Starting phenix.real_space_refine
on Wed Feb 12 18:13:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pd7_17602/02_2025/8pd7_17602.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pd7_17602/02_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_17602/02_2025/8pd7_17602.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pd7_17602/02_2025/8pd7_17602.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pd7_17602/02_2025/8pd7_17602.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pd7_17602/02_2025/8pd7_17602.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.35, per 1000 atoms: 0.66
  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: 2.10
  Conformation dependent library (CDL) restraints added in 964.5 milliseconds
  

  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: 0.92
  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: 2.57

  Time building geometry restraints manager: 2.45 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:             1.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     22.190
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.480
-------------------------------------------------------------------------------
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= 0.188
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.26), 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
 TRP   0.012   0.001   TRP A1112 
 HIS   0.005   0.001   HIS A1120 
 PHE   0.024   0.001   PHE A 802 
 TYR   0.013   0.001   TYR A1153 
 ARG   0.002   0.000   ARG A 899 

*********************** 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  : 0.858 
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: 0.7515 (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: 0.5952 (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: 0.6486 (ttm)
REVERT: A  881 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7461 (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: 0.7980 (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: 0.7798 (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: 0.6906 (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: 0.2283
  time to fit residues: 86.0134
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  : 0.887 
-------------------------------------------------------------------------------
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 86 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 48 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9980
   chunk 92 optimal weight:    0.5980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 869 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.130944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.110780 restraints weight = 11337.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 1.56
r_work: 0.3170 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.1819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8280  Z= 0.282
  Angle     :  0.542   7.115  11232  Z= 0.289
  Chirality :  0.041   0.139   1349
  Planarity :  0.004   0.045   1385
  Dihedral  :  4.272  20.391   1099
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  :  9.74 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.26), residues: 1016
  helix:  1.53 (0.19), residues: 729
  sheet: -0.27 (0.72), residues: 43
  loop :  0.32 (0.43), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 635 
 HIS   0.012   0.002   HIS A 132 
 PHE   0.019   0.002   PHE A 598 
 TYR   0.018   0.002   TYR A1153 
 ARG   0.004   0.001   ARG A 479 

*********************** 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
  266 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 245
  time to evaluate  : 1.005 
Fit side-chains
REVERT: A  155 ASP cc_start: 0.7755 (t70) cc_final: 0.7555 (t70)
REVERT: A  205 MET cc_start: 0.7821 (mtp) cc_final: 0.7524 (mmt)
REVERT: A  218 LYS cc_start: 0.7836 (ttmm) cc_final: 0.7563 (ttmm)
REVERT: A  233 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7568 (tt0)
REVERT: A  443 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7791 (tm-30)
REVERT: A  492 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8036 (mm)
REVERT: A  533 SER cc_start: 0.8505 (p) cc_final: 0.7755 (m)
REVERT: A  579 MET cc_start: 0.6649 (tpp) cc_final: 0.6374 (tpp)
REVERT: A  591 LYS cc_start: 0.8548 (mtpp) cc_final: 0.8348 (mtmm)
REVERT: A  646 ARG cc_start: 0.7605 (ttp-170) cc_final: 0.7363 (ttp-170)
REVERT: A  697 MET cc_start: 0.6163 (tpt) cc_final: 0.5844 (tpt)
REVERT: A  814 THR cc_start: 0.8591 (p) cc_final: 0.8309 (m)
REVERT: A 1050 LYS cc_start: 0.8387 (mttt) cc_final: 0.8151 (mttp)
REVERT: A 1104 MET cc_start: 0.7872 (mmm) cc_final: 0.7622 (mmm)
REVERT: A 1119 LEU cc_start: 0.8545 (mt) cc_final: 0.8098 (mt)
REVERT: A 1143 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6696 (mt-10)
REVERT: A 1144 ASP cc_start: 0.7557 (p0) cc_final: 0.7162 (p0)
REVERT: A 1171 VAL cc_start: 0.8230 (t) cc_final: 0.7738 (m)
REVERT: A 1183 GLU cc_start: 0.7608 (tt0) cc_final: 0.7223 (mt-10)
  outliers start: 21
  outliers final: 9
  residues processed: 248
  average time/residue: 0.2274
  time to fit residues: 74.7692
Evaluate side-chains
  234 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 224
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
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  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 50 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 78 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 95 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 98 optimal weight:    6.9990
   chunk 84 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 101 optimal weight:    0.8980
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 636 GLN
A 869 HIS
** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.126244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.106687 restraints weight = 11693.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 1.48
r_work: 0.3172 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3027 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.2383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8280  Z= 0.340
  Angle     :  0.527   7.076  11232  Z= 0.284
  Chirality :  0.041   0.138   1349
  Planarity :  0.004   0.045   1385
  Dihedral  :  4.109  19.605   1097
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 11.44 %
    Favored  : 85.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.26), residues: 1016
  helix:  1.46 (0.19), residues: 736
  sheet:  0.18 (0.74), residues: 43
  loop :  0.15 (0.43), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 278 
 HIS   0.010   0.001   HIS A1120 
 PHE   0.016   0.002   PHE A 625 
 TYR   0.014   0.002   TYR A1153 
 ARG   0.004   0.000   ARG A 479 

*********************** 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
  252 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 226
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 HIS cc_start: 0.7612 (t70) cc_final: 0.7287 (t70)
REVERT: A  155 ASP cc_start: 0.7870 (t70) cc_final: 0.7594 (p0)
REVERT: A  205 MET cc_start: 0.7792 (mtp) cc_final: 0.7409 (mmt)
REVERT: A  218 LYS cc_start: 0.7791 (ttmm) cc_final: 0.7524 (ttmm)
REVERT: A  233 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7451 (tt0)
REVERT: A  443 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7729 (tm-30)
REVERT: A  492 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8121 (mm)
REVERT: A  579 MET cc_start: 0.6696 (tpp) cc_final: 0.6375 (tpp)
REVERT: A  646 ARG cc_start: 0.7532 (ttp-170) cc_final: 0.7295 (ttp-170)
REVERT: A  688 ILE cc_start: 0.8184 (mt) cc_final: 0.7979 (mp)
REVERT: A  697 MET cc_start: 0.6131 (tpt) cc_final: 0.5793 (tpt)
REVERT: A  814 THR cc_start: 0.8580 (p) cc_final: 0.8341 (m)
REVERT: A  866 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7292 (tm-30)
REVERT: A  932 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7968 (tt)
REVERT: A 1104 MET cc_start: 0.7981 (mmm) cc_final: 0.7611 (mmm)
REVERT: A 1119 LEU cc_start: 0.8531 (mt) cc_final: 0.8100 (mt)
REVERT: A 1143 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6559 (mt-10)
REVERT: A 1144 ASP cc_start: 0.7594 (p0) cc_final: 0.7165 (p0)
REVERT: A 1171 VAL cc_start: 0.8257 (t) cc_final: 0.7789 (m)
REVERT: A 1183 GLU cc_start: 0.7617 (tt0) cc_final: 0.7291 (mt-10)
  outliers start: 26
  outliers final: 17
  residues processed: 234
  average time/residue: 0.2407
  time to fit residues: 74.1887
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  : 0.915 
-------------------------------------------------------------------------------
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  228 THR
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  293 ILE
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  900 GLN
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 38 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 65 optimal weight:    4.9990
   chunk 25 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 64 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 99 optimal weight:    0.0980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 869 HIS
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 = 0.3588 r_free = 0.3588 target = 0.129434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.110528 restraints weight = 11580.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 1.43
r_work: 0.3208 rms_B_bonded: 1.90 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: 0.7795
moved from start:          0.2657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8280  Z= 0.192
  Angle     :  0.472   6.621  11232  Z= 0.252
  Chirality :  0.038   0.138   1349
  Planarity :  0.004   0.058   1385
  Dihedral  :  3.923  17.800   1097
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 13.36 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.26), residues: 1016
  helix:  1.81 (0.19), residues: 731
  sheet:  0.02 (0.70), residues: 43
  loop :  0.39 (0.43), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 278 
 HIS   0.007   0.001   HIS A1120 
 PHE   0.021   0.001   PHE A 625 
 TYR   0.013   0.001   TYR A1153 
 ARG   0.005   0.000   ARG A 887 

*********************** 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
  253 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 226
  time to evaluate  : 0.866 
Fit side-chains
REVERT: A  155 ASP cc_start: 0.7809 (t70) cc_final: 0.7507 (p0)
REVERT: A  218 LYS cc_start: 0.7739 (ttmm) cc_final: 0.7481 (ttmm)
REVERT: A  233 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7386 (tt0)
REVERT: A  443 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7695 (tm-30)
REVERT: A  444 ASN cc_start: 0.8313 (t0) cc_final: 0.7979 (t0)
REVERT: A  492 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8038 (mm)
REVERT: A  533 SER cc_start: 0.8443 (p) cc_final: 0.7635 (m)
REVERT: A  579 MET cc_start: 0.6598 (tpp) cc_final: 0.6251 (tpp)
REVERT: A  583 ARG cc_start: 0.7852 (ttp80) cc_final: 0.7308 (ttt90)
REVERT: A  646 ARG cc_start: 0.7540 (ttp-170) cc_final: 0.7302 (ttp-170)
REVERT: A  697 MET cc_start: 0.6150 (tpt) cc_final: 0.5833 (tpt)
REVERT: A  746 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7426 (tm-30)
REVERT: A  812 ARG cc_start: 0.7725 (ttt180) cc_final: 0.7504 (ttt180)
REVERT: A  866 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7276 (tm-30)
REVERT: A 1062 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8605 (p)
REVERT: A 1104 MET cc_start: 0.8000 (mmm) cc_final: 0.7763 (mmm)
REVERT: A 1119 LEU cc_start: 0.8488 (mt) cc_final: 0.8060 (mt)
REVERT: A 1143 GLU cc_start: 0.6755 (mt-10) cc_final: 0.6381 (mt-10)
REVERT: A 1144 ASP cc_start: 0.7677 (p0) cc_final: 0.7231 (p0)
REVERT: A 1171 VAL cc_start: 0.8223 (t) cc_final: 0.7740 (m)
  outliers start: 27
  outliers final: 11
  residues processed: 235
  average time/residue: 0.2354
  time to fit residues: 72.1769
Evaluate side-chains
  236 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 223
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  228 THR
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  591 LYS
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  876 LEU
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 87 optimal weight:    0.6980
   chunk 57 optimal weight:    0.7980
   chunk 64 optimal weight:    0.8980
   chunk 90 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 869 HIS
A 886 GLN
** 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 = 0.3587 r_free = 0.3587 target = 0.129111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.109761 restraints weight = 11382.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 1.50
r_work: 0.3192 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.2861

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= 0.219
  Angle     :  0.481   6.410  11232  Z= 0.254
  Chirality :  0.039   0.138   1349
  Planarity :  0.004   0.045   1385
  Dihedral  :  3.847  17.519   1097
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 13.82 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.14 (0.26), residues: 1016
  helix:  1.87 (0.19), residues: 732
  sheet:  0.26 (0.73), residues: 43
  loop :  0.39 (0.42), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 278 
 HIS   0.008   0.001   HIS A 981 
 PHE   0.019   0.001   PHE A 766 
 TYR   0.012   0.001   TYR A1153 
 ARG   0.003   0.000   ARG A 887 

*********************** 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
  253 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 224
  time to evaluate  : 0.888 
Fit side-chains
REVERT: A  129 ASP cc_start: 0.7934 (m-30) cc_final: 0.7586 (m-30)
REVERT: A  155 ASP cc_start: 0.7855 (t70) cc_final: 0.7511 (p0)
REVERT: A  218 LYS cc_start: 0.7772 (ttmm) cc_final: 0.7492 (ttmm)
REVERT: A  233 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7449 (tt0)
REVERT: A  443 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7718 (tm-30)
REVERT: A  444 ASN cc_start: 0.8338 (t0) cc_final: 0.7982 (t0)
REVERT: A  492 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8049 (mm)
REVERT: A  533 SER cc_start: 0.8184 (p) cc_final: 0.7729 (m)
REVERT: A  579 MET cc_start: 0.6615 (tpp) cc_final: 0.6247 (tpp)
REVERT: A  646 ARG cc_start: 0.7566 (ttp-170) cc_final: 0.7325 (ttp-170)
REVERT: A  697 MET cc_start: 0.6133 (tpt) cc_final: 0.5812 (tpt)
REVERT: A  746 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7472 (tm-30)
REVERT: A  857 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6832 (ttm)
REVERT: A  866 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7062 (tm-30)
REVERT: A  932 LEU cc_start: 0.8064 (tt) cc_final: 0.7802 (tt)
REVERT: A 1062 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8624 (p)
REVERT: A 1104 MET cc_start: 0.8030 (mmm) cc_final: 0.7779 (mmm)
REVERT: A 1119 LEU cc_start: 0.8504 (mt) cc_final: 0.8076 (mt)
REVERT: A 1143 GLU cc_start: 0.6693 (mt-10) cc_final: 0.6310 (mt-10)
REVERT: A 1144 ASP cc_start: 0.7689 (p0) cc_final: 0.7265 (p0)
REVERT: A 1171 VAL cc_start: 0.8215 (t) cc_final: 0.7746 (m)
REVERT: A 1190 ARG cc_start: 0.7239 (mmt-90) cc_final: 0.6989 (mmt-90)
  outliers start: 29
  outliers final: 18
  residues processed: 232
  average time/residue: 0.2342
  time to fit residues: 70.9120
Evaluate side-chains
  241 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 220
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  216 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  476 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  591 LYS
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  857 MET
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  900 GLN
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 96 optimal weight:    5.9990
   chunk 28 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 87 optimal weight:    0.4980
   chunk 73 optimal weight:    0.6980
   chunk 70 optimal weight:    0.0060
   chunk 53 optimal weight:    2.9990
   chunk 82 optimal weight:    0.5980
   chunk 88 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0570
   overall best weight:    0.3714

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

Flipped N/Q/H residues before XYZ refinement:
A 869 HIS
A 908 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.131614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.112595 restraints weight = 11469.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 1.40
r_work: 0.3212 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.3079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8280  Z= 0.148
  Angle     :  0.450   6.196  11232  Z= 0.238
  Chirality :  0.037   0.137   1349
  Planarity :  0.003   0.043   1385
  Dihedral  :  3.698  17.091   1097
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 14.61 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.44 (0.27), residues: 1016
  helix:  2.10 (0.19), residues: 733
  sheet:  0.56 (0.77), residues: 42
  loop :  0.44 (0.43), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 278 
 HIS   0.005   0.001   HIS A 869 
 PHE   0.019   0.001   PHE A 766 
 TYR   0.012   0.001   TYR A1153 
 ARG   0.004   0.000   ARG A 976 

*********************** 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
  256 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 227
  time to evaluate  : 0.866 
Fit side-chains
REVERT: A  155 ASP cc_start: 0.7757 (t70) cc_final: 0.7552 (p0)
REVERT: A  161 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.7216 (mpp-170)
REVERT: A  205 MET cc_start: 0.7819 (mmm) cc_final: 0.7455 (mmm)
REVERT: A  218 LYS cc_start: 0.7703 (ttmm) cc_final: 0.7405 (ttmm)
REVERT: A  233 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7232 (tt0)
REVERT: A  444 ASN cc_start: 0.8308 (t0) cc_final: 0.8032 (t0)
REVERT: A  492 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8003 (mm)
REVERT: A  527 THR cc_start: 0.8740 (t) cc_final: 0.8537 (t)
REVERT: A  531 GLU cc_start: 0.7270 (tm-30) cc_final: 0.6571 (tm-30)
REVERT: A  533 SER cc_start: 0.8216 (p) cc_final: 0.7633 (m)
REVERT: A  579 MET cc_start: 0.6559 (tpp) cc_final: 0.6183 (tpp)
REVERT: A  621 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6856 (mp0)
REVERT: A  646 ARG cc_start: 0.7500 (ttp-170) cc_final: 0.7258 (ttp-170)
REVERT: A  697 MET cc_start: 0.6168 (tpt) cc_final: 0.5861 (tpt)
REVERT: A  746 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7528 (tm-30)
REVERT: A  863 ILE cc_start: 0.8064 (mm) cc_final: 0.7825 (mt)
REVERT: A  866 GLU cc_start: 0.7378 (tm-30) cc_final: 0.6914 (tm-30)
REVERT: A  870 ILE cc_start: 0.8167 (mt) cc_final: 0.7862 (mt)
REVERT: A  916 LEU cc_start: 0.8492 (mt) cc_final: 0.8289 (mp)
REVERT: A  932 LEU cc_start: 0.8034 (tt) cc_final: 0.7779 (tt)
REVERT: A  974 LYS cc_start: 0.8413 (ttpt) cc_final: 0.8209 (mtpt)
REVERT: A 1062 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8587 (p)
REVERT: A 1063 VAL cc_start: 0.8381 (t) cc_final: 0.8139 (t)
REVERT: A 1104 MET cc_start: 0.7957 (mmm) cc_final: 0.7754 (mmm)
REVERT: A 1119 LEU cc_start: 0.8490 (mt) cc_final: 0.8053 (mt)
REVERT: A 1143 GLU cc_start: 0.6565 (mt-10) cc_final: 0.6181 (mt-10)
REVERT: A 1144 ASP cc_start: 0.7567 (p0) cc_final: 0.7149 (p0)
REVERT: A 1171 VAL cc_start: 0.8196 (t) cc_final: 0.7724 (m)
  outliers start: 29
  outliers final: 14
  residues processed: 237
  average time/residue: 0.2204
  time to fit residues: 69.0302
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  : 0.947 
-------------------------------------------------------------------------------
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  169 LEU
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  479 ARG
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  591 LYS
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  808 LEU
Chi-restraints excluded: chain A residue  837 TYR
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 89 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 44 optimal weight:    0.4980
   chunk 71 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 94 optimal weight:    0.6980
   chunk 92 optimal weight:    0.5980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 140 GLN
A 187 ASN
A 636 GLN
A 869 HIS
** A1106 GLN ** 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 = 0.3586 r_free = 0.3586 target = 0.129078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.109183 restraints weight = 11515.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 1.57
r_work: 0.3181 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.3154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8280  Z= 0.265
  Angle     :  0.508   7.198  11232  Z= 0.264
  Chirality :  0.040   0.138   1349
  Planarity :  0.003   0.045   1385
  Dihedral  :  3.777  17.037   1097
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 16.19 %
    Favored  : 81.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.18 (0.26), residues: 1016
  helix:  1.90 (0.19), residues: 734
  sheet:  0.68 (0.76), residues: 43
  loop :  0.27 (0.42), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 278 
 HIS   0.008   0.001   HIS A1120 
 PHE   0.018   0.001   PHE A 766 
 TYR   0.011   0.001   TYR A1088 
 ARG   0.005   0.000   ARG A 903 

*********************** 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
  257 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 234
  time to evaluate  : 0.926 
Fit side-chains
REVERT: A  155 ASP cc_start: 0.7865 (t70) cc_final: 0.7551 (p0)
REVERT: A  205 MET cc_start: 0.7907 (mmm) cc_final: 0.7433 (mmm)
REVERT: A  218 LYS cc_start: 0.7763 (ttmm) cc_final: 0.7497 (ttmm)
REVERT: A  233 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7443 (tt0)
REVERT: A  347 VAL cc_start: 0.8693 (p) cc_final: 0.8486 (t)
REVERT: A  383 MET cc_start: 0.7765 (tpp) cc_final: 0.7444 (tpp)
REVERT: A  444 ASN cc_start: 0.8220 (t0) cc_final: 0.7999 (t0)
REVERT: A  492 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8057 (mm)
REVERT: A  579 MET cc_start: 0.6627 (tpp) cc_final: 0.6244 (tpp)
REVERT: A  621 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6949 (mp0)
REVERT: A  646 ARG cc_start: 0.7583 (ttp-170) cc_final: 0.7304 (ttp-170)
REVERT: A  697 MET cc_start: 0.6201 (tpt) cc_final: 0.5891 (tpt)
REVERT: A  746 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7405 (tm-30)
REVERT: A  810 MET cc_start: 0.5814 (ppp) cc_final: 0.5506 (ppp)
REVERT: A  866 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7170 (tm-30)
REVERT: A  924 GLU cc_start: 0.7710 (tt0) cc_final: 0.7370 (tp30)
REVERT: A 1063 VAL cc_start: 0.8446 (t) cc_final: 0.8164 (t)
REVERT: A 1104 MET cc_start: 0.8045 (mmm) cc_final: 0.7831 (mmm)
REVERT: A 1119 LEU cc_start: 0.8512 (mt) cc_final: 0.8094 (mt)
REVERT: A 1143 GLU cc_start: 0.6702 (mt-10) cc_final: 0.6290 (mt-10)
REVERT: A 1144 ASP cc_start: 0.7598 (p0) cc_final: 0.7183 (p0)
REVERT: A 1171 VAL cc_start: 0.8192 (t) cc_final: 0.7715 (m)
  outliers start: 23
  outliers final: 18
  residues processed: 243
  average time/residue: 0.2206
  time to fit residues: 71.5086
Evaluate side-chains
  247 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 228
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
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  228 THR
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  476 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  603 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  876 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 64 optimal weight:    0.0000
   chunk 57 optimal weight:    5.9990
   chunk 73 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 96 optimal weight:    5.9990
   chunk 85 optimal weight:    0.0370
   chunk 38 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0770
   overall best weight:    0.3820

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

Flipped N/Q/H residues before XYZ refinement:
A 140 GLN
A 869 HIS
A 877 GLN
** 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 = 0.3615 r_free = 0.3615 target = 0.131209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.111933 restraints weight = 11544.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 1.48
r_work: 0.3239 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3101 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.3295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8280  Z= 0.158
  Angle     :  0.481   6.938  11232  Z= 0.251
  Chirality :  0.038   0.176   1349
  Planarity :  0.003   0.044   1385
  Dihedral  :  3.680  17.257   1097
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 16.87 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.46 (0.27), residues: 1016
  helix:  2.13 (0.19), residues: 733
  sheet:  0.72 (0.79), residues: 42
  loop :  0.34 (0.42), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 278 
 HIS   0.006   0.001   HIS A 869 
 PHE   0.020   0.001   PHE A 766 
 TYR   0.012   0.001   TYR A1153 
 ARG   0.004   0.000   ARG A 903 

*********************** 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
  254 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 229
  time to evaluate  : 0.859 
Fit side-chains
REVERT: A  113 LEU cc_start: 0.8662 (tp) cc_final: 0.8398 (tt)
REVERT: A  155 ASP cc_start: 0.7810 (t70) cc_final: 0.7574 (p0)
REVERT: A  161 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7287 (mpp-170)
REVERT: A  218 LYS cc_start: 0.7719 (ttmm) cc_final: 0.7421 (ttmm)
REVERT: A  233 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7270 (tt0)
REVERT: A  492 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8016 (mm)
REVERT: A  531 GLU cc_start: 0.7543 (tm-30) cc_final: 0.6984 (tm-30)
REVERT: A  579 MET cc_start: 0.6529 (tpp) cc_final: 0.6161 (tpp)
REVERT: A  621 GLU cc_start: 0.7319 (mt-10) cc_final: 0.7111 (mt-10)
REVERT: A  646 ARG cc_start: 0.7489 (ttp-170) cc_final: 0.7223 (ttp-170)
REVERT: A  697 MET cc_start: 0.6135 (tpt) cc_final: 0.5820 (tpt)
REVERT: A  746 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7527 (tm-30)
REVERT: A  810 MET cc_start: 0.5851 (ppp) cc_final: 0.5363 (ppp)
REVERT: A  863 ILE cc_start: 0.8087 (mm) cc_final: 0.7817 (mt)
REVERT: A  866 GLU cc_start: 0.7377 (tm-30) cc_final: 0.7065 (tm-30)
REVERT: A  924 GLU cc_start: 0.7635 (tt0) cc_final: 0.7321 (tp30)
REVERT: A  932 LEU cc_start: 0.8047 (tt) cc_final: 0.7761 (tt)
REVERT: A 1033 GLU cc_start: 0.7711 (tt0) cc_final: 0.7331 (tp30)
REVERT: A 1062 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8598 (p)
REVERT: A 1063 VAL cc_start: 0.8384 (t) cc_final: 0.8140 (t)
REVERT: A 1104 MET cc_start: 0.7996 (mmm) cc_final: 0.7777 (mmm)
REVERT: A 1119 LEU cc_start: 0.8488 (mt) cc_final: 0.8076 (mt)
REVERT: A 1143 GLU cc_start: 0.6548 (mt-10) cc_final: 0.6145 (mt-10)
REVERT: A 1144 ASP cc_start: 0.7514 (p0) cc_final: 0.7138 (p0)
REVERT: A 1171 VAL cc_start: 0.8202 (t) cc_final: 0.7714 (m)
  outliers start: 25
  outliers final: 16
  residues processed: 238
  average time/residue: 0.2138
  time to fit residues: 68.3664
Evaluate side-chains
  245 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 226
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
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  169 LEU
Chi-restraints excluded: chain A residue  220 LEU
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  476 THR
Chi-restraints excluded: chain A residue  479 ARG
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  591 LYS
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  931 GLU
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1062 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 92 optimal weight:    0.4980
   chunk 31 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 61 optimal weight:    6.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 869 HIS
** 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 = 0.3599 r_free = 0.3599 target = 0.129933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.110206 restraints weight = 11762.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 1.57
r_work: 0.3189 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.3312

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= 0.232
  Angle     :  0.515   8.313  11232  Z= 0.266
  Chirality :  0.039   0.137   1349
  Planarity :  0.003   0.044   1385
  Dihedral  :  3.700  17.889   1097
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 18.12 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.26), residues: 1016
  helix:  1.99 (0.19), residues: 737
  sheet:  0.73 (0.77), residues: 43
  loop :  0.30 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 278 
 HIS   0.007   0.001   HIS A1120 
 PHE   0.018   0.001   PHE A 766 
 TYR   0.012   0.001   TYR A1153 
 ARG   0.006   0.000   ARG A 887 

*********************** 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
  242 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 222
  time to evaluate  : 0.896 
Fit side-chains
REVERT: A  155 ASP cc_start: 0.7860 (t70) cc_final: 0.7466 (p0)
REVERT: A  161 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7327 (mpp-170)
REVERT: A  218 LYS cc_start: 0.7737 (ttmm) cc_final: 0.7429 (ttmm)
REVERT: A  233 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7410 (tt0)
REVERT: A  383 MET cc_start: 0.7755 (tpp) cc_final: 0.7450 (tpp)
REVERT: A  444 ASN cc_start: 0.8268 (t0) cc_final: 0.8049 (t0)
REVERT: A  492 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8016 (mm)
REVERT: A  531 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7033 (tm-30)
REVERT: A  579 MET cc_start: 0.6558 (tpp) cc_final: 0.6192 (tpp)
REVERT: A  621 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7243 (mt-10)
REVERT: A  646 ARG cc_start: 0.7521 (ttp-170) cc_final: 0.7236 (ttp-170)
REVERT: A  697 MET cc_start: 0.6176 (tpt) cc_final: 0.5865 (tpt)
REVERT: A  746 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7532 (tm-30)
REVERT: A  810 MET cc_start: 0.5824 (ppp) cc_final: 0.5341 (ppp)
REVERT: A  863 ILE cc_start: 0.8142 (mm) cc_final: 0.7892 (mt)
REVERT: A  866 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7130 (tm-30)
REVERT: A  924 GLU cc_start: 0.7809 (tt0) cc_final: 0.7421 (tp30)
REVERT: A 1033 GLU cc_start: 0.7759 (tt0) cc_final: 0.7354 (tp30)
REVERT: A 1062 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8704 (p)
REVERT: A 1119 LEU cc_start: 0.8526 (mt) cc_final: 0.8089 (mt)
REVERT: A 1126 LEU cc_start: 0.8143 (tt) cc_final: 0.7919 (tp)
REVERT: A 1143 GLU cc_start: 0.6620 (mt-10) cc_final: 0.6160 (mt-10)
REVERT: A 1144 ASP cc_start: 0.7529 (p0) cc_final: 0.7145 (p0)
REVERT: A 1171 VAL cc_start: 0.8193 (t) cc_final: 0.7701 (m)
  outliers start: 20
  outliers final: 12
  residues processed: 230
  average time/residue: 0.2251
  time to fit residues: 68.9756
Evaluate side-chains
  237 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 222
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
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  169 LEU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  476 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  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 1058 THR
Chi-restraints excluded: chain A residue 1062 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 71 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9980
   chunk 72 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 869 HIS
** 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 = 0.3603 r_free = 0.3603 target = 0.130280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.110514 restraints weight = 11510.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 1.55
r_work: 0.3197 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.3357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8280  Z= 0.217
  Angle     :  0.514  10.000  11232  Z= 0.264
  Chirality :  0.039   0.138   1349
  Planarity :  0.003   0.045   1385
  Dihedral  :  3.685  17.761   1097
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 18.01 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.36 (0.27), residues: 1016
  helix:  2.04 (0.19), residues: 737
  sheet:  0.80 (0.80), residues: 42
  loop :  0.28 (0.42), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1112 
 HIS   0.008   0.001   HIS A 869 
 PHE   0.021   0.001   PHE A 766 
 TYR   0.013   0.001   TYR A1153 
 ARG   0.006   0.000   ARG A 887 

********************** 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
  243 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 224
  time to evaluate  : 0.829 
Fit side-chains
REVERT: A  155 ASP cc_start: 0.7863 (t70) cc_final: 0.7416 (p0)
REVERT: A  161 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7316 (mpp-170)
REVERT: A  205 MET cc_start: 0.7833 (mmm) cc_final: 0.7630 (mtp)
REVERT: A  216 LEU cc_start: 0.7814 (mt) cc_final: 0.7519 (mp)
REVERT: A  218 LYS cc_start: 0.7732 (ttmm) cc_final: 0.7425 (ttmm)
REVERT: A  233 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7395 (tt0)
REVERT: A  383 MET cc_start: 0.7760 (tpp) cc_final: 0.7462 (tpp)
REVERT: A  492 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8001 (mm)
REVERT: A  531 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7062 (tm-30)
REVERT: A  579 MET cc_start: 0.6573 (tpp) cc_final: 0.6205 (tpp)
REVERT: A  646 ARG cc_start: 0.7540 (ttp-170) cc_final: 0.7253 (ttp-170)
REVERT: A  697 MET cc_start: 0.6197 (tpt) cc_final: 0.5886 (tpt)
REVERT: A  746 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7527 (tm-30)
REVERT: A  810 MET cc_start: 0.5833 (ppp) cc_final: 0.5378 (ppp)
REVERT: A  863 ILE cc_start: 0.8107 (mm) cc_final: 0.7879 (mt)
REVERT: A  866 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7216 (tm-30)
REVERT: A  932 LEU cc_start: 0.8072 (tt) cc_final: 0.7801 (tt)
REVERT: A 1033 GLU cc_start: 0.7774 (tt0) cc_final: 0.7362 (tp30)
REVERT: A 1062 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8723 (p)
REVERT: A 1119 LEU cc_start: 0.8497 (mt) cc_final: 0.8077 (mt)
REVERT: A 1143 GLU cc_start: 0.6643 (mt-10) cc_final: 0.6183 (mt-10)
REVERT: A 1144 ASP cc_start: 0.7513 (p0) cc_final: 0.7161 (p0)
REVERT: A 1171 VAL cc_start: 0.8206 (t) cc_final: 0.7721 (m)
  outliers start: 19
  outliers final: 15
  residues processed: 231
  average time/residue: 0.2231
  time to fit residues: 68.3407
Evaluate side-chains
  239 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 221
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
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  169 LEU
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  476 THR
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  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
Chi-restraints excluded: chain A residue 1062 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 87 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 101 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 59 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 869 HIS
** 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 = 0.3594 r_free = 0.3594 target = 0.129655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.109876 restraints weight = 11666.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 1.56
r_work: 0.3193 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3049 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.3385

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= 0.246
  Angle     :  0.529   8.977  11232  Z= 0.273
  Chirality :  0.039   0.138   1349
  Planarity :  0.004   0.052   1385
  Dihedral  :  3.736  17.631   1097
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 18.23 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.27 (0.26), residues: 1016
  helix:  1.99 (0.19), residues: 737
  sheet:  0.86 (0.79), residues: 43
  loop :  0.19 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1112 
 HIS   0.008   0.001   HIS A 869 
 PHE   0.022   0.001   PHE A 766 
 TYR   0.012   0.001   TYR A1153 
 ARG   0.006   0.000   ARG A 887 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4426.06 seconds
wall clock time: 78 minutes 56.42 seconds (4736.42 seconds total)