Starting phenix.real_space_refine
on Wed Feb 12 18:15:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pd3_17599/02_2025/8pd3_17599.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pd3_17599/02_2025/8pd3_17599.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pd3_17599/02_2025/8pd3_17599.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pd3_17599/02_2025/8pd3_17599.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pd3_17599/02_2025/8pd3_17599.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pd3_17599/02_2025/8pd3_17599.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.027
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    5303      2.51       5
     N    1346      2.21       5
     O    1431      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  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': 30, 'TRANS': 997}
          Chain breaks: 5
  Time building chain proxies: 5.11, per 1000 atoms: 0.63
  Number of scatterers: 8121
  At special positions: 0
  Unit cell: (79.42, 113.696, 125.4, 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    1431      8.00
     N    1346      7.00
     C    5303      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: 2.11
  Conformation dependent library (CDL) restraints added in 966.8 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:  1940

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 4 sheets defined
      76.7% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 76 through 95
      removed outlier: 3.945A  pdb=" N   PHE A  80 " --> pdb=" O   LYS A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 118
      removed outlier: 3.971A  pdb=" N   VAL A 105 " --> pdb=" O   PRO A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.582A  pdb=" N   GLU A 124 " --> pdb=" O   VAL A 120 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   HIS A 126 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
      removed outlier: 4.965A  pdb=" N   ASP A 129 " --> pdb=" O   GLU A 125 " (cutoff:3.500A)
      removed outlier: 5.078A  pdb=" N   VAL A 130 " --> pdb=" O   HIS A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 154
      removed outlier: 4.412A  pdb=" N   GLN A 140 " --> pdb=" O   HIS A 136 " (cutoff:3.500A)
      Proline residue:  A 144  - end of helix
      removed outlier: 3.985A  pdb=" N   MET A 154 " --> pdb=" O   SER A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 161
    Processing helix  chain 'A' and resid 162 through 171
      removed outlier: 3.561A  pdb=" N   VAL A 166 " --> pdb=" O   SER A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 188
    Processing helix  chain 'A' and resid 194 through 206
    Processing helix  chain 'A' and resid 210 through 221
      removed outlier: 3.996A  pdb=" N   LEU A 216 " --> pdb=" O   ALA A 212 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ASP A 219 " --> pdb=" O   ALA A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 254
      removed outlier: 3.742A  pdb=" N   ILE A 229 " --> pdb=" O   GLN A 225 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   VAL A 243 " --> pdb=" O   GLY A 239 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LYS A 250 " --> pdb=" O   ASN A 246 " (cutoff:3.500A)
      removed outlier: 3.720A  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 318
      removed outlier: 3.594A  pdb=" N   GLU A 300 " --> pdb=" O   ASP A 296 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   TYR A 312 " --> pdb=" O   THR A 308 " (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: 3.632A  pdb=" N   PHE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   ARG A 351 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   THR A 373 " --> pdb=" O   GLY A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 411
      removed outlier: 3.885A  pdb=" N   TRP A 385 " --> pdb=" O   ASP A 381 " (cutoff:3.500A)
      removed outlier: 3.836A  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 446
    Processing helix  chain 'A' and resid 449 through 469
      removed outlier: 4.224A  pdb=" N   SER A 453 " --> pdb=" O   ASP A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 481
      removed outlier: 4.836A  pdb=" N   GLN A 475 " --> pdb=" O   ALA A 471 " (cutoff:3.500A)
      removed outlier: 5.437A  pdb=" N   THR A 476 " --> pdb=" O   THR A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 513
    Processing helix  chain 'A' and resid 514 through 519
      removed outlier: 6.265A  pdb=" N   PHE A 517 " --> pdb=" O   SER A 514 " (cutoff:3.500A)
      removed outlier: 3.678A  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 620
    Processing helix  chain 'A' and resid 627 through 636
      removed outlier: 4.438A  pdb=" N   LYS A 633 " --> pdb=" O   ASP A 629 " (cutoff:3.500A)
      removed outlier: 5.104A  pdb=" N   SER A 634 " --> pdb=" O   ASP A 630 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   TRP A 635 " --> pdb=" O   LEU A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 653
      removed outlier: 3.504A  pdb=" N   TRP A 643 " --> pdb=" O   GLY A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 706
      removed outlier: 4.342A  pdb=" N   VAL A 682 " --> pdb=" O   MET A 678 " (cutoff:3.500A)
      removed outlier: 4.982A  pdb=" N   VAL A 693 " --> pdb=" O   VAL A 689 " (cutoff:3.500A)
      Proline residue:  A 694  - end of helix
      removed outlier: 4.405A  pdb=" N   PHE A 699 " --> pdb=" O   ILE A 695 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   VAL A 701 " --> pdb=" O   MET A 697 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LYS A 704 " --> pdb=" O   VAL A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 755
      removed outlier: 3.753A  pdb=" N   ASP A 730 " --> pdb=" O   GLN A 726 " (cutoff:3.500A)
      removed outlier: 5.694A  pdb=" N   ALA A 731 " --> pdb=" O   LYS A 727 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   LEU A 732 " --> pdb=" O   ILE A 728 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ARG A 733 " --> pdb=" O   GLU A 729 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   TYR A 737 " --> pdb=" O   ARG A 733 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 756 through 760
      removed outlier: 3.944A  pdb=" N   ILE A 759 " --> pdb=" O   ARG A 756 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 784
      removed outlier: 3.936A  pdb=" N   LYS A 765 " --> pdb=" O   SER A 761 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   PHE A 766 " --> pdb=" O   HIS A 762 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ASP A 767 " --> pdb=" O   TRP A 763 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   LEU A 771 " --> pdb=" O   ASP A 767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 794 through 797
    Processing helix  chain 'A' and resid 798 through 811
      removed outlier: 3.911A  pdb=" N   ARG A 806 " --> pdb=" O   PHE A 802 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   ARG A 809 " --> pdb=" O   LEU A 805 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   LEU A 811 " --> pdb=" O   GLY A 807 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 813 through 852
      Proline residue:  A 819  - end of helix
      removed outlier: 3.600A  pdb=" N   LYS A 852 " --> pdb=" O   GLU A 848 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 857
    Processing helix  chain 'A' and resid 860 through 889
      removed outlier: 3.630A  pdb=" N   GLN A 877 " --> pdb=" O   THR A 873 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   GLN A 886 " --> pdb=" O   LEU A 882 " (cutoff:3.500A)
      removed outlier: 3.769A  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 923 through 942
      removed outlier: 3.526A  pdb=" N   THR A 933 " --> pdb=" O   LYS A 929 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LEU A 941 " --> pdb=" O   LYS A 937 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   MET A 942 " --> pdb=" O   MET A 938 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 952 through 959
      removed outlier: 3.641A  pdb=" N   LEU A 956 " --> pdb=" O   PRO A 952 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU A 957 " --> pdb=" O   PRO A 953 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   LYS A 958 " --> pdb=" O   GLU A 954 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 960 through 964
    Processing helix  chain 'A' and resid 966 through 977
    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 1107
      removed outlier: 3.617A  pdb=" N   ARG A1097 " --> pdb=" O   VAL A1093 " (cutoff:3.500A)
      Proline residue:  A1101  - end of helix
    Processing helix  chain 'A' and resid 1113 through 1123
      removed outlier: 3.710A  pdb=" N   ARG A1123 " --> pdb=" O   LEU A1119 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982
      removed outlier: 6.460A  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: 6.816A  pdb=" N   VAL A 987 " --> pdb=" O   CYS A1059 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   CYS A1059 " --> pdb=" O   VAL A 987 " (cutoff:3.500A)
      removed outlier: 3.848A  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: 6.689A  pdb=" N   ARG A1185 " --> pdb=" O   ILE A1148 " (cutoff:3.500A)
      removed outlier: 4.001A  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

    570 hydrogen bonds defined for protein.
    1668 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: 2.73

  Time building geometry restraints manager: 2.48 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2574
        1.35 -     1.46: 1857
        1.46 -     1.58: 3772
        1.58 -     1.70: 0
        1.70 -     1.81: 76
  Bond restraints: 8279
  Sorted by residual:
  bond pdb=" N   LEU A  70 "
       pdb=" CA  LEU A  70 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.86e+00
  bond pdb=" CA  ILE A 488 "
       pdb=" CB  ILE A 488 "
    ideal  model  delta    sigma   weight residual
    1.534  1.524  0.010 6.80e-03 2.16e+04 2.26e+00
  bond pdb=" CB  GLU A1071 "
       pdb=" CG  GLU A1071 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.92e-01
  bond pdb=" CB  GLU A 994 "
       pdb=" CG  GLU A 994 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 8.91e-01
  bond pdb=" CB  ARG A 733 "
       pdb=" CG  ARG A 733 "
    ideal  model  delta    sigma   weight residual
    1.520  1.547 -0.027 3.00e-02 1.11e+03 8.25e-01
  ... (remaining 8274 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 10993
        1.58 -     3.16: 196
        3.16 -     4.74: 32
        4.74 -     6.32: 7
        6.32 -     7.90: 1
  Bond angle restraints: 11229
  Sorted by residual:
  angle pdb=" N   VAL A 130 "
        pdb=" CA  VAL A 130 "
        pdb=" C   VAL A 130 "
      ideal   model   delta    sigma   weight residual
     112.12  109.15    2.97 8.40e-01 1.42e+00 1.25e+01
  angle pdb=" C   LEU A 817 "
        pdb=" N   ILE A 818 "
        pdb=" CA  ILE A 818 "
      ideal   model   delta    sigma   weight residual
     120.24  122.24   -2.00 6.30e-01 2.52e+00 1.00e+01
  angle pdb=" C   ILE A 818 "
        pdb=" CA  ILE A 818 "
        pdb=" CB  ILE A 818 "
      ideal   model   delta    sigma   weight residual
     114.35  111.02    3.33 1.06e+00 8.90e-01 9.90e+00
  angle pdb=" CA  ARG A 733 "
        pdb=" CB  ARG A 733 "
        pdb=" CG  ARG A 733 "
      ideal   model   delta    sigma   weight residual
     114.10  119.90   -5.80 2.00e+00 2.50e-01 8.40e+00
  angle pdb=" CB  MET A 925 "
        pdb=" CG  MET A 925 "
        pdb=" SD  MET A 925 "
      ideal   model   delta    sigma   weight residual
     112.70  120.60   -7.90 3.00e+00 1.11e-01 6.94e+00
  ... (remaining 11224 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.71: 4439
       16.71 -    33.43: 400
       33.43 -    50.14: 83
       50.14 -    66.85: 14
       66.85 -    83.57: 7
  Dihedral angle restraints: 4943
    sinusoidal: 1952
      harmonic: 2991
  Sorted by residual:
  dihedral pdb=" CA  ARG A1162 "
           pdb=" C   ARG A1162 "
           pdb=" N   SER A1163 "
           pdb=" CA  SER A1163 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.64  -24.36     0      5.00e+00 4.00e-02 2.37e+01
  dihedral pdb=" CA  LEU A 805 "
           pdb=" C   LEU A 805 "
           pdb=" N   ARG A 806 "
           pdb=" CA  ARG A 806 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.21   22.79     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  ASN A 448 "
           pdb=" C   ASN A 448 "
           pdb=" N   ASP A 449 "
           pdb=" CA  ASP A 449 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.52   19.48     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 4940 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 873
       0.032 -    0.063: 326
       0.063 -    0.095: 110
       0.095 -    0.127: 37
       0.127 -    0.158: 4
  Chirality restraints: 1350
  Sorted by residual:
  chirality pdb=" CA  ILE A 948 "
            pdb=" N   ILE A 948 "
            pdb=" C   ILE A 948 "
            pdb=" CB  ILE A 948 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.25e-01
  chirality pdb=" CA  ILE A 742 "
            pdb=" N   ILE A 742 "
            pdb=" C   ILE A 742 "
            pdb=" CB  ILE A 742 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.48e-01
  chirality pdb=" CA  ASN A 448 "
            pdb=" N   ASN A 448 "
            pdb=" C   ASN A 448 "
            pdb=" CB  ASN A 448 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.47e-01
  ... (remaining 1347 not shown)

  Planarity restraints: 1383
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 120 "    0.045 5.00e-02 4.00e+02   6.77e-02 7.33e+00
        pdb=" N   PRO A 121 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO A 121 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 121 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A1163 "    0.029 5.00e-02 4.00e+02   4.46e-02 3.18e+00
        pdb=" N   PRO A1164 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A1164 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A1164 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 733 "    0.142 9.50e-02 1.11e+02   6.37e-02 2.57e+00
        pdb=" NE  ARG A 733 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 733 "    0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 733 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 733 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1380 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1377
        2.76 -     3.30: 8397
        3.30 -     3.83: 12765
        3.83 -     4.37: 15061
        4.37 -     4.90: 26259
  Nonbonded interactions: 63859
  Sorted by model distance:
  nonbonded pdb=" N   GLU A 954 "
            pdb=" OE1 GLU A 954 "
     model   vdw
     2.227 3.120
  nonbonded pdb=" N   GLU A 994 "
            pdb=" OE1 GLU A 994 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" O   PHE A 254 "
            pdb=" NE2 GLN A 256 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" OD1 ASN A 237 "
            pdb=" N   ASP A 238 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" N   GLU A1071 "
            pdb=" OE1 GLU A1071 "
     model   vdw
     2.273 3.120
  ... (remaining 63854 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:             1.820
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     22.020
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
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   0.035   8279  Z= 0.180
  Angle     :  0.560   7.902  11229  Z= 0.307
  Chirality :  0.039   0.158   1350
  Planarity :  0.004   0.068   1383
  Dihedral  : 13.667  83.567   3003
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.86 %
    Favored  : 89.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.70 (0.26), residues: 1016
  helix:  0.81 (0.19), residues: 725
  sheet:  0.93 (0.84), residues: 38
  loop : -0.35 (0.37), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 635 
 HIS   0.006   0.001   HIS A 132 
 PHE   0.018   0.001   PHE A 740 
 TYR   0.010   0.001   TYR A1178 
 ARG   0.007   0.001   ARG A 573 

*********************** 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
  219 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 219
  time to evaluate  : 0.890 
Fit side-chains
REVERT: A  113 LEU cc_start: 0.7467 (tt) cc_final: 0.7187 (tp)
REVERT: A  128 ARG cc_start: 0.7103 (ttm170) cc_final: 0.6867 (ttm-80)
REVERT: A  160 MET cc_start: 0.6836 (mmt) cc_final: 0.6409 (mmm)
REVERT: A  176 VAL cc_start: 0.7544 (p) cc_final: 0.7255 (m)
REVERT: A  346 GLU cc_start: 0.6953 (tt0) cc_final: 0.6704 (tt0)
REVERT: A  375 LYS cc_start: 0.7810 (mtmt) cc_final: 0.7339 (mtmm)
REVERT: A  385 TRP cc_start: 0.7977 (m100) cc_final: 0.7460 (m100)
REVERT: A  579 MET cc_start: 0.6806 (tpt) cc_final: 0.6169 (tpt)
REVERT: A  624 GLN cc_start: 0.7425 (mm-40) cc_final: 0.6997 (mm-40)
REVERT: A  684 ILE cc_start: 0.7616 (mm) cc_final: 0.7388 (mt)
REVERT: A  697 MET cc_start: 0.6534 (mmm) cc_final: 0.5858 (mmm)
REVERT: A  852 LYS cc_start: 0.8200 (mmtm) cc_final: 0.7998 (mmmt)
REVERT: A  972 PHE cc_start: 0.7776 (t80) cc_final: 0.7446 (t80)
REVERT: A 1054 ASN cc_start: 0.8049 (t0) cc_final: 0.7819 (t0)
REVERT: A 1133 HIS cc_start: 0.6011 (t70) cc_final: 0.5781 (t-90)
REVERT: A 1173 LYS cc_start: 0.7030 (ttmt) cc_final: 0.6603 (ttmm)
REVERT: A 1183 GLU cc_start: 0.7767 (tt0) cc_final: 0.7538 (tt0)
REVERT: A 1185 ARG cc_start: 0.7807 (mmm160) cc_final: 0.7465 (mmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 219
  average time/residue: 0.2556
  time to fit residues: 71.7502
Evaluate side-chains
  205 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 26 optimal weight:    0.4980
   chunk 52 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0870
   chunk 30 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   chunk 59 optimal weight:    3.9990
   chunk 92 optimal weight:    0.6980
   overall best weight:    0.5960

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

Flipped N/Q/H residues before XYZ refinement:
A 335 ASN
A 374 GLN
A 636 GLN
A 691 ASN
A 886 GLN
A 981 HIS
A1114 GLN
A1120 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.135455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.113098 restraints weight = 11025.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 1.87
r_work: 0.3205 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.1631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8279  Z= 0.207
  Angle     :  0.547   7.673  11229  Z= 0.292
  Chirality :  0.041   0.167   1350
  Planarity :  0.004   0.058   1383
  Dihedral  :  4.191  19.391   1097
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 12.78 %
    Favored  : 85.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.68 (0.26), residues: 1016
  helix:  1.56 (0.19), residues: 730
  sheet:  1.18 (1.05), residues: 28
  loop : -0.02 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 278 
 HIS   0.003   0.001   HIS A1133 
 PHE   0.017   0.002   PHE A1136 
 TYR   0.014   0.001   TYR A 267 
 ARG   0.005   0.001   ARG A 903 

*********************** 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
  222 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 207
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
REVERT: A  160 MET cc_start: 0.7328 (mmt) cc_final: 0.6984 (mmm)
REVERT: A  176 VAL cc_start: 0.8458 (p) cc_final: 0.8055 (m)
REVERT: A  186 MET cc_start: 0.7782 (mtp) cc_final: 0.7543 (mtp)
REVERT: A  187 ASN cc_start: 0.8073 (m-40) cc_final: 0.7805 (m-40)
REVERT: A  217 LEU cc_start: 0.8272 (mp) cc_final: 0.7915 (mp)
REVERT: A  385 TRP cc_start: 0.8380 (m100) cc_final: 0.8106 (m100)
REVERT: A  579 MET cc_start: 0.7581 (tpt) cc_final: 0.7160 (tpt)
REVERT: A  684 ILE cc_start: 0.8207 (mm) cc_final: 0.7887 (mt)
REVERT: A  697 MET cc_start: 0.6208 (mmm) cc_final: 0.5541 (mmm)
REVERT: A  736 ASN cc_start: 0.7586 (m-40) cc_final: 0.6993 (m-40)
REVERT: A  958 LYS cc_start: 0.7960 (ttpp) cc_final: 0.7412 (ttpp)
REVERT: A  990 ARG cc_start: 0.7847 (ttm110) cc_final: 0.7209 (ttm110)
REVERT: A 1054 ASN cc_start: 0.8349 (t0) cc_final: 0.8052 (t0)
REVERT: A 1142 LEU cc_start: 0.5670 (tt) cc_final: 0.5446 (tp)
REVERT: A 1173 LYS cc_start: 0.7829 (ttmt) cc_final: 0.7546 (ttmm)
REVERT: A 1191 ASN cc_start: 0.7516 (m-40) cc_final: 0.7292 (m-40)
  outliers start: 15
  outliers final: 4
  residues processed: 217
  average time/residue: 0.2457
  time to fit residues: 69.3261
Evaluate side-chains
  199 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 195
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  430 LEU
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:    0.9980
   chunk 78 optimal weight:    0.5980
   chunk 41 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9990
   chunk 79 optimal weight:    0.5980
   chunk 98 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 75 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 101 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 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 600 HIS
** A 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 832 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.134284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.111688 restraints weight = 11239.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 1.90
r_work: 0.3197 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8279  Z= 0.234
  Angle     :  0.509   6.884  11229  Z= 0.271
  Chirality :  0.040   0.153   1350
  Planarity :  0.004   0.052   1383
  Dihedral  :  4.022  18.743   1097
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 14.93 %
    Favored  : 83.48 %
  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:  1.78 (0.26), residues: 1016
  helix:  1.68 (0.19), residues: 726
  sheet:  0.64 (0.81), residues: 43
  loop : -0.12 (0.39), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 278 
 HIS   0.006   0.001   HIS A1120 
 PHE   0.014   0.001   PHE A1136 
 TYR   0.009   0.001   TYR A 309 
 ARG   0.008   0.001   ARG A 887 

*********************** 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
  220 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 206
  time to evaluate  : 0.858 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 MET cc_start: 0.7458 (mmt) cc_final: 0.7135 (mmm)
REVERT: A  176 VAL cc_start: 0.8407 (p) cc_final: 0.8035 (m)
REVERT: A  186 MET cc_start: 0.7937 (mtp) cc_final: 0.7703 (mtp)
REVERT: A  205 MET cc_start: 0.8288 (mmm) cc_final: 0.8027 (mmp)
REVERT: A  217 LEU cc_start: 0.8210 (mp) cc_final: 0.7819 (mp)
REVERT: A  383 MET cc_start: 0.7524 (mmp) cc_final: 0.7282 (mmp)
REVERT: A  385 TRP cc_start: 0.8363 (m100) cc_final: 0.8121 (m100)
REVERT: A  579 MET cc_start: 0.7475 (tpt) cc_final: 0.7150 (tpt)
REVERT: A  584 LEU cc_start: 0.8544 (mt) cc_final: 0.8330 (mm)
REVERT: A  684 ILE cc_start: 0.8191 (mm) cc_final: 0.7873 (mt)
REVERT: A  697 MET cc_start: 0.6212 (mmm) cc_final: 0.5597 (mmm)
REVERT: A  769 PHE cc_start: 0.7491 (t80) cc_final: 0.7223 (t80)
REVERT: A  958 LYS cc_start: 0.8028 (ttpp) cc_final: 0.7465 (ttpp)
REVERT: A  990 ARG cc_start: 0.7819 (ttm110) cc_final: 0.7171 (ttm110)
REVERT: A 1037 THR cc_start: 0.8470 (t) cc_final: 0.8106 (m)
REVERT: A 1173 LYS cc_start: 0.7851 (ttmt) cc_final: 0.7543 (ttmm)
REVERT: A 1191 ASN cc_start: 0.7528 (m-40) cc_final: 0.7286 (m-40)
  outliers start: 14
  outliers final: 7
  residues processed: 213
  average time/residue: 0.2324
  time to fit residues: 64.6137
Evaluate side-chains
  208 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 201
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  652 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 99 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   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 165 GLN
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 691 ASN
A 832 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.134084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.111497 restraints weight = 11133.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 1.90
r_work: 0.3195 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8279  Z= 0.220
  Angle     :  0.486   6.682  11229  Z= 0.258
  Chirality :  0.040   0.148   1350
  Planarity :  0.004   0.048   1383
  Dihedral  :  3.884  18.944   1097
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 14.71 %
    Favored  : 82.81 %
  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:  1.94 (0.26), residues: 1016
  helix:  1.82 (0.19), residues: 726
  sheet:  0.60 (0.81), residues: 43
  loop : -0.11 (0.39), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 278 
 HIS   0.006   0.001   HIS A1120 
 PHE   0.018   0.001   PHE A 972 
 TYR   0.009   0.001   TYR A 309 
 ARG   0.003   0.000   ARG A 573 

*********************** 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
  228 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 206
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
REVERT: A  160 MET cc_start: 0.7491 (mmt) cc_final: 0.7172 (mmm)
REVERT: A  176 VAL cc_start: 0.8375 (p) cc_final: 0.8018 (m)
REVERT: A  186 MET cc_start: 0.8015 (mtp) cc_final: 0.7770 (mtp)
REVERT: A  217 LEU cc_start: 0.8183 (mp) cc_final: 0.7772 (mp)
REVERT: A  383 MET cc_start: 0.7553 (mmp) cc_final: 0.7327 (mmp)
REVERT: A  385 TRP cc_start: 0.8357 (m100) cc_final: 0.8154 (m100)
REVERT: A  579 MET cc_start: 0.7438 (tpt) cc_final: 0.7124 (tpt)
REVERT: A  584 LEU cc_start: 0.8520 (mt) cc_final: 0.8319 (mm)
REVERT: A  624 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7516 (tt0)
REVERT: A  684 ILE cc_start: 0.8167 (mm) cc_final: 0.7838 (mt)
REVERT: A  958 LYS cc_start: 0.8069 (ttpp) cc_final: 0.7481 (ttpp)
REVERT: A  990 ARG cc_start: 0.7856 (ttm110) cc_final: 0.7328 (ttm110)
REVERT: A 1037 THR cc_start: 0.8458 (t) cc_final: 0.8113 (m)
REVERT: A 1054 ASN cc_start: 0.8334 (t0) cc_final: 0.8084 (t0)
REVERT: A 1173 LYS cc_start: 0.7864 (ttmt) cc_final: 0.7585 (ttmm)
REVERT: A 1183 GLU cc_start: 0.8070 (tt0) cc_final: 0.7863 (tt0)
  outliers start: 22
  outliers final: 17
  residues processed: 217
  average time/residue: 0.2293
  time to fit residues: 65.3523
Evaluate side-chains
  217 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 200
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  652 ILE
Chi-restraints excluded: chain A residue  822 ILE
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  865 ARG
Chi-restraints excluded: chain A residue 1082 LEU
Chi-restraints excluded: chain A residue 1188 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 87 optimal weight:    0.8980
   chunk 57 optimal weight:    6.9990
   chunk 64 optimal weight:    9.9990
   chunk 90 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 47 optimal weight:    2.9990
   chunk 24 optimal weight:    0.4980
   chunk 26 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 39 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   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 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 691 ASN
A 832 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.133652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.111178 restraints weight = 11079.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 1.90
r_work: 0.3195 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8279  Z= 0.211
  Angle     :  0.482   7.698  11229  Z= 0.254
  Chirality :  0.039   0.144   1350
  Planarity :  0.004   0.048   1383
  Dihedral  :  3.846  18.384   1097
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 15.05 %
    Favored  : 82.01 %
  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:  2.08 (0.26), residues: 1016
  helix:  1.93 (0.19), residues: 727
  sheet:  0.67 (0.94), residues: 33
  loop : -0.03 (0.38), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 278 
 HIS   0.005   0.001   HIS A1120 
 PHE   0.014   0.001   PHE A 769 
 TYR   0.011   0.001   TYR A 984 
 ARG   0.005   0.000   ARG A1190 

*********************** 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
  233 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 207
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 MET cc_start: 0.7481 (mmt) cc_final: 0.7143 (mmm)
REVERT: A  176 VAL cc_start: 0.8357 (p) cc_final: 0.8009 (m)
REVERT: A  186 MET cc_start: 0.8057 (mtp) cc_final: 0.7821 (mtp)
REVERT: A  205 MET cc_start: 0.8268 (mmm) cc_final: 0.8037 (mmp)
REVERT: A  217 LEU cc_start: 0.8154 (mp) cc_final: 0.7741 (mp)
REVERT: A  383 MET cc_start: 0.7615 (mmp) cc_final: 0.7292 (mmp)
REVERT: A  624 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7508 (tt0)
REVERT: A  684 ILE cc_start: 0.8165 (mm) cc_final: 0.7827 (mt)
REVERT: A  697 MET cc_start: 0.6443 (mmm) cc_final: 0.6058 (tmm)
REVERT: A  736 ASN cc_start: 0.7702 (m-40) cc_final: 0.7242 (m-40)
REVERT: A  881 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8077 (mt-10)
REVERT: A  958 LYS cc_start: 0.8066 (ttpp) cc_final: 0.7463 (ttpp)
REVERT: A  990 ARG cc_start: 0.7914 (ttm110) cc_final: 0.7406 (ttm110)
REVERT: A 1037 THR cc_start: 0.8469 (t) cc_final: 0.8117 (m)
REVERT: A 1054 ASN cc_start: 0.8314 (t0) cc_final: 0.8042 (t0)
REVERT: A 1173 LYS cc_start: 0.7862 (ttmt) cc_final: 0.7561 (ttmm)
REVERT: A 1183 GLU cc_start: 0.8071 (tt0) cc_final: 0.7856 (tt0)
  outliers start: 26
  outliers final: 20
  residues processed: 222
  average time/residue: 0.2480
  time to fit residues: 71.9332
Evaluate side-chains
  221 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 201
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  506 ASN
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  652 ILE
Chi-restraints excluded: chain A residue  691 ASN
Chi-restraints excluded: chain A residue  809 ARG
Chi-restraints excluded: chain A residue  822 ILE
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  865 ARG
Chi-restraints excluded: chain A residue 1142 LEU
Chi-restraints excluded: chain A residue 1188 VAL
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:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9980
   chunk 73 optimal weight:    0.6980
   chunk 70 optimal weight:    3.9990
   chunk 53 optimal weight:    0.4980
   chunk 82 optimal weight:    0.9990
   chunk 88 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 832 GLN
A1074 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.133682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.111200 restraints weight = 11150.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 1.90
r_work: 0.3192 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3029 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.2643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   8279  Z= 0.230
  Angle     :  0.483   8.899  11229  Z= 0.255
  Chirality :  0.039   0.145   1350
  Planarity :  0.004   0.049   1383
  Dihedral  :  3.834  18.711   1097
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 15.72 %
    Favored  : 81.22 %
  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:  2.10 (0.26), residues: 1016
  helix:  1.95 (0.19), residues: 727
  sheet:  0.58 (0.94), residues: 33
  loop : -0.03 (0.39), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 278 
 HIS   0.006   0.001   HIS A1120 
 PHE   0.016   0.001   PHE A 254 
 TYR   0.013   0.001   TYR A1125 
 ARG   0.002   0.000   ARG A1092 

*********************** 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
  230 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 203
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 MET cc_start: 0.7480 (mmt) cc_final: 0.7156 (mmm)
REVERT: A  176 VAL cc_start: 0.8352 (p) cc_final: 0.8007 (m)
REVERT: A  186 MET cc_start: 0.8103 (mtp) cc_final: 0.7871 (mtp)
REVERT: A  217 LEU cc_start: 0.8150 (mp) cc_final: 0.7736 (mp)
REVERT: A  383 MET cc_start: 0.7610 (mmp) cc_final: 0.7275 (mmp)
REVERT: A  579 MET cc_start: 0.7549 (tpt) cc_final: 0.7092 (tpt)
REVERT: A  624 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7569 (tt0)
REVERT: A  684 ILE cc_start: 0.8174 (mm) cc_final: 0.7809 (mt)
REVERT: A  685 ASN cc_start: 0.8295 (m-40) cc_final: 0.8015 (m-40)
REVERT: A  697 MET cc_start: 0.6485 (mmm) cc_final: 0.6092 (mmm)
REVERT: A  736 ASN cc_start: 0.7699 (m-40) cc_final: 0.7243 (m-40)
REVERT: A  881 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8091 (mt-10)
REVERT: A  958 LYS cc_start: 0.8097 (ttpp) cc_final: 0.7501 (ttpp)
REVERT: A  990 ARG cc_start: 0.7923 (ttm110) cc_final: 0.7411 (ttm110)
REVERT: A 1037 THR cc_start: 0.8457 (t) cc_final: 0.8117 (m)
REVERT: A 1054 ASN cc_start: 0.8299 (t0) cc_final: 0.8023 (t0)
REVERT: A 1173 LYS cc_start: 0.7858 (ttmt) cc_final: 0.7555 (ttmm)
REVERT: A 1183 GLU cc_start: 0.8062 (tt0) cc_final: 0.7841 (tt0)
  outliers start: 27
  outliers final: 22
  residues processed: 218
  average time/residue: 0.2385
  time to fit residues: 67.7159
Evaluate side-chains
  222 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 200
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  506 ASN
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  652 ILE
Chi-restraints excluded: chain A residue  822 ILE
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  865 ARG
Chi-restraints excluded: chain A residue 1082 LEU
Chi-restraints excluded: chain A residue 1109 PHE
Chi-restraints excluded: chain A residue 1142 LEU
Chi-restraints excluded: chain A residue 1188 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 44 optimal weight:    0.6980
   chunk 71 optimal weight:    0.3980
   chunk 48 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 94 optimal weight:    0.5980
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 132 HIS
A 374 GLN
A1074 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.134539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.111948 restraints weight = 11102.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 1.90
r_work: 0.3193 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3031 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.2787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8279  Z= 0.186
  Angle     :  0.467   7.357  11229  Z= 0.247
  Chirality :  0.039   0.152   1350
  Planarity :  0.004   0.048   1383
  Dihedral  :  3.755  18.382   1097
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 16.52 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.14 (0.19), residues: 717
  sheet:  0.83 (0.97), residues: 28
  loop :  0.14 (0.38), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 278 
 HIS   0.004   0.001   HIS A1120 
 PHE   0.014   0.001   PHE A 254 
 TYR   0.017   0.001   TYR A 267 
 ARG   0.008   0.000   ARG A 161 

*********************** 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
  227 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 203
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 MET cc_start: 0.7426 (mmt) cc_final: 0.7104 (mmm)
REVERT: A  176 VAL cc_start: 0.8330 (p) cc_final: 0.7992 (m)
REVERT: A  186 MET cc_start: 0.8073 (mtp) cc_final: 0.7850 (mtp)
REVERT: A  200 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7778 (ttm)
REVERT: A  205 MET cc_start: 0.8271 (mmm) cc_final: 0.8008 (mmp)
REVERT: A  217 LEU cc_start: 0.8147 (mp) cc_final: 0.7732 (mp)
REVERT: A  383 MET cc_start: 0.7560 (mmp) cc_final: 0.7224 (mmp)
REVERT: A  579 MET cc_start: 0.7480 (tpt) cc_final: 0.7155 (tpt)
REVERT: A  624 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7551 (tt0)
REVERT: A  684 ILE cc_start: 0.8153 (mm) cc_final: 0.7776 (mt)
REVERT: A  685 ASN cc_start: 0.8312 (m-40) cc_final: 0.8026 (m-40)
REVERT: A  697 MET cc_start: 0.6493 (mmm) cc_final: 0.6117 (mmm)
REVERT: A  736 ASN cc_start: 0.7689 (m-40) cc_final: 0.7212 (m-40)
REVERT: A  832 GLN cc_start: 0.8441 (tp40) cc_final: 0.8238 (tp40)
REVERT: A  881 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8099 (mt-10)
REVERT: A  958 LYS cc_start: 0.8100 (ttpp) cc_final: 0.7498 (ttpp)
REVERT: A  990 ARG cc_start: 0.7958 (ttm110) cc_final: 0.7439 (ttm110)
REVERT: A 1037 THR cc_start: 0.8438 (t) cc_final: 0.8102 (m)
REVERT: A 1054 ASN cc_start: 0.8312 (t0) cc_final: 0.8037 (t0)
REVERT: A 1173 LYS cc_start: 0.7867 (ttmt) cc_final: 0.7561 (ttmm)
REVERT: A 1182 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7476 (mm-30)
  outliers start: 24
  outliers final: 22
  residues processed: 216
  average time/residue: 0.2405
  time to fit residues: 67.8079
Evaluate side-chains
  224 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 201
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  506 ASN
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  652 ILE
Chi-restraints excluded: chain A residue  822 ILE
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  865 ARG
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1109 PHE
Chi-restraints excluded: chain A residue 1142 LEU
Chi-restraints excluded: chain A residue 1188 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 57 optimal weight:    5.9990
   chunk 73 optimal weight:    0.5980
   chunk 5 optimal weight:    0.4980
   chunk 1 optimal weight:    1.9990
   chunk 96 optimal weight:    0.5980
   chunk 85 optimal weight:    1.9990
   chunk 38 optimal weight:    0.2980
   chunk 19 optimal weight:    0.9990
   chunk 100 optimal weight:    0.1980
   chunk 97 optimal weight:    0.8980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A 374 GLN
A1074 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.135813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.113358 restraints weight = 11134.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 1.89
r_work: 0.3219 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3060 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8279  Z= 0.161
  Angle     :  0.467   9.796  11229  Z= 0.243
  Chirality :  0.038   0.153   1350
  Planarity :  0.004   0.048   1383
  Dihedral  :  3.668  19.138   1097
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 16.86 %
    Favored  : 80.54 %
  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:  2.49 (0.27), residues: 1016
  helix:  2.21 (0.19), residues: 720
  sheet:  0.95 (0.98), residues: 28
  loop :  0.23 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 278 
 HIS   0.004   0.001   HIS A1133 
 PHE   0.013   0.001   PHE A 254 
 TYR   0.013   0.001   TYR A 267 
 ARG   0.008   0.000   ARG A 161 

*********************** 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
  227 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 204
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
REVERT: A  160 MET cc_start: 0.7430 (mmt) cc_final: 0.7109 (mmm)
REVERT: A  176 VAL cc_start: 0.8323 (p) cc_final: 0.8005 (m)
REVERT: A  186 MET cc_start: 0.8007 (mtp) cc_final: 0.7768 (mtp)
REVERT: A  200 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7787 (ttm)
REVERT: A  205 MET cc_start: 0.8246 (mmm) cc_final: 0.7976 (mmp)
REVERT: A  217 LEU cc_start: 0.8191 (mp) cc_final: 0.7774 (mp)
REVERT: A  338 LYS cc_start: 0.8343 (mtmt) cc_final: 0.8040 (mtmm)
REVERT: A  383 MET cc_start: 0.7549 (mmp) cc_final: 0.7212 (mmp)
REVERT: A  579 MET cc_start: 0.7464 (tpt) cc_final: 0.7124 (tpt)
REVERT: A  584 LEU cc_start: 0.8437 (mm) cc_final: 0.8093 (mp)
REVERT: A  624 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7534 (tt0)
REVERT: A  684 ILE cc_start: 0.8177 (mm) cc_final: 0.7789 (mt)
REVERT: A  685 ASN cc_start: 0.8332 (m-40) cc_final: 0.8075 (m-40)
REVERT: A  697 MET cc_start: 0.6525 (mmm) cc_final: 0.6145 (tmm)
REVERT: A  736 ASN cc_start: 0.7670 (m-40) cc_final: 0.7200 (m-40)
REVERT: A  769 PHE cc_start: 0.7460 (t80) cc_final: 0.7242 (t80)
REVERT: A  832 GLN cc_start: 0.8431 (tp40) cc_final: 0.8210 (tp40)
REVERT: A  857 MET cc_start: 0.7995 (tpp) cc_final: 0.7663 (tpp)
REVERT: A  958 LYS cc_start: 0.8095 (ttpp) cc_final: 0.7490 (ttpp)
REVERT: A  990 ARG cc_start: 0.7969 (ttm110) cc_final: 0.7463 (ttm110)
REVERT: A 1037 THR cc_start: 0.8413 (t) cc_final: 0.8082 (m)
REVERT: A 1054 ASN cc_start: 0.8316 (t0) cc_final: 0.8042 (t0)
REVERT: A 1173 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7554 (ttmm)
REVERT: A 1182 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7466 (mm-30)
  outliers start: 23
  outliers final: 17
  residues processed: 216
  average time/residue: 0.2331
  time to fit residues: 66.1975
Evaluate side-chains
  218 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 200
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  506 ASN
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  822 ILE
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  865 ARG
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1142 LEU
Chi-restraints excluded: chain A residue 1188 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 67 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 39 optimal weight:    0.3980
   chunk 0 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   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 374 GLN
A1074 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.134440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.112054 restraints weight = 11233.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 1.89
r_work: 0.3206 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8279  Z= 0.225
  Angle     :  0.488   7.092  11229  Z= 0.255
  Chirality :  0.040   0.149   1350
  Planarity :  0.004   0.049   1383
  Dihedral  :  3.731  18.957   1097
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 17.42 %
    Favored  : 80.20 %
  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:  2.33 (0.26), residues: 1016
  helix:  2.08 (0.19), residues: 725
  sheet:  1.14 (0.97), residues: 28
  loop :  0.14 (0.39), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 278 
 HIS   0.006   0.001   HIS A1120 
 PHE   0.012   0.001   PHE A 254 
 TYR   0.013   0.001   TYR A 267 
 ARG   0.008   0.000   ARG A 161 

*********************** 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
  220 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 199
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 MET cc_start: 0.7444 (mmt) cc_final: 0.7119 (mmm)
REVERT: A  176 VAL cc_start: 0.8334 (p) cc_final: 0.8009 (m)
REVERT: A  186 MET cc_start: 0.8081 (mtp) cc_final: 0.7845 (mtp)
REVERT: A  200 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7796 (ttm)
REVERT: A  205 MET cc_start: 0.8248 (mmm) cc_final: 0.8014 (mmp)
REVERT: A  217 LEU cc_start: 0.8190 (mp) cc_final: 0.7777 (mp)
REVERT: A  383 MET cc_start: 0.7572 (mmp) cc_final: 0.7247 (mmp)
REVERT: A  579 MET cc_start: 0.7476 (tpt) cc_final: 0.7179 (tpt)
REVERT: A  624 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7536 (tt0)
REVERT: A  684 ILE cc_start: 0.8191 (mm) cc_final: 0.7814 (mt)
REVERT: A  685 ASN cc_start: 0.8287 (m-40) cc_final: 0.8031 (m-40)
REVERT: A  697 MET cc_start: 0.6563 (mmm) cc_final: 0.6196 (tmm)
REVERT: A  736 ASN cc_start: 0.7690 (m-40) cc_final: 0.7221 (m-40)
REVERT: A  769 PHE cc_start: 0.7482 (t80) cc_final: 0.7242 (t80)
REVERT: A  857 MET cc_start: 0.7980 (tpp) cc_final: 0.7660 (tpp)
REVERT: A  958 LYS cc_start: 0.8110 (ttpp) cc_final: 0.7507 (ttpp)
REVERT: A 1037 THR cc_start: 0.8440 (t) cc_final: 0.8102 (m)
REVERT: A 1045 MET cc_start: 0.8207 (tpp) cc_final: 0.7965 (mmm)
REVERT: A 1173 LYS cc_start: 0.7873 (ttmt) cc_final: 0.7575 (ttmm)
REVERT: A 1182 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7488 (mm-30)
  outliers start: 21
  outliers final: 17
  residues processed: 213
  average time/residue: 0.2310
  time to fit residues: 64.4545
Evaluate side-chains
  214 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 196
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  506 ASN
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  822 ILE
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  865 ARG
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1109 PHE
Chi-restraints excluded: chain A residue 1142 LEU
Chi-restraints excluded: chain A residue 1188 VAL
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:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 71 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9980
   chunk 72 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 832 GLN
A1074 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.134311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.111959 restraints weight = 11021.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 1.88
r_work: 0.3192 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.2940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8279  Z= 0.228
  Angle     :  0.500   8.616  11229  Z= 0.259
  Chirality :  0.040   0.219   1350
  Planarity :  0.004   0.049   1383
  Dihedral  :  3.741  18.994   1097
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 17.19 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.38 (0.26), residues: 1016
  helix:  2.09 (0.19), residues: 721
  sheet:  1.10 (0.98), residues: 28
  loop :  0.29 (0.39), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 278 
 HIS   0.006   0.001   HIS A1120 
 PHE   0.019   0.001   PHE A 254 
 TYR   0.012   0.001   TYR A 267 
 ARG   0.009   0.000   ARG A 161 

********************** 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
  210 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 192
  time to evaluate  : 0.858 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 MET cc_start: 0.7460 (mmt) cc_final: 0.7137 (mmm)
REVERT: A  176 VAL cc_start: 0.8342 (p) cc_final: 0.8018 (m)
REVERT: A  186 MET cc_start: 0.8083 (mtp) cc_final: 0.7845 (mtp)
REVERT: A  205 MET cc_start: 0.8247 (mmm) cc_final: 0.8022 (mmp)
REVERT: A  383 MET cc_start: 0.7588 (mmp) cc_final: 0.7251 (mmp)
REVERT: A  579 MET cc_start: 0.7464 (tpt) cc_final: 0.7109 (tpt)
REVERT: A  624 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7547 (tt0)
REVERT: A  684 ILE cc_start: 0.8192 (mm) cc_final: 0.7777 (mt)
REVERT: A  685 ASN cc_start: 0.8311 (m-40) cc_final: 0.8052 (m-40)
REVERT: A  697 MET cc_start: 0.6544 (mmm) cc_final: 0.6182 (tmm)
REVERT: A  736 ASN cc_start: 0.7699 (m-40) cc_final: 0.7226 (m-40)
REVERT: A  769 PHE cc_start: 0.7490 (t80) cc_final: 0.7256 (t80)
REVERT: A  812 ARG cc_start: 0.8472 (ptm-80) cc_final: 0.8049 (ttt180)
REVERT: A  857 MET cc_start: 0.7976 (tpp) cc_final: 0.7649 (tpp)
REVERT: A  958 LYS cc_start: 0.8112 (ttpp) cc_final: 0.7509 (ttpp)
REVERT: A 1037 THR cc_start: 0.8403 (t) cc_final: 0.8054 (m)
REVERT: A 1045 MET cc_start: 0.8195 (tpp) cc_final: 0.7945 (mmm)
REVERT: A 1173 LYS cc_start: 0.7854 (ttmt) cc_final: 0.7554 (ttmm)
REVERT: A 1182 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7482 (mm-30)
  outliers start: 18
  outliers final: 18
  residues processed: 204
  average time/residue: 0.2504
  time to fit residues: 66.2113
Evaluate side-chains
  209 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 191
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  506 ASN
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  822 ILE
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  865 ARG
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1109 PHE
Chi-restraints excluded: chain A residue 1142 LEU
Chi-restraints excluded: chain A residue 1188 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 101 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A1074 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.134602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.112121 restraints weight = 11120.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 1.89
r_work: 0.3171 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.2968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8279  Z= 0.227
  Angle     :  0.503   8.442  11229  Z= 0.261
  Chirality :  0.041   0.342   1350
  Planarity :  0.004   0.049   1383
  Dihedral  :  3.752  18.911   1097
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 16.86 %
    Favored  : 80.88 %
  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:  2.34 (0.26), residues: 1016
  helix:  2.07 (0.19), residues: 722
  sheet:  1.03 (0.99), residues: 28
  loop :  0.26 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 278 
 HIS   0.006   0.001   HIS A1120 
 PHE   0.018   0.001   PHE A 254 
 TYR   0.012   0.001   TYR A 267 
 ARG   0.010   0.000   ARG A 161 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4407.89 seconds
wall clock time: 78 minutes 50.80 seconds (4730.80 seconds total)