Starting phenix.real_space_refine
on Wed Mar  4 14:06:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yna_33956/03_2026/7yna_33956.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yna_33956/03_2026/7yna_33956.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yna_33956/03_2026/7yna_33956.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yna_33956/03_2026/7yna_33956.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yna_33956/03_2026/7yna_33956.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yna_33956/03_2026/7yna_33956.cif"
  }
  resolution = 3.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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: 5
    Type Number    sf(0)   Gaussians
     P      63      5.49       5
     S      57      5.16       5
     C    8468      2.51       5
     N    2454      2.21       5
     O    2742      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13784
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 12447
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1536, 12447
          Classifications: {'peptide': 1536}
          Link IDs: {'PTRANS': 84, 'TRANS': 1451}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 810
          Classifications: {'RNA': 38}
          Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 6, 'rna3p_pur': 7, 'rna3p_pyr': 11}
          Link IDs: {'rna2p': 20, 'rna3p': 17}
    Chain: "C"
      Number of atoms: 527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 527
          Classifications: {'RNA': 25}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 12}
          Link IDs: {'rna2p': 3, 'rna3p': 21}
  Time building chain proxies: 3.49, per 1000 atoms: 0.25
  Number of scatterers: 13784
  At special positions: 0
  Unit cell: (92.02, 171.2, 132.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      57     16.00
     P      63     15.00
     O    2742      8.00
     N    2454      7.00
     C    8468      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.27
  Conformation dependent library (CDL) restraints added in 692.1 milliseconds
  

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2858

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 20 sheets defined
      22.2% alpha, 15.3% beta
      16 base pairs and 23 stacking pairs defined.
    Time for finding SS restraints: 1.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 58 through 74
      removed outlier: 3.510A  pdb=" N   THR A  74 " --> pdb=" O   GLU A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 77
      No H-bonds generated for 'chain 'A' and resid 75 through 77'
    Processing helix  chain 'A' and resid 123 through 130
    Processing helix  chain 'A' and resid 163 through 167
    Processing helix  chain 'A' and resid 213 through 225
    Processing helix  chain 'A' and resid 261 through 276
    Processing helix  chain 'A' and resid 281 through 290
    Processing helix  chain 'A' and resid 291 through 295
      removed outlier: 4.037A  pdb=" N   ARG A 294 " --> pdb=" O   SER A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 302
      removed outlier: 3.945A  pdb=" N   LEU A 302 " --> pdb=" O   VAL A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 336
    Processing helix  chain 'A' and resid 344 through 365
      removed outlier: 4.080A  pdb=" N   ASP A 365 " --> pdb=" O   LEU A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 459
      removed outlier: 3.613A  pdb=" N   VAL A 447 " --> pdb=" O   PRO A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 554
    Processing helix  chain 'A' and resid 562 through 566
    Processing helix  chain 'A' and resid 587 through 594
      removed outlier: 3.562A  pdb=" N   ASN A 594 " --> pdb=" O   ASP A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 607
    Processing helix  chain 'A' and resid 642 through 649
    Processing helix  chain 'A' and resid 675 through 688
      removed outlier: 3.651A  pdb=" N   PHE A 679 " --> pdb=" O   LYS A 675 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 709 through 713
    Processing helix  chain 'A' and resid 780 through 784
    Processing helix  chain 'A' and resid 787 through 801
    Processing helix  chain 'A' and resid 809 through 813
      removed outlier: 3.650A  pdb=" N   GLY A 813 " --> pdb=" O   SER A 810 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 946 through 962
      removed outlier: 3.986A  pdb=" N   LEU A 950 " --> pdb=" O   PRO A 946 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   THR A 962 " --> pdb=" O   TYR A 958 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1101 through 1109
      removed outlier: 4.178A  pdb=" N   GLU A1106 " --> pdb=" O   ASN A1102 " (cutoff:3.500A)
      removed outlier: 5.389A  pdb=" N   LYS A1107 " --> pdb=" O   PHE A1103 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LEU A1108 " --> pdb=" O   ASP A1104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1231 through 1246
      removed outlier: 3.980A  pdb=" N   ARG A1235 " --> pdb=" O   PRO A1231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1259 through 1265
    Processing helix  chain 'A' and resid 1300 through 1305
      removed outlier: 4.132A  pdb=" N   MET A1305 " --> pdb=" O   GLY A1302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1420 through 1427
      removed outlier: 3.975A  pdb=" N   ILE A1424 " --> pdb=" O   ALA A1420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1466 through 1476
      removed outlier: 3.646A  pdb=" N   GLN A1476 " --> pdb=" O   ILE A1472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1515 through 1517
      No H-bonds generated for 'chain 'A' and resid 1515 through 1517'
    Processing helix  chain 'A' and resid 1518 through 1534
    Processing helix  chain 'A' and resid 1538 through 1548
    Processing helix  chain 'A' and resid 1565 through 1569
      removed outlier: 4.032A  pdb=" N   ASP A1568 " --> pdb=" O   ARG A1565 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ASP A1569 " --> pdb=" O   LYS A1566 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1565 through 1569'
    Processing helix  chain 'A' and resid 1575 through 1580
    Processing helix  chain 'A' and resid 1588 through 1595
      removed outlier: 3.569A  pdb=" N   THR A1594 " --> pdb=" O   GLN A1590 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150
    Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17
      removed outlier: 3.709A  pdb=" N   MET A  17 " --> pdb=" O   TYR A 190 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   TYR A 190 " --> pdb=" O   MET A  17 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ARG A 171 " --> pdb=" O   ALA A 189 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 44
    Processing sheet with id=AA4, first strand: chain 'A' and resid 483 through 484
      removed outlier: 3.630A  pdb=" N   TYR A 577 " --> pdb=" O   ASN A 611 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ASN A 611 " --> pdb=" O   TYR A 577 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 527 through 529
    Processing sheet with id=AA6, first strand: chain 'A' and resid 497 through 504
      removed outlier: 3.742A  pdb=" N   GLU A 497 " --> pdb=" O   VAL A 521 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   ARG A 503 " --> pdb=" O   ALA A 515 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   ALA A 515 " --> pdb=" O   ARG A 503 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 723 through 724
      removed outlier: 3.743A  pdb=" N   VAL A 630 " --> pdb=" O   GLY A 774 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   ASN A 629 " --> pdb=" O   ILE A 822 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   ILE A 822 " --> pdb=" O   ASN A 629 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   SER A 631 " --> pdb=" O   LEU A 820 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   LEU A 820 " --> pdb=" O   SER A 631 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   GLU A 633 " --> pdb=" O   LYS A 818 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 659 through 660
      removed outlier: 3.518A  pdb=" N   LEU A 728 " --> pdb=" O   TYR A 674 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 739 through 744
      removed outlier: 3.594A  pdb=" N   PHE A 757 " --> pdb=" O   HIS A 741 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   LYS A 755 " --> pdb=" O   ALA A 743 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 861 through 862
    Processing sheet with id=AB2, first strand: chain 'A' and resid 944 through 945
      removed outlier: 3.603A  pdb=" N   SER A1363 " --> pdb=" O   SER A1455 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 944 through 945
      removed outlier: 3.603A  pdb=" N   SER A1363 " --> pdb=" O   SER A1455 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 976 through 978
    Processing sheet with id=AB5, first strand: chain 'A' and resid 991 through 993
      removed outlier: 4.035A  pdb=" N   VAL A1275 " --> pdb=" O   GLY A 993 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   TYR A1276 " --> pdb=" O   ILE A1287 " (cutoff:3.500A)
      removed outlier: 4.728A  pdb=" N   ILE A1287 " --> pdb=" O   TYR A1276 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   LYS A1278 " --> pdb=" O   GLU A1285 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1001 through 1011
      removed outlier: 8.390A  pdb=" N   ALA A1129 " --> pdb=" O   THR A1008 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   ARG A1010 " --> pdb=" O   ALA A1129 " (cutoff:3.500A)
      removed outlier: 19.405A  pdb=" N   CYS A1143 " --> pdb=" O   LYS A1223 " (cutoff:3.500A)
      removed outlier: 14.370A  pdb=" N   LYS A1223 " --> pdb=" O   CYS A1143 " (cutoff:3.500A)
      removed outlier: 9.178A  pdb=" N   GLU A1145 " --> pdb=" O   ASP A1221 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ASP A1221 " --> pdb=" O   GLU A1145 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   PHE A1220 " --> pdb=" O   GLU A1007 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   GLU A1007 " --> pdb=" O   PHE A1220 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   LEU A1222 " --> pdb=" O   PHE A1005 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   PHE A1005 " --> pdb=" O   LEU A1222 " (cutoff:3.500A)
      removed outlier: 7.752A  pdb=" N   GLU A1224 " --> pdb=" O   GLN A1003 " (cutoff:3.500A)
      removed outlier: 8.512A  pdb=" N   GLN A1003 " --> pdb=" O   GLU A1224 " (cutoff:3.500A)
      removed outlier: 10.121A  pdb=" N   GLU A1226 " --> pdb=" O   HIS A1001 " (cutoff:3.500A)
      removed outlier: 8.960A  pdb=" N   HIS A1001 " --> pdb=" O   GLU A1226 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1044 through 1047
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1070 through 1071
    Processing sheet with id=AB9, first strand: chain 'A' and resid 1081 through 1086
      removed outlier: 3.670A  pdb=" N   LEU A1096 " --> pdb=" O   PHE A1083 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   VAL A1085 " --> pdb=" O   PHE A1094 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 1200 through 1202
    Processing sheet with id=AC2, first strand: chain 'A' and resid 1385 through 1387

    307 hydrogen bonds defined for protein.
    825 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      40 hydrogen bonds
      80 hydrogen bond angles
      0 basepair planarities
      16 basepair parallelities
      23 stacking parallelities
  Total time for adding SS restraints: 3.07

  Time building geometry restraints manager: 1.67 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3596
        1.33 -     1.45: 2944
        1.45 -     1.57: 7491
        1.57 -     1.69: 124
        1.69 -     1.81: 82
  Bond restraints: 14237
  Sorted by residual:
  bond pdb=" C   CYS A1560 "
       pdb=" N   TYR A1561 "
    ideal  model  delta    sigma   weight residual
    1.331  1.267  0.064 2.07e-02 2.33e+03 9.42e+00
  bond pdb=" N   CYS A 965 "
       pdb=" CA  CYS A 965 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.22e-02 6.72e+03 7.06e+00
  bond pdb=" N   CYS A 706 "
       pdb=" CA  CYS A 706 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.034 1.30e-02 5.92e+03 6.87e+00
  bond pdb=" N   CYS A 711 "
       pdb=" CA  CYS A 711 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.033 1.29e-02 6.01e+03 6.68e+00
  bond pdb=" N   CYS A 708 "
       pdb=" CA  CYS A 708 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.25e-02 6.40e+03 6.19e+00
  ... (remaining 14232 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 19113
        2.23 -     4.45: 342
        4.45 -     6.68: 25
        6.68 -     8.91: 3
        8.91 -    11.13: 1
  Bond angle restraints: 19484
  Sorted by residual:
  angle pdb=" N   SER A1080 "
        pdb=" CA  SER A1080 "
        pdb=" C   SER A1080 "
      ideal   model   delta    sigma   weight residual
     108.34  113.35   -5.01 1.31e+00 5.83e-01 1.46e+01
  angle pdb=" N   LYS A1586 "
        pdb=" CA  LYS A1586 "
        pdb=" C   LYS A1586 "
      ideal   model   delta    sigma   weight residual
     114.75  110.41    4.34 1.26e+00 6.30e-01 1.18e+01
  angle pdb=" CA  CYS A 708 "
        pdb=" C   CYS A 708 "
        pdb=" O   CYS A 708 "
      ideal   model   delta    sigma   weight residual
     121.55  118.02    3.53 1.06e+00 8.90e-01 1.11e+01
  angle pdb=" N   GLN A 884 "
        pdb=" CA  GLN A 884 "
        pdb=" C   GLN A 884 "
      ideal   model   delta    sigma   weight residual
     110.80  103.99    6.81 2.13e+00 2.20e-01 1.02e+01
  angle pdb=" C   SER A1403 "
        pdb=" N   ASP A1404 "
        pdb=" CA  ASP A1404 "
      ideal   model   delta    sigma   weight residual
     121.54  115.60    5.94 1.91e+00 2.74e-01 9.69e+00
  ... (remaining 19479 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.14: 8376
       34.14 -    68.28: 289
       68.28 -   102.42: 35
      102.42 -   136.56: 2
      136.56 -   170.70: 1
  Dihedral angle restraints: 8703
    sinusoidal: 4272
      harmonic: 4431
  Sorted by residual:
  dihedral pdb=" CA  HIS A 383 "
           pdb=" C   HIS A 383 "
           pdb=" N   GLY A 384 "
           pdb=" CA  GLY A 384 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.48  -23.52     0      5.00e+00 4.00e-02 2.21e+01
  dihedral pdb=" CA  LEU A 173 "
           pdb=" C   LEU A 173 "
           pdb=" N   ASN A 174 "
           pdb=" CA  ASN A 174 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.20  -20.80     0      5.00e+00 4.00e-02 1.73e+01
  dihedral pdb=" C4'   U B -14 "
           pdb=" C3'   U B -14 "
           pdb=" O3'   U B -14 "
           pdb=" P     G B -13 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -110.00   60.70 -170.70     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 8700 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1524
       0.048 -    0.097: 440
       0.097 -    0.145: 103
       0.145 -    0.193: 13
       0.193 -    0.241: 4
  Chirality restraints: 2084
  Sorted by residual:
  chirality pdb=" C3'   U B -14 "
            pdb=" C4'   U B -14 "
            pdb=" O3'   U B -14 "
            pdb=" C2'   U B -14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.50   -0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" C1'   A B  13 "
            pdb=" O4'   A B  13 "
            pdb=" C2'   A B  13 "
            pdb=" N9    A B  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.25    0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  CYS A1342 "
            pdb=" N   CYS A1342 "
            pdb=" C   CYS A1342 "
            pdb=" CB  CYS A1342 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.00e+00
  ... (remaining 2081 not shown)

  Planarity restraints: 2315
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 863 "   -0.052 5.00e-02 4.00e+02   7.89e-02 9.96e+00
        pdb=" N   PRO A 864 "    0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO A 864 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 864 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B   9 "   -0.037 2.00e-02 2.50e+03   1.69e-02 8.56e+00
        pdb=" N9    G B   9 "    0.043 2.00e-02 2.50e+03
        pdb=" C8    G B   9 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    G B   9 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    G B   9 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G B   9 "   -0.006 2.00e-02 2.50e+03
        pdb=" O6    G B   9 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    G B   9 "   -0.005 2.00e-02 2.50e+03
        pdb=" C2    G B   9 "    0.005 2.00e-02 2.50e+03
        pdb=" N2    G B   9 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G B   9 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    G B   9 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A1311 "   -0.013 2.00e-02 2.50e+03   2.62e-02 6.87e+00
        pdb=" C   PRO A1311 "    0.045 2.00e-02 2.50e+03
        pdb=" O   PRO A1311 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   CYS A1312 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 2312 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 609
        2.69 -     3.25: 13133
        3.25 -     3.80: 20329
        3.80 -     4.35: 25821
        4.35 -     4.90: 44074
  Nonbonded interactions: 103966
  Sorted by model distance:
  nonbonded pdb=" O2'   A B  11 "
            pdb=" O4'   C B  12 "
     model   vdw
     2.143 3.040
  nonbonded pdb=" OG  SER A 445 "
            pdb=" OP1   A B  -2 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" NZ  LYS A1004 "
            pdb=" O   PHE A1005 "
     model   vdw
     2.229 3.120
  nonbonded pdb=" NE2 HIS A 931 "
            pdb=" OG1 THR A1444 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" NH1 ARG A 974 "
            pdb=" O   ASP A1298 "
     model   vdw
     2.241 3.120
  ... (remaining 103961 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.670
  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:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     16.100
  Find NCS groups from input model:        0.060
  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:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
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      :  0.007   0.064  14237  Z= 0.293
  Angle     :  0.729  11.132  19484  Z= 0.406
  Chirality :  0.048   0.241   2084
  Planarity :  0.005   0.079   2315
  Dihedral  : 16.960 170.704   5845
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 16.06 %
    Favored  : 83.81 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  7.22 %
    Favored  : 92.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.75 (0.17), residues: 1526
  helix: -1.14 (0.28), residues: 300
  sheet: -3.22 (0.26), residues: 281
  loop : -4.07 (0.15), residues: 945

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 444 
 TYR   0.021   0.002   TYR A 863 
 PHE   0.015   0.002   PHE A 528 
 TRP   0.015   0.002   TRP A1600 
 HIS   0.005   0.002   HIS A1473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00655 (14237)
  covalent geometry    : angle       0.72934 (19484)
  hydrogen bonds       : bond        0.21404 (  342)
  hydrogen bonds       : angle       6.95324 (  905)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.496 
Fit side-chains
REVERT: A  311 ASP cc_start: 0.8125 (t0) cc_final: 0.7676 (t70)
REVERT: A 1065 ARG cc_start: 0.8012 (mmm160) cc_final: 0.7252 (ttm170)
REVERT: A 1211 MET cc_start: 0.7960 (tmm) cc_final: 0.7124 (tmm)
REVERT: A 1270 LYS cc_start: 0.7649 (mmmt) cc_final: 0.7340 (mttm)
REVERT: A 1342 CYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7846 (p)
  outliers start: 8
  outliers final: 3
  residues processed: 74
  average time/residue: 0.1716
  time to fit residues: 17.4630
Evaluate side-chains
  48 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 CYS
Chi-restraints excluded: chain A residue  708 CYS
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue 1342 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    0.5980
   chunk 149 optimal weight:    3.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 118 ASN
A 306 HIS
A 456 GLN
A 586 ASN
A1027 GLN
A1095 HIS
A1136 ASN
A1207 ASN
A1417 HIS
A1419 HIS
A1452 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.081419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.061286 restraints weight = 36638.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.063345 restraints weight = 19957.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.064652 restraints weight = 13954.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.065462 restraints weight = 11240.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.065899 restraints weight = 9836.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.1093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  14237  Z= 0.133
  Angle     :  0.616  11.983  19484  Z= 0.320
  Chirality :  0.044   0.213   2084
  Planarity :  0.005   0.066   2315
  Dihedral  : 16.259 164.850   2639
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.42 %
    Favored  : 89.58 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 10.12 %
    Favored  : 89.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.77 (0.19), residues: 1526
  helix:  0.26 (0.31), residues: 311
  sheet: -2.50 (0.28), residues: 275
  loop : -3.73 (0.16), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 393 
 TYR   0.011   0.001   TYR A 863 
 PHE   0.010   0.001   PHE A 776 
 TRP   0.011   0.001   TRP A1600 
 HIS   0.005   0.001   HIS A1149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (14237)
  covalent geometry    : angle       0.61573 (19484)
  hydrogen bonds       : bond        0.04695 (  342)
  hydrogen bonds       : angle       4.72925 (  905)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.575 
Fit side-chains
REVERT: A  305 ASP cc_start: 0.7313 (t0) cc_final: 0.6860 (t0)
REVERT: A  410 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7716 (pp)
REVERT: A  989 ASP cc_start: 0.8142 (t70) cc_final: 0.7918 (t0)
REVERT: A 1065 ARG cc_start: 0.7846 (mmm160) cc_final: 0.7203 (ttm170)
REVERT: A 1211 MET cc_start: 0.7970 (tmm) cc_final: 0.7258 (tmm)
REVERT: A 1270 LYS cc_start: 0.7630 (mmmt) cc_final: 0.7376 (mttm)
  outliers start: 5
  outliers final: 3
  residues processed: 69
  average time/residue: 0.1498
  time to fit residues: 15.0337
Evaluate side-chains
  54 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 CYS
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue 1479 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 9 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 122 optimal weight:    9.9990
   chunk 100 optimal weight:    0.7980
   chunk 102 optimal weight:    3.9990
   chunk 56 optimal weight:    7.9990
   chunk 104 optimal weight:    0.7980
   chunk 156 optimal weight:   10.0000
   chunk 94 optimal weight:   20.0000
   chunk 36 optimal weight:    5.9990
   overall best weight:    3.5186

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

Flipped N/Q/H residues before XYZ refinement:
A1246 ASN
A1483 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.078501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.058313 restraints weight = 37610.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.060292 restraints weight = 20690.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.061530 restraints weight = 14609.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.062263 restraints weight = 11863.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.062689 restraints weight = 10483.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.1076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051  14237  Z= 0.281
  Angle     :  0.700  11.264  19484  Z= 0.364
  Chirality :  0.048   0.249   2084
  Planarity :  0.006   0.078   2315
  Dihedral  : 16.237 167.025   2637
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.42 %
    Favored  : 85.58 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 13.84 %
    Favored  : 84.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.63 (0.19), residues: 1526
  helix:  0.31 (0.31), residues: 316
  sheet: -2.35 (0.27), residues: 292
  loop : -3.66 (0.16), residues: 918

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 444 
 TYR   0.023   0.002   TYR A 863 
 PHE   0.017   0.002   PHE A 658 
 TRP   0.015   0.002   TRP A1600 
 HIS   0.006   0.002   HIS A1473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00649 (14237)
  covalent geometry    : angle       0.70020 (19484)
  hydrogen bonds       : bond        0.05719 (  342)
  hydrogen bonds       : angle       4.74213 (  905)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 45
  time to evaluate  : 0.479 
Fit side-chains
REVERT: A   60 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9123 (tt)
REVERT: A  410 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7980 (pp)
REVERT: A  989 ASP cc_start: 0.8220 (t70) cc_final: 0.7906 (t0)
REVERT: A 1065 ARG cc_start: 0.7940 (mmm160) cc_final: 0.7340 (ttm170)
REVERT: A 1211 MET cc_start: 0.8040 (tmm) cc_final: 0.7145 (tmm)
REVERT: A 1270 LYS cc_start: 0.7705 (mmmt) cc_final: 0.7424 (mttm)
REVERT: A 1533 TRP cc_start: 0.8352 (OUTLIER) cc_final: 0.7932 (m-10)
  outliers start: 21
  outliers final: 13
  residues processed: 65
  average time/residue: 0.1275
  time to fit residues: 12.5756
Evaluate side-chains
  63 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 47
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   86 CYS
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  968 ILE
Chi-restraints excluded: chain A residue 1008 THR
Chi-restraints excluded: chain A residue 1087 THR
Chi-restraints excluded: chain A residue 1156 VAL
Chi-restraints excluded: chain A residue 1479 LYS
Chi-restraints excluded: chain A residue 1533 TRP
Chi-restraints excluded: chain A residue 1600 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 135 optimal weight:    1.9990
   chunk 7 optimal weight:    7.9990
   chunk 104 optimal weight:    6.9990
   chunk 25 optimal weight:    0.6980
   chunk 95 optimal weight:    8.9990
   chunk 114 optimal weight:    9.9990
   chunk 36 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 134 optimal weight:    4.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 208 ASN
A1105 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.080258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.059982 restraints weight = 37300.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.062028 restraints weight = 20128.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.063335 restraints weight = 14066.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.064138 restraints weight = 11337.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.064629 restraints weight = 9928.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8560
moved from start:          0.1307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  14237  Z= 0.168
  Angle     :  0.613  11.618  19484  Z= 0.317
  Chirality :  0.044   0.218   2084
  Planarity :  0.005   0.070   2315
  Dihedral  : 16.141 165.244   2637
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.14 %
    Favored  : 88.86 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 15.25 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.23 (0.20), residues: 1526
  helix:  0.80 (0.31), residues: 310
  sheet: -2.08 (0.29), residues: 287
  loop : -3.44 (0.17), residues: 929

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 393 
 TYR   0.013   0.001   TYR A 863 
 PHE   0.013   0.001   PHE A 776 
 TRP   0.014   0.001   TRP A1600 
 HIS   0.005   0.001   HIS A1473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (14237)
  covalent geometry    : angle       0.61332 (19484)
  hydrogen bonds       : bond        0.04520 (  342)
  hydrogen bonds       : angle       4.35504 (  905)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 47
  time to evaluate  : 0.511 
Fit side-chains
REVERT: A  410 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7582 (pp)
REVERT: A  989 ASP cc_start: 0.8233 (t70) cc_final: 0.7949 (t0)
REVERT: A 1065 ARG cc_start: 0.7946 (mmm160) cc_final: 0.7273 (ttm170)
REVERT: A 1211 MET cc_start: 0.7996 (tmm) cc_final: 0.7230 (tmm)
REVERT: A 1270 LYS cc_start: 0.7660 (mmmt) cc_final: 0.7387 (mttm)
  outliers start: 28
  outliers final: 18
  residues processed: 74
  average time/residue: 0.1140
  time to fit residues: 13.1093
Evaluate side-chains
  64 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 45
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 CYS
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue 1087 THR
Chi-restraints excluded: chain A residue 1156 VAL
Chi-restraints excluded: chain A residue 1367 ASP
Chi-restraints excluded: chain A residue 1390 LEU
Chi-restraints excluded: chain A residue 1397 THR
Chi-restraints excluded: chain A residue 1436 ILE
Chi-restraints excluded: chain A residue 1479 LYS
Chi-restraints excluded: chain A residue 1500 VAL
Chi-restraints excluded: chain A residue 1600 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0000
   chunk 82 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 103 optimal weight:    6.9990
   chunk 152 optimal weight:    2.9990
   chunk 150 optimal weight:    9.9990
   chunk 147 optimal weight:    0.9980
   chunk 143 optimal weight:    5.9990
   chunk 129 optimal weight:    4.9990
   overall best weight:    1.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.081463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.061388 restraints weight = 36914.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.063437 restraints weight = 20037.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.064742 restraints weight = 14020.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.065543 restraints weight = 11309.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.065977 restraints weight = 9927.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.1565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  14237  Z= 0.136
  Angle     :  0.576  11.852  19484  Z= 0.296
  Chirality :  0.043   0.203   2084
  Planarity :  0.005   0.063   2315
  Dihedral  : 16.034 164.231   2637
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.75 %
    Favored  : 89.25 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 15.92 %
    Favored  : 82.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.88 (0.20), residues: 1526
  helix:  1.16 (0.32), residues: 311
  sheet: -1.82 (0.30), residues: 286
  loop : -3.26 (0.17), residues: 929

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 393 
 TYR   0.011   0.001   TYR A 313 
 PHE   0.011   0.001   PHE A 776 
 TRP   0.011   0.001   TRP A1600 
 HIS   0.005   0.001   HIS A1473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (14237)
  covalent geometry    : angle       0.57562 (19484)
  hydrogen bonds       : bond        0.03913 (  342)
  hydrogen bonds       : angle       4.07586 (  905)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 49
  time to evaluate  : 0.561 
Fit side-chains
REVERT: A  410 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7454 (pp)
REVERT: A  989 ASP cc_start: 0.8150 (t70) cc_final: 0.7935 (t0)
REVERT: A 1065 ARG cc_start: 0.7893 (mmm160) cc_final: 0.7316 (ttm170)
REVERT: A 1270 LYS cc_start: 0.7656 (mmmt) cc_final: 0.7333 (mttm)
  outliers start: 27
  outliers final: 21
  residues processed: 74
  average time/residue: 0.1266
  time to fit residues: 14.2151
Evaluate side-chains
  69 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 47
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  861 VAL
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue  968 ILE
Chi-restraints excluded: chain A residue 1156 VAL
Chi-restraints excluded: chain A residue 1305 MET
Chi-restraints excluded: chain A residue 1386 VAL
Chi-restraints excluded: chain A residue 1390 LEU
Chi-restraints excluded: chain A residue 1397 THR
Chi-restraints excluded: chain A residue 1436 ILE
Chi-restraints excluded: chain A residue 1479 LYS
Chi-restraints excluded: chain A residue 1491 MET
Chi-restraints excluded: chain A residue 1500 VAL
Chi-restraints excluded: chain A residue 1600 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 14 optimal weight:    0.0040
   chunk 110 optimal weight:    7.9990
   chunk 107 optimal weight:   20.0000
   chunk 78 optimal weight:    3.9990
   chunk 17 optimal weight:    6.9990
   chunk 72 optimal weight:    8.9990
   chunk 44 optimal weight:    1.9990
   chunk 73 optimal weight:    5.9990
   chunk 129 optimal weight:    4.9990
   chunk 153 optimal weight:   10.0000
   overall best weight:    3.4000

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

Flipped N/Q/H residues before XYZ refinement:
A 306 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.078425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.058407 restraints weight = 37238.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.060374 restraints weight = 20153.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.061610 restraints weight = 14130.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.062324 restraints weight = 11452.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.062841 restraints weight = 10115.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.1430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042  14237  Z= 0.271
  Angle     :  0.686  10.752  19484  Z= 0.354
  Chirality :  0.047   0.242   2084
  Planarity :  0.005   0.071   2315
  Dihedral  : 16.083 166.309   2636
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.76 %
    Favored  : 86.24 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.22 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.97 (0.20), residues: 1526
  helix:  0.97 (0.31), residues: 310
  sheet: -1.66 (0.30), residues: 283
  loop : -3.34 (0.17), residues: 933

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 393 
 TYR   0.020   0.002   TYR A 863 
 PHE   0.017   0.002   PHE A1540 
 TRP   0.013   0.002   TRP A1600 
 HIS   0.006   0.002   HIS A1149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00626 (14237)
  covalent geometry    : angle       0.68629 (19484)
  hydrogen bonds       : bond        0.05266 (  342)
  hydrogen bonds       : angle       4.46123 (  905)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 44
  time to evaluate  : 0.542 
Fit side-chains
REVERT: A  410 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7812 (pp)
REVERT: A  989 ASP cc_start: 0.8210 (t70) cc_final: 0.7887 (t0)
REVERT: A 1065 ARG cc_start: 0.7936 (mmm160) cc_final: 0.7341 (ttm170)
REVERT: A 1211 MET cc_start: 0.8218 (tmm) cc_final: 0.6832 (tmm)
REVERT: A 1270 LYS cc_start: 0.7675 (mmmt) cc_final: 0.7415 (mttm)
REVERT: A 1283 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.7153 (m-10)
REVERT: A 1444 THR cc_start: 0.9522 (OUTLIER) cc_final: 0.9267 (m)
REVERT: A 1473 HIS cc_start: 0.8420 (OUTLIER) cc_final: 0.7942 (t-90)
REVERT: A 1533 TRP cc_start: 0.8335 (OUTLIER) cc_final: 0.7847 (m-10)
  outliers start: 42
  outliers final: 27
  residues processed: 82
  average time/residue: 0.1134
  time to fit residues: 14.4474
Evaluate side-chains
  74 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 42
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 CYS
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  861 VAL
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue  968 ILE
Chi-restraints excluded: chain A residue 1087 THR
Chi-restraints excluded: chain A residue 1103 PHE
Chi-restraints excluded: chain A residue 1156 VAL
Chi-restraints excluded: chain A residue 1283 TYR
Chi-restraints excluded: chain A residue 1305 MET
Chi-restraints excluded: chain A residue 1367 ASP
Chi-restraints excluded: chain A residue 1386 VAL
Chi-restraints excluded: chain A residue 1397 THR
Chi-restraints excluded: chain A residue 1436 ILE
Chi-restraints excluded: chain A residue 1444 THR
Chi-restraints excluded: chain A residue 1446 GLU
Chi-restraints excluded: chain A residue 1473 HIS
Chi-restraints excluded: chain A residue 1479 LYS
Chi-restraints excluded: chain A residue 1500 VAL
Chi-restraints excluded: chain A residue 1533 TRP
Chi-restraints excluded: chain A residue 1600 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 129 optimal weight:    2.9990
   chunk 103 optimal weight:   10.0000
   chunk 37 optimal weight:    0.0970
   chunk 36 optimal weight:    0.7980
   chunk 127 optimal weight:    0.9980
   chunk 113 optimal weight:    0.0020
   chunk 154 optimal weight:    3.9990
   chunk 91 optimal weight:    0.6980
   chunk 137 optimal weight:    0.9990
   overall best weight:    0.4786

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

Flipped N/Q/H residues before XYZ refinement:
** A  21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.082685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.063046 restraints weight = 36520.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.065074 restraints weight = 19864.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.066356 restraints weight = 13879.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.067159 restraints weight = 11162.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.067555 restraints weight = 9755.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.1882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  14237  Z= 0.101
  Angle     :  0.555  12.204  19484  Z= 0.284
  Chirality :  0.041   0.184   2084
  Planarity :  0.005   0.058   2315
  Dihedral  : 15.979 162.862   2636
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.11 %
    Favored  : 90.89 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 17.34 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.52 (0.21), residues: 1526
  helix:  1.51 (0.32), residues: 309
  sheet: -1.38 (0.31), residues: 277
  loop : -3.10 (0.17), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 393 
 TYR   0.011   0.001   TYR A 492 
 PHE   0.010   0.001   PHE A1407 
 TRP   0.009   0.001   TRP A1466 
 HIS   0.004   0.001   HIS A1473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 (14237)
  covalent geometry    : angle       0.55501 (19484)
  hydrogen bonds       : bond        0.03387 (  342)
  hydrogen bonds       : angle       3.86251 (  905)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 48
  time to evaluate  : 0.520 
Fit side-chains
REVERT: A  410 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7907 (pt)
REVERT: A  989 ASP cc_start: 0.8103 (t70) cc_final: 0.7875 (t0)
REVERT: A 1211 MET cc_start: 0.8130 (tmm) cc_final: 0.7724 (tmm)
REVERT: A 1270 LYS cc_start: 0.7588 (mmmt) cc_final: 0.7229 (mttm)
REVERT: A 1444 THR cc_start: 0.9475 (OUTLIER) cc_final: 0.9198 (m)
REVERT: A 1473 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.7840 (t-90)
  outliers start: 26
  outliers final: 17
  residues processed: 72
  average time/residue: 0.1225
  time to fit residues: 13.4302
Evaluate side-chains
  62 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 42
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  729 VAL
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  861 VAL
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue  968 ILE
Chi-restraints excluded: chain A residue 1087 THR
Chi-restraints excluded: chain A residue 1103 PHE
Chi-restraints excluded: chain A residue 1156 VAL
Chi-restraints excluded: chain A residue 1305 MET
Chi-restraints excluded: chain A residue 1444 THR
Chi-restraints excluded: chain A residue 1473 HIS
Chi-restraints excluded: chain A residue 1479 LYS
Chi-restraints excluded: chain A residue 1600 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 22 optimal weight:    0.0000
   chunk 49 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 84 optimal weight:    5.9990
   chunk 111 optimal weight:    8.9990
   chunk 114 optimal weight:    9.9990
   chunk 110 optimal weight:    6.9990
   chunk 154 optimal weight:    6.9990
   chunk 54 optimal weight:    7.9990
   chunk 15 optimal weight:    3.9990
   chunk 131 optimal weight:    0.8980
   overall best weight:    1.9790

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.081248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.061086 restraints weight = 36751.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.063155 restraints weight = 19623.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.064436 restraints weight = 13543.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.065162 restraints weight = 10938.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.065723 restraints weight = 9638.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  14237  Z= 0.169
  Angle     :  0.587  11.662  19484  Z= 0.303
  Chirality :  0.043   0.211   2084
  Planarity :  0.005   0.062   2315
  Dihedral  : 15.908 164.494   2636
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.07 %
    Favored  : 88.93 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 17.26 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.49 (0.21), residues: 1526
  helix:  1.53 (0.32), residues: 309
  sheet: -1.50 (0.30), residues: 289
  loop : -3.04 (0.18), residues: 928

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 393 
 TYR   0.012   0.001   TYR A 492 
 PHE   0.013   0.001   PHE A 528 
 TRP   0.010   0.001   TRP A1600 
 HIS   0.005   0.001   HIS A1473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (14237)
  covalent geometry    : angle       0.58743 (19484)
  hydrogen bonds       : bond        0.04023 (  342)
  hydrogen bonds       : angle       3.99965 (  905)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 42
  time to evaluate  : 0.550 
Fit side-chains
REVERT: A  410 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7441 (pp)
REVERT: A  989 ASP cc_start: 0.8202 (t70) cc_final: 0.7921 (t0)
REVERT: A 1211 MET cc_start: 0.8161 (tmm) cc_final: 0.7127 (tmm)
REVERT: A 1270 LYS cc_start: 0.7620 (mmmt) cc_final: 0.7310 (mttm)
REVERT: A 1473 HIS cc_start: 0.8381 (OUTLIER) cc_final: 0.7879 (t-90)
REVERT: A 1533 TRP cc_start: 0.8185 (OUTLIER) cc_final: 0.7765 (m-10)
  outliers start: 31
  outliers final: 21
  residues processed: 69
  average time/residue: 0.1093
  time to fit residues: 12.3375
Evaluate side-chains
  65 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 41
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  861 VAL
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue  968 ILE
Chi-restraints excluded: chain A residue 1087 THR
Chi-restraints excluded: chain A residue 1103 PHE
Chi-restraints excluded: chain A residue 1156 VAL
Chi-restraints excluded: chain A residue 1305 MET
Chi-restraints excluded: chain A residue 1436 ILE
Chi-restraints excluded: chain A residue 1473 HIS
Chi-restraints excluded: chain A residue 1479 LYS
Chi-restraints excluded: chain A residue 1491 MET
Chi-restraints excluded: chain A residue 1533 TRP
Chi-restraints excluded: chain A residue 1600 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   chunk 88 optimal weight:    9.9990
   chunk 31 optimal weight:    6.9990
   chunk 75 optimal weight:    0.0670
   chunk 152 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   chunk 108 optimal weight:    6.9990
   chunk 18 optimal weight:    4.9990
   chunk 124 optimal weight:    0.0980
   chunk 70 optimal weight:    1.9990
   overall best weight:    2.0324

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.080920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.060747 restraints weight = 37212.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.062788 restraints weight = 19801.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.064085 restraints weight = 13724.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.064878 restraints weight = 11020.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.065260 restraints weight = 9643.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.1773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  14237  Z= 0.171
  Angle     :  0.595  11.606  19484  Z= 0.307
  Chirality :  0.043   0.215   2084
  Planarity :  0.005   0.063   2315
  Dihedral  : 15.904 165.180   2636
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.40 %
    Favored  : 88.60 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 17.63 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.42 (0.21), residues: 1526
  helix:  1.52 (0.32), residues: 309
  sheet: -1.30 (0.31), residues: 277
  loop : -3.01 (0.18), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 393 
 TYR   0.012   0.001   TYR A 863 
 PHE   0.013   0.001   PHE A 776 
 TRP   0.009   0.001   TRP A  42 
 HIS   0.005   0.001   HIS A1473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 (14237)
  covalent geometry    : angle       0.59486 (19484)
  hydrogen bonds       : bond        0.04146 (  342)
  hydrogen bonds       : angle       4.01210 (  905)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 41
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
REVERT: A  410 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7432 (pp)
REVERT: A  989 ASP cc_start: 0.8194 (t70) cc_final: 0.7852 (t0)
REVERT: A 1211 MET cc_start: 0.8157 (tmm) cc_final: 0.7125 (tmm)
REVERT: A 1270 LYS cc_start: 0.7625 (mmmt) cc_final: 0.7320 (mttm)
REVERT: A 1473 HIS cc_start: 0.8404 (OUTLIER) cc_final: 0.7941 (t-90)
  outliers start: 28
  outliers final: 24
  residues processed: 66
  average time/residue: 0.1156
  time to fit residues: 12.2372
Evaluate side-chains
  67 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 41
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  861 VAL
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue  968 ILE
Chi-restraints excluded: chain A residue 1087 THR
Chi-restraints excluded: chain A residue 1103 PHE
Chi-restraints excluded: chain A residue 1156 VAL
Chi-restraints excluded: chain A residue 1305 MET
Chi-restraints excluded: chain A residue 1436 ILE
Chi-restraints excluded: chain A residue 1446 GLU
Chi-restraints excluded: chain A residue 1473 HIS
Chi-restraints excluded: chain A residue 1479 LYS
Chi-restraints excluded: chain A residue 1491 MET
Chi-restraints excluded: chain A residue 1600 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 102 optimal weight:    7.9990
   chunk 146 optimal weight:    0.4980
   chunk 47 optimal weight:    0.7980
   chunk 77 optimal weight:    0.4980
   chunk 98 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 120 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   chunk 26 optimal weight:    4.9990
   chunk 67 optimal weight:    0.2980
   chunk 84 optimal weight:    4.9990
   overall best weight:    1.0182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.082749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.062726 restraints weight = 36661.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.064839 restraints weight = 19457.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.066177 restraints weight = 13339.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.066999 restraints weight = 10676.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.067391 restraints weight = 9290.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.2011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  14237  Z= 0.113
  Angle     :  0.551  12.196  19484  Z= 0.283
  Chirality :  0.042   0.195   2084
  Planarity :  0.004   0.060   2315
  Dihedral  : 15.844 163.868   2636
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.70 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 17.78 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.22 (0.21), residues: 1526
  helix:  1.72 (0.32), residues: 309
  sheet: -1.23 (0.31), residues: 275
  loop : -2.86 (0.18), residues: 942

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 393 
 TYR   0.010   0.001   TYR A 313 
 PHE   0.010   0.001   PHE A 747 
 TRP   0.008   0.001   TRP A  42 
 HIS   0.005   0.001   HIS A1473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (14237)
  covalent geometry    : angle       0.55055 (19484)
  hydrogen bonds       : bond        0.03443 (  342)
  hydrogen bonds       : angle       3.77538 (  905)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 45
  time to evaluate  : 0.535 
Fit side-chains
REVERT: A  410 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7889 (pt)
REVERT: A  989 ASP cc_start: 0.8145 (t70) cc_final: 0.7864 (t0)
REVERT: A 1211 MET cc_start: 0.8109 (tmm) cc_final: 0.6898 (tmm)
REVERT: A 1270 LYS cc_start: 0.7573 (mmmt) cc_final: 0.7335 (mttm)
REVERT: A 1473 HIS cc_start: 0.8360 (OUTLIER) cc_final: 0.7889 (t-90)
  outliers start: 25
  outliers final: 23
  residues processed: 67
  average time/residue: 0.1133
  time to fit residues: 12.1575
Evaluate side-chains
  68 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 43
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  861 VAL
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue  968 ILE
Chi-restraints excluded: chain A residue 1087 THR
Chi-restraints excluded: chain A residue 1103 PHE
Chi-restraints excluded: chain A residue 1156 VAL
Chi-restraints excluded: chain A residue 1305 MET
Chi-restraints excluded: chain A residue 1397 THR
Chi-restraints excluded: chain A residue 1436 ILE
Chi-restraints excluded: chain A residue 1446 GLU
Chi-restraints excluded: chain A residue 1473 HIS
Chi-restraints excluded: chain A residue 1479 LYS
Chi-restraints excluded: chain A residue 1491 MET
Chi-restraints excluded: chain A residue 1600 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 125 optimal weight:    1.9990
   chunk 109 optimal weight:    6.9990
   chunk 52 optimal weight:    5.9990
   chunk 77 optimal weight:    0.2980
   chunk 64 optimal weight:    6.9990
   chunk 94 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0050
   chunk 27 optimal weight:    8.9990
   chunk 1 optimal weight:    5.9990
   chunk 128 optimal weight:    0.5980
   overall best weight:    1.3798

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.082250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.062189 restraints weight = 36935.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.064258 restraints weight = 19650.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.065626 restraints weight = 13541.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.066435 restraints weight = 10766.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.066820 restraints weight = 9389.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.1999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14237  Z= 0.133
  Angle     :  0.564  11.895  19484  Z= 0.289
  Chirality :  0.042   0.205   2084
  Planarity :  0.005   0.061   2315
  Dihedral  : 15.815 164.407   2636
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.55 %
    Favored  : 89.45 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.56 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.17 (0.21), residues: 1526
  helix:  1.76 (0.32), residues: 309
  sheet: -1.20 (0.31), residues: 280
  loop : -2.84 (0.18), residues: 937

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 393 
 TYR   0.011   0.001   TYR A 313 
 PHE   0.014   0.001   PHE A1219 
 TRP   0.008   0.001   TRP A1180 
 HIS   0.005   0.001   HIS A1473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (14237)
  covalent geometry    : angle       0.56353 (19484)
  hydrogen bonds       : bond        0.03665 (  342)
  hydrogen bonds       : angle       3.80581 (  905)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2060.85 seconds
wall clock time: 36 minutes 36.61 seconds (2196.61 seconds total)