t)
REVERT: A 1104 MET cc_start: 0.8020 (mmm) cc_final: 0.7800 (mmm)
REVERT: A 1119 LEU cc_start: 0.8508 (mt) cc_final: 0.8076 (mt)
REVERT: A 1143 GLU cc_start: 0.6670 (mt-10) cc_final: 0.6296 (mt-10)
REVERT: A 1144 ASP cc_start: 0.7575 (p0) cc_final: 0.7216 (p0)
REVERT: A 1171 VAL cc_start: 0.8221 (t) cc_final: 0.7767 (m)
  outliers start: 20
  outliers final: 13
  residues processed: 235
  average time/residue: 0.0984
  time to fit residues: 30.9811
Evaluate side-chains
  241 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 226
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  161 ARG
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  479 ARG
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  838 ASP
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  931 GLU
Chi-restraints excluded: chain A residue 1058 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 80 optimal weight:    2.9990
   chunk 86 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 60 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.129751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.110146 restraints weight = 11543.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 1.54
r_work: 0.3199 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.3226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8280  Z= 0.154
  Angle     :  0.517  10.820  11232  Z= 0.269
  Chirality :  0.039   0.141   1349
  Planarity :  0.003   0.045   1385
  Dihedral  :  3.682  16.150   1097
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 17.10 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.33 (0.26), residues: 1016
  helix:  2.00 (0.19), residues: 738
  sheet:  0.65 (0.76), residues: 42
  loop :  0.36 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 903 
 TYR   0.012   0.001   TYR A1035 
 PHE   0.025   0.002   PHE A 201 
 TRP   0.012   0.001   TRP A 278 
 HIS   0.007   0.001   HIS A1120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 8280)
  covalent geometry    : angle       0.51695 (11232)
  hydrogen bonds       : bond        0.03981 (  581)
  hydrogen bonds       : angle       3.79142 ( 1701)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 234
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A  155 ASP cc_start: 0.7806 (t70) cc_final: 0.7449 (p0)
REVERT: A  161 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7171 (mpp-170)
REVERT: A  205 MET cc_start: 0.7901 (mpp) cc_final: 0.7161 (mmm)
REVERT: A  218 LYS cc_start: 0.7740 (ttmm) cc_final: 0.7453 (ttmm)
REVERT: A  233 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7425 (tt0)
REVERT: A  237 ASN cc_start: 0.8499 (t0) cc_final: 0.8287 (m-40)
REVERT: A  347 VAL cc_start: 0.8682 (p) cc_final: 0.8470 (t)
REVERT: A  443 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7639 (tp30)
REVERT: A  492 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8010 (mm)
REVERT: A  531 GLU cc_start: 0.7486 (tm-30) cc_final: 0.6897 (tm-30)
REVERT: A  579 MET cc_start: 0.6643 (tpp) cc_final: 0.6280 (tpp)
REVERT: A  583 ARG cc_start: 0.7852 (ttp80) cc_final: 0.7369 (ttt90)
REVERT: A  621 GLU cc_start: 0.7328 (mt-10) cc_final: 0.7051 (mt-10)
REVERT: A  623 ASP cc_start: 0.8225 (t0) cc_final: 0.7979 (t0)
REVERT: A  646 ARG cc_start: 0.7518 (ttp-170) cc_final: 0.7254 (ttp-170)
REVERT: A  697 MET cc_start: 0.6196 (tpt) cc_final: 0.5878 (tpt)
REVERT: A  765 LYS cc_start: 0.8066 (mtmt) cc_final: 0.7548 (mttm)
REVERT: A  863 ILE cc_start: 0.8200 (mm) cc_final: 0.7986 (mt)
REVERT: A  866 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7109 (tm-30)
REVERT: A 1063 VAL cc_start: 0.8453 (t) cc_final: 0.8171 (t)
REVERT: A 1119 LEU cc_start: 0.8531 (mt) cc_final: 0.8121 (mt)
REVERT: A 1143 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6382 (mt-10)
REVERT: A 1144 ASP cc_start: 0.7578 (p0) cc_final: 0.7320 (p0)
REVERT: A 1171 VAL cc_start: 0.8197 (t) cc_final: 0.7727 (m)
  outliers start: 23
  outliers final: 15
  residues processed: 239
  average time/residue: 0.1002
  time to fit residues: 31.6085
Evaluate side-chains
  245 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 228
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  161 ARG
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  479 ARG
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  742 ILE
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  838 ASP
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  931 GLU
Chi-restraints excluded: chain A residue 1058 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 73 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 99 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.130225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.110955 restraints weight = 11598.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 1.49
r_work: 0.3196 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.3296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8280  Z= 0.155
  Angle     :  0.522  10.014  11232  Z= 0.271
  Chirality :  0.039   0.141   1349
  Planarity :  0.003   0.045   1385
  Dihedral  :  3.725  15.880   1097
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 17.78 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.25 (0.26), residues: 1016
  helix:  1.95 (0.19), residues: 738
  sheet:  0.67 (0.75), residues: 42
  loop :  0.30 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 903 
 TYR   0.011   0.001   TYR A1153 
 PHE   0.030   0.002   PHE A 201 
 TRP   0.012   0.001   TRP A 278 
 HIS   0.007   0.001   HIS A1120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 8280)
  covalent geometry    : angle       0.52179 (11232)
  hydrogen bonds       : bond        0.03986 (  581)
  hydrogen bonds       : angle       3.80493 ( 1701)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 223
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A  155 ASP cc_start: 0.7814 (t70) cc_final: 0.7451 (p0)
REVERT: A  161 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7160 (mpp-170)
REVERT: A  205 MET cc_start: 0.7782 (mpp) cc_final: 0.7463 (mtm)
REVERT: A  218 LYS cc_start: 0.7739 (ttmm) cc_final: 0.7442 (ttmm)
REVERT: A  233 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7403 (tt0)
REVERT: A  237 ASN cc_start: 0.8463 (t0) cc_final: 0.8236 (m-40)
REVERT: A  347 VAL cc_start: 0.8695 (p) cc_final: 0.8478 (t)
REVERT: A  492 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8037 (mm)
REVERT: A  531 GLU cc_start: 0.7480 (tm-30) cc_final: 0.6921 (tm-30)
REVERT: A  579 MET cc_start: 0.6622 (tpp) cc_final: 0.6260 (tpp)
REVERT: A  623 ASP cc_start: 0.8191 (t0) cc_final: 0.7933 (t0)
REVERT: A  646 ARG cc_start: 0.7529 (ttp-170) cc_final: 0.7259 (ttp-170)
REVERT: A  697 MET cc_start: 0.6213 (tpt) cc_final: 0.5890 (tpt)
REVERT: A  810 MET cc_start: 0.5762 (ppp) cc_final: 0.5493 (ppp)
REVERT: A  863 ILE cc_start: 0.8208 (mm) cc_final: 0.8000 (mt)
REVERT: A  866 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7070 (tm-30)
REVERT: A  870 ILE cc_start: 0.8229 (mt) cc_final: 0.7923 (mt)
REVERT: A 1119 LEU cc_start: 0.8534 (mt) cc_final: 0.8100 (mt)
REVERT: A 1143 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6377 (mt-10)
REVERT: A 1144 ASP cc_start: 0.7509 (p0) cc_final: 0.7270 (p0)
REVERT: A 1171 VAL cc_start: 0.8174 (t) cc_final: 0.7718 (m)
REVERT: A 1174 LEU cc_start: 0.7781 (mt) cc_final: 0.7385 (mt)
  outliers start: 19
  outliers final: 15
  residues processed: 226
  average time/residue: 0.0887
  time to fit residues: 26.8415
Evaluate side-chains
  239 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 222
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  161 ARG
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  479 ARG
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  742 ILE
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  838 ASP
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  900 GLN
Chi-restraints excluded: chain A residue  931 GLU
Chi-restraints excluded: chain A residue 1058 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 91 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 63 optimal weight:    5.9990
   chunk 64 optimal weight:    7.9990
   chunk 32 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 89 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.130076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.110415 restraints weight = 11562.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 1.54
r_work: 0.3199 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.3356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8280  Z= 0.148
  Angle     :  0.524  10.183  11232  Z= 0.270
  Chirality :  0.039   0.138   1349
  Planarity :  0.003   0.044   1385
  Dihedral  :  3.711  16.000   1097
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 18.23 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.28 (0.26), residues: 1016
  helix:  1.99 (0.19), residues: 738
  sheet:  0.59 (0.75), residues: 42
  loop :  0.25 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 903 
 TYR   0.012   0.001   TYR A1153 
 PHE   0.025   0.002   PHE A 201 
 TRP   0.012   0.001   TRP A 278 
 HIS   0.007   0.001   HIS A1120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 8280)
  covalent geometry    : angle       0.52416 (11232)
  hydrogen bonds       : bond        0.03927 (  581)
  hydrogen bonds       : angle       3.77819 ( 1701)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2035.76 seconds
wall clock time: 35 minutes 25.90 seconds (2125.90 seconds total)