Starting phenix.real_space_refine
on Wed Feb  4 16:03:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k4c_62054/02_2026/9k4c_62054.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k4c_62054/02_2026/9k4c_62054.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k4c_62054/02_2026/9k4c_62054.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k4c_62054/02_2026/9k4c_62054.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k4c_62054/02_2026/9k4c_62054.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k4c_62054/02_2026/9k4c_62054.map"
  }
  resolution = 3.84
  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=   0.003 sd=   0.033
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     149      5.49       5
     S      18      5.16       5
     C    6781      2.51       5
     N    2039      2.21       5
     O    2538      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11525
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1015, 8326
          Classifications: {'peptide': 1015}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 26, 'TRANS': 988}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 783
          Classifications: {'DNA': 38}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 37}
    Chain: "C"
      Number of atoms: 305
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 305
          Classifications: {'DNA': 15}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 14}
    Chain: "D"
      Number of atoms: 2111
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 2111
          Classifications: {'RNA': 99}
          Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 49, 'rna3p_pyr': 39}
          Link IDs: {'rna2p': 11, 'rna3p': 87}
  Time building chain proxies: 2.11, per 1000 atoms: 0.18
  Number of scatterers: 11525
  At special positions: 0
  Unit cell: (120.288, 115.992, 111.696, 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      18     16.00
     P     149     15.00
     O    2538      8.00
     N    2039      7.00
     C    6781      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.69
  Conformation dependent library (CDL) restraints added in 295.9 milliseconds
  

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1932

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 6 sheets defined
      56.1% alpha, 8.2% beta
      54 base pairs and 80 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 94
      removed outlier: 4.754A  pdb=" N   ASN A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 5.356A  pdb=" N   GLU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   LYS A  92 " --> pdb=" O   ASN A  88 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   VAL A  93 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 103
    Processing helix  chain 'A' and resid 121 through 132
    Processing helix  chain 'A' and resid 134 through 145
      removed outlier: 3.639A  pdb=" N   LEU A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 164
      removed outlier: 3.521A  pdb=" N   PHE A 164 " --> pdb=" O   HIS A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 306
    Processing helix  chain 'A' and resid 315 through 343
      removed outlier: 3.638A  pdb=" N   ALA A 319 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 352
      removed outlier: 4.408A  pdb=" N   LYS A 348 " --> pdb=" O   PRO A 344 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   GLU A 349 " --> pdb=" O   GLU A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 364
    Processing helix  chain 'A' and resid 368 through 383
      Proline residue:  A 378  - end of helix
      removed outlier: 3.658A  pdb=" N   MET A 383 " --> pdb=" O   ILE A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 396
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.665A  pdb=" N   ASN A 407 " --> pdb=" O   THR A 404 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   GLY A 408 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   SER A 409 " --> pdb=" O   ASP A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 427
      removed outlier: 4.288A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 436
    Processing helix  chain 'A' and resid 436 through 446
    Processing helix  chain 'A' and resid 477 through 482
      removed outlier: 3.670A  pdb=" N   VAL A 481 " --> pdb=" O   ASN A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 494
    Processing helix  chain 'A' and resid 512 through 526
      removed outlier: 4.046A  pdb=" N   LYS A 526 " --> pdb=" O   ASN A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 552
    Processing helix  chain 'A' and resid 560 through 568
    Processing helix  chain 'A' and resid 591 through 602
    Processing helix  chain 'A' and resid 603 through 609
    Processing helix  chain 'A' and resid 612 through 626
      removed outlier: 3.522A  pdb=" N   PHE A 626 " --> pdb=" O   THR A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 637
    Processing helix  chain 'A' and resid 638 through 643
      removed outlier: 4.745A  pdb=" N   HIS A 641 " --> pdb=" O   THR A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 654
      removed outlier: 3.664A  pdb=" N   ARG A 654 " --> pdb=" O   GLN A 650 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 669
    Processing helix  chain 'A' and resid 678 through 685
    Processing helix  chain 'A' and resid 686 through 690
      removed outlier: 4.244A  pdb=" N   ALA A 689 " --> pdb=" O   ASP A 686 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ASN A 690 " --> pdb=" O   GLY A 687 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 686 through 690'
    Processing helix  chain 'A' and resid 692 through 699
      removed outlier: 3.559A  pdb=" N   ILE A 697 " --> pdb=" O   PHE A 693 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   HIS A 698 " --> pdb=" O   MET A 694 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 702 through 712
      removed outlier: 4.426A  pdb=" N   GLU A 706 " --> pdb=" O   LEU A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 726
    Processing helix  chain 'A' and resid 730 through 751
      removed outlier: 3.699A  pdb=" N   LYS A 734 " --> pdb=" O   SER A 730 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   MET A 751 " --> pdb=" O   LEU A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 917 through 940
      removed outlier: 3.923A  pdb=" N   LEU A 921 " --> pdb=" O   ILE A 917 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   THR A 928 " --> pdb=" O   THR A 924 " (cutoff:3.500A)
      removed outlier: 5.313A  pdb=" N   LYS A 929 " --> pdb=" O   ARG A 925 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   HIS A 930 " --> pdb=" O   GLN A 926 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ASN A 940 " --> pdb=" O   ASP A 936 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 959 through 970
      removed outlier: 4.260A  pdb=" N   VAL A 963 " --> pdb=" O   LYS A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 981 through 999
      removed outlier: 3.634A  pdb=" N   LEU A 997 " --> pdb=" O   VAL A 993 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ILE A 998 " --> pdb=" O   GLY A 994 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1079 through 1088
    Processing helix  chain 'A' and resid 1127 through 1132
    Processing helix  chain 'A' and resid 1170 through 1177
      removed outlier: 3.760A  pdb=" N   ASN A1177 " --> pdb=" O   SER A1173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1185
    Processing helix  chain 'A' and resid 1191 through 1195
    Processing helix  chain 'A' and resid 1207 through 1209
      No H-bonds generated for 'chain 'A' and resid 1207 through 1209'
    Processing helix  chain 'A' and resid 1229 through 1241
    Processing helix  chain 'A' and resid 1248 through 1262
      removed outlier: 3.526A  pdb=" N   HIS A1262 " --> pdb=" O   PHE A1258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1264 through 1281
      removed outlier: 3.614A  pdb=" N   GLU A1268 " --> pdb=" O   HIS A1264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1283 through 1297
    Processing helix  chain 'A' and resid 1301 through 1313
      removed outlier: 3.606A  pdb=" N   HIS A1311 " --> pdb=" O   GLU A1307 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LEU A1312 " --> pdb=" O   ASN A1308 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   PHE A1313 " --> pdb=" O   ILE A1309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1314 through 1316
      No H-bonds generated for 'chain 'A' and resid 1314 through 1316'
    Processing helix  chain 'A' and resid 1339 through 1344
      removed outlier: 3.644A  pdb=" N   VAL A1342 " --> pdb=" O   THR A1339 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ASP A1344 " --> pdb=" O   GLU A1341 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957
      removed outlier: 3.508A  pdb=" N   TRP A  18 " --> pdb=" O   GLY A  49 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   VAL A1095 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33
    Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36
      removed outlier: 6.738A  pdb=" N   LEU A  35 " --> pdb=" O   ARG A1359 " (cutoff:3.500A)
      removed outlier: 8.371A  pdb=" N   ASP A1361 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   SER A1202 " --> pdb=" O   LEU A1214 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 528 through 531
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 5.045A  pdb=" N   LYS A1156 " --> pdb=" O   GLU A1150 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   GLU A1150 " --> pdb=" O   LYS A1156 " (cutoff:3.500A)
      removed outlier: 5.607A  pdb=" N   LYS A1158 " --> pdb=" O   LYS A1148 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   LYS A1148 " --> pdb=" O   LYS A1158 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   VAL A1160 " --> pdb=" O   VAL A1146 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   VAL A1146 " --> pdb=" O   VAL A1160 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   GLU A1162 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
      removed outlier: 5.113A  pdb=" N   LEU A1144 " --> pdb=" O   GLU A1162 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   LEU A1164 " --> pdb=" O   SER A1142 " (cutoff:3.500A)
      removed outlier: 5.389A  pdb=" N   SER A1142 " --> pdb=" O   LEU A1164 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   ILE A1166 " --> pdb=" O   ALA A1140 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1324 through 1326
      removed outlier: 3.890A  pdb=" N   PHE A1324 " --> pdb=" O   ILE A1331 " (cutoff:3.500A)

    379 hydrogen bonds defined for protein.
    1104 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      136 hydrogen bonds
      264 hydrogen bond angles
      0 basepair planarities
      54 basepair parallelities
      80 stacking parallelities
  Total time for adding SS restraints: 2.18

  Time building geometry restraints manager: 0.93 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: 1942
        1.33 -     1.45: 3733
        1.45 -     1.57: 6055
        1.57 -     1.69: 298
        1.69 -     1.81: 34
  Bond restraints: 12062
  Sorted by residual:
  bond pdb=" CD  GLN A 933 "
       pdb=" OE1 GLN A 933 "
    ideal  model  delta    sigma   weight residual
    1.231  1.208  0.023 1.90e-02 2.77e+03 1.44e+00
  bond pdb=" CG  GLN A 933 "
       pdb=" CD  GLN A 933 "
    ideal  model  delta    sigma   weight residual
    1.516  1.491  0.025 2.50e-02 1.60e+03 1.02e+00
  bond pdb=" C3'  DG B   7 "
       pdb=" O3'  DG B   7 "
    ideal  model  delta    sigma   weight residual
    1.422  1.450 -0.028 3.00e-02 1.11e+03 8.92e-01
  bond pdb=" CA  ILE A 312 "
       pdb=" CB  ILE A 312 "
    ideal  model  delta    sigma   weight residual
    1.530  1.540 -0.009 1.05e-02 9.07e+03 8.11e-01
  bond pdb=" CG1 ILE A 927 "
       pdb=" CD1 ILE A 927 "
    ideal  model  delta    sigma   weight residual
    1.513  1.479  0.034 3.90e-02 6.57e+02 7.80e-01
  ... (remaining 12057 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 16344
        1.21 -     2.43: 533
        2.43 -     3.64: 61
        3.64 -     4.85: 7
        4.85 -     6.07: 3
  Bond angle restraints: 16948
  Sorted by residual:
  angle pdb=" N   GLN A 933 "
        pdb=" CA  GLN A 933 "
        pdb=" CB  GLN A 933 "
      ideal   model   delta    sigma   weight residual
     110.28  116.35   -6.07 1.55e+00 4.16e-01 1.53e+01
  angle pdb=" CA  GLN A 933 "
        pdb=" CB  GLN A 933 "
        pdb=" CG  GLN A 933 "
      ideal   model   delta    sigma   weight residual
     114.10  119.99   -5.89 2.00e+00 2.50e-01 8.67e+00
  angle pdb=" C   ALA A 932 "
        pdb=" N   GLN A 933 "
        pdb=" CA  GLN A 933 "
      ideal   model   delta    sigma   weight residual
     120.31  115.94    4.37 1.52e+00 4.33e-01 8.25e+00
  angle pdb=" N   ILE A 312 "
        pdb=" CA  ILE A 312 "
        pdb=" C   ILE A 312 "
      ideal   model   delta    sigma   weight residual
     107.37  110.75   -3.38 1.42e+00 4.96e-01 5.67e+00
  angle pdb=" N   VAL A1280 "
        pdb=" CA  VAL A1280 "
        pdb=" C   VAL A1280 "
      ideal   model   delta    sigma   weight residual
     109.34  113.82   -4.48 2.08e+00 2.31e-01 4.64e+00
  ... (remaining 16943 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.19: 6798
       29.19 -    58.38: 383
       58.38 -    87.57: 91
       87.57 -   116.75: 0
      116.75 -   145.94: 1
  Dihedral angle restraints: 7273
    sinusoidal: 4290
      harmonic: 2983
  Sorted by residual:
  dihedral pdb=" CA  ILE A 927 "
           pdb=" C   ILE A 927 "
           pdb=" N   THR A 928 "
           pdb=" CA  THR A 928 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.78  -24.22     0      5.00e+00 4.00e-02 2.35e+01
  dihedral pdb=" C4'  DG B   7 "
           pdb=" C3'  DG B   7 "
           pdb=" O3'  DG B   7 "
           pdb=" P    DA B   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   74.06  145.94     1      3.50e+01 8.16e-04 1.43e+01
  dihedral pdb=" CA  PHE A  86 "
           pdb=" C   PHE A  86 "
           pdb=" N   SER A  87 "
           pdb=" CA  SER A  87 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.60  -16.40     0      5.00e+00 4.00e-02 1.08e+01
  ... (remaining 7270 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1427
       0.031 -    0.061: 373
       0.061 -    0.092: 100
       0.092 -    0.122: 56
       0.122 -    0.153: 3
  Chirality restraints: 1959
  Sorted by residual:
  chirality pdb=" C1'   A D  67 "
            pdb=" O4'   A D  67 "
            pdb=" C2'   A D  67 "
            pdb=" N9    A D  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.30    0.15 2.00e-01 2.50e+01 5.84e-01
  chirality pdb=" CA  VAL A  27 "
            pdb=" N   VAL A  27 "
            pdb=" C   VAL A  27 "
            pdb=" CB  VAL A  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.91e-01
  chirality pdb=" CA  GLN A 933 "
            pdb=" N   GLN A 933 "
            pdb=" C   GLN A 933 "
            pdb=" CB  GLN A 933 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 3.98e-01
  ... (remaining 1956 not shown)

  Planarity restraints: 1601
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A1228 "   -0.027 5.00e-02 4.00e+02   4.15e-02 2.76e+00
        pdb=" N   PRO A1229 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A1229 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A1229 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  67 "    0.022 2.00e-02 2.50e+03   9.81e-03 2.65e+00
        pdb=" N9    A D  67 "   -0.022 2.00e-02 2.50e+03
        pdb=" C8    A D  67 "   -0.007 2.00e-02 2.50e+03
        pdb=" N7    A D  67 "    0.003 2.00e-02 2.50e+03
        pdb=" C5    A D  67 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    A D  67 "    0.003 2.00e-02 2.50e+03
        pdb=" N6    A D  67 "    0.005 2.00e-02 2.50e+03
        pdb=" N1    A D  67 "   -0.000 2.00e-02 2.50e+03
        pdb=" C2    A D  67 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    A D  67 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    A D  67 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U D  68 "    0.016 2.00e-02 2.50e+03   8.74e-03 1.72e+00
        pdb=" N1    U D  68 "   -0.020 2.00e-02 2.50e+03
        pdb=" C2    U D  68 "   -0.002 2.00e-02 2.50e+03
        pdb=" O2    U D  68 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    U D  68 "    0.001 2.00e-02 2.50e+03
        pdb=" C4    U D  68 "    0.002 2.00e-02 2.50e+03
        pdb=" O4    U D  68 "    0.004 2.00e-02 2.50e+03
        pdb=" C5    U D  68 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    U D  68 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1598 not shown)

  Histogram of nonbonded interaction distances:
        1.30 -     2.02: 3
        2.02 -     2.74: 917
        2.74 -     3.46: 15378
        3.46 -     4.18: 28686
        4.18 -     4.90: 45719
  Nonbonded interactions: 90703
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A  44 "
            pdb=" O6    G D  94 "
     model   vdw
     1.298 3.120
  nonbonded pdb=" NH1 ARG A 340 "
            pdb=" OP1   A D  43 "
     model   vdw
     1.298 3.120
  nonbonded pdb=" NH1 ARG A  71 "
            pdb=" N4    C D  20 "
     model   vdw
     1.352 3.200
  nonbonded pdb=" O2   DC B  16 "
            pdb=" N2    G D  22 "
     model   vdw
     2.095 2.496
  nonbonded pdb=" NH1 ARG A  71 "
            pdb=" C4    C D  20 "
     model   vdw
     2.172 3.340
  ... (remaining 90698 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.050
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
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      :  0.002   0.034  12062  Z= 0.123
  Angle     :  0.507   6.069  16948  Z= 0.304
  Chirality :  0.034   0.153   1959
  Planarity :  0.003   0.042   1601
  Dihedral  : 16.789 145.943   5341
  Min Nonbonded Distance : 1.298

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  1.35 (0.26), residues: 1007
  helix:  1.76 (0.24), residues: 487
  sheet:  1.10 (0.47), residues: 91
  loop : -0.10 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 400 
 TYR   0.009   0.001   TYR A 347 
 PHE   0.010   0.001   PHE A1276 
 TRP   0.005   0.001   TRP A 476 
 HIS   0.006   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 (12062)
  covalent geometry    : angle       0.50652 (16948)
  hydrogen bonds       : bond        0.15656 (  515)
  hydrogen bonds       : angle       5.65881 ( 1368)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 PHE cc_start: 0.8698 (m-80) cc_final: 0.8171 (m-10)
REVERT: A  549 VAL cc_start: 0.9213 (t) cc_final: 0.9001 (m)
REVERT: A  569 PHE cc_start: 0.9082 (m-80) cc_final: 0.8793 (m-10)
REVERT: A  587 PHE cc_start: 0.8104 (m-80) cc_final: 0.7646 (m-80)
REVERT: A  629 ARG cc_start: 0.8696 (mtt180) cc_final: 0.8454 (mmm-85)
REVERT: A  964 SER cc_start: 0.9599 (t) cc_final: 0.9376 (p)
REVERT: A  981 TYR cc_start: 0.7725 (m-10) cc_final: 0.7198 (m-10)
REVERT: A 1164 LEU cc_start: 0.8497 (tp) cc_final: 0.8135 (tp)
REVERT: A 1352 ILE cc_start: 0.9141 (tt) cc_final: 0.8891 (tt)
REVERT: A 1357 GLU cc_start: 0.6695 (pt0) cc_final: 0.6109 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 190
  average time/residue: 0.1180
  time to fit residues: 30.3482
Evaluate side-chains
  111 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:   20.0000
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:   20.0000
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:   10.0000
   chunk 100 optimal weight:    6.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  99 HIS
A 354 GLN
** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 612 ASN
A1101 GLN
A1297 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.042550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.030772 restraints weight = 98202.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.031814 restraints weight = 54125.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.032521 restraints weight = 36951.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.032995 restraints weight = 28655.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.033288 restraints weight = 24266.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.3626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  12062  Z= 0.246
  Angle     :  0.703  13.215  16948  Z= 0.370
  Chirality :  0.039   0.191   1959
  Planarity :  0.005   0.060   1601
  Dihedral  : 19.590 152.859   3176
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  :  8.32 %
    Favored  : 89.17 %
  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:  0.77 (0.26), residues: 1007
  helix:  1.24 (0.23), residues: 515
  sheet:  1.56 (0.54), residues: 69
  loop : -0.54 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 395 
 TYR   0.014   0.002   TYR A 430 
 PHE   0.019   0.002   PHE A1204 
 TRP   0.009   0.002   TRP A 464 
 HIS   0.010   0.002   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 (12062)
  covalent geometry    : angle       0.70309 (16948)
  hydrogen bonds       : bond        0.05790 (  515)
  hydrogen bonds       : angle       4.84551 ( 1368)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7070 (tmm) cc_final: 0.6842 (tmm)
REVERT: A   60 GLU cc_start: 0.9773 (pm20) cc_final: 0.9146 (pm20)
REVERT: A  161 MET cc_start: 0.9459 (mmm) cc_final: 0.9184 (mmt)
REVERT: A  321 MET cc_start: 0.9648 (mmm) cc_final: 0.9309 (mmm)
REVERT: A  371 GLU cc_start: 0.9466 (mt-10) cc_final: 0.9236 (pt0)
REVERT: A  398 LEU cc_start: 0.9784 (OUTLIER) cc_final: 0.9311 (pp)
REVERT: A  524 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9205 (pp)
REVERT: A  587 PHE cc_start: 0.8442 (m-80) cc_final: 0.7735 (m-80)
REVERT: A  629 ARG cc_start: 0.9282 (mtt180) cc_final: 0.8696 (mmt90)
REVERT: A  631 MET cc_start: 0.9403 (tpt) cc_final: 0.9158 (mtt)
REVERT: A  936 ASP cc_start: 0.9735 (t0) cc_final: 0.9402 (m-30)
REVERT: A  951 ARG cc_start: 0.9469 (mpp-170) cc_final: 0.9190 (mmt90)
REVERT: A 1204 PHE cc_start: 0.9625 (m-10) cc_final: 0.9237 (m-10)
REVERT: A 1324 PHE cc_start: 0.8012 (p90) cc_final: 0.7501 (p90)
  outliers start: 23
  outliers final: 11
  residues processed: 112
  average time/residue: 0.1016
  time to fit residues: 16.0069
Evaluate side-chains
  85 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  364 ASP
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  507 VAL
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue 1260 GLU
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1337 THR
Chi-restraints excluded: chain A residue 1349 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 3 optimal weight:   20.0000
   chunk 55 optimal weight:    0.0980
   chunk 15 optimal weight:    5.9990
   chunk 43 optimal weight:   30.0000
   chunk 75 optimal weight:   20.0000
   chunk 41 optimal weight:   30.0000
   chunk 14 optimal weight:    0.1980
   chunk 87 optimal weight:   20.0000
   chunk 20 optimal weight:    7.9990
   chunk 42 optimal weight:    5.9990
   overall best weight:    3.0586

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

Flipped N/Q/H residues before XYZ refinement:
A 309 ASN
** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 985 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.042789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.031145 restraints weight = 95999.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.032234 restraints weight = 51076.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.032940 restraints weight = 34254.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.033468 restraints weight = 26409.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.033774 restraints weight = 22122.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.4239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12062  Z= 0.133
  Angle     :  0.561  12.261  16948  Z= 0.296
  Chirality :  0.036   0.153   1959
  Planarity :  0.004   0.061   1601
  Dihedral  : 19.518 156.627   3176
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  9.41 %
    Favored  : 89.06 %
  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:  0.96 (0.26), residues: 1007
  helix:  1.49 (0.23), residues: 521
  sheet:  1.14 (0.51), residues: 85
  loop : -0.59 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 925 
 TYR   0.017   0.001   TYR A 517 
 PHE   0.018   0.001   PHE A1276 
 TRP   0.003   0.001   TRP A 476 
 HIS   0.006   0.001   HIS A 930 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (12062)
  covalent geometry    : angle       0.56099 (16948)
  hydrogen bonds       : bond        0.04215 (  515)
  hydrogen bonds       : angle       4.41432 ( 1368)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7180 (tmm) cc_final: 0.6841 (tmm)
REVERT: A   60 GLU cc_start: 0.9583 (pm20) cc_final: 0.9363 (pm20)
REVERT: A  161 MET cc_start: 0.9479 (mmm) cc_final: 0.9097 (mmt)
REVERT: A  371 GLU cc_start: 0.9495 (mt-10) cc_final: 0.9277 (pt0)
REVERT: A  398 LEU cc_start: 0.9774 (tt) cc_final: 0.9334 (pp)
REVERT: A  495 MET cc_start: 0.9201 (mpp) cc_final: 0.8931 (pmm)
REVERT: A  524 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9193 (pp)
REVERT: A  587 PHE cc_start: 0.8601 (m-80) cc_final: 0.8051 (m-80)
REVERT: A  629 ARG cc_start: 0.9270 (mtt180) cc_final: 0.8849 (mmt-90)
REVERT: A  631 MET cc_start: 0.9410 (tpt) cc_final: 0.9045 (mmm)
REVERT: A  648 MET cc_start: 0.9531 (mmm) cc_final: 0.9323 (mmm)
REVERT: A  652 LYS cc_start: 0.9615 (tttt) cc_final: 0.8750 (tttm)
REVERT: A  939 MET cc_start: 0.6866 (ptt) cc_final: 0.6434 (ptt)
REVERT: A  951 ARG cc_start: 0.9526 (mpp-170) cc_final: 0.9258 (mmt90)
REVERT: A 1096 LYS cc_start: 0.9049 (tptt) cc_final: 0.8582 (ttmm)
REVERT: A 1214 LEU cc_start: 0.9517 (mp) cc_final: 0.9165 (mt)
REVERT: A 1228 LEU cc_start: 0.9067 (tp) cc_final: 0.8528 (tt)
  outliers start: 14
  outliers final: 9
  residues processed: 97
  average time/residue: 0.0962
  time to fit residues: 13.4959
Evaluate side-chains
  78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  500 LYS
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  694 MET
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1349 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 82 optimal weight:    6.9990
   chunk 97 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 48 optimal weight:   20.0000
   chunk 90 optimal weight:    7.9990
   chunk 68 optimal weight:    9.9990
   chunk 49 optimal weight:   10.0000
   chunk 2 optimal weight:    8.9990
   chunk 8 optimal weight:    6.9990
   chunk 105 optimal weight:   20.0000
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1349 HIS ** 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 = 0.3072 r_free = 0.3072 target = 0.040084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.028944 restraints weight = 101709.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.029941 restraints weight = 55002.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.030581 restraints weight = 37240.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.031058 restraints weight = 29023.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.031337 restraints weight = 24479.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.5424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  12062  Z= 0.201
  Angle     :  0.602  11.670  16948  Z= 0.321
  Chirality :  0.037   0.166   1959
  Planarity :  0.004   0.067   1601
  Dihedral  : 19.741 155.820   3176
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 10.07 %
    Favored  : 87.31 %
  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:  0.69 (0.26), residues: 1007
  helix:  1.22 (0.22), residues: 518
  sheet:  1.79 (0.57), residues: 65
  loop : -0.68 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  63 
 TYR   0.014   0.002   TYR A 943 
 PHE   0.031   0.002   PHE A1276 
 TRP   0.006   0.001   TRP A 659 
 HIS   0.006   0.002   HIS A 930 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (12062)
  covalent geometry    : angle       0.60167 (16948)
  hydrogen bonds       : bond        0.05112 (  515)
  hydrogen bonds       : angle       4.50588 ( 1368)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 77
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7511 (tmm) cc_final: 0.7187 (tmm)
REVERT: A   60 GLU cc_start: 0.9601 (pm20) cc_final: 0.9363 (pm20)
REVERT: A   90 MET cc_start: 0.9483 (tpt) cc_final: 0.9225 (tpp)
REVERT: A  161 MET cc_start: 0.9536 (mmm) cc_final: 0.9151 (mmt)
REVERT: A  383 MET cc_start: 0.7371 (mtt) cc_final: 0.7169 (ttt)
REVERT: A  524 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9244 (pp)
REVERT: A  629 ARG cc_start: 0.9356 (mtt180) cc_final: 0.8759 (mmt-90)
REVERT: A  631 MET cc_start: 0.9425 (tpt) cc_final: 0.9131 (mtt)
REVERT: A  746 GLU cc_start: 0.9238 (mm-30) cc_final: 0.9023 (mm-30)
REVERT: A  951 ARG cc_start: 0.9559 (mpp-170) cc_final: 0.9265 (mmt90)
REVERT: A 1169 MET cc_start: 0.9672 (tpp) cc_final: 0.9367 (tpp)
REVERT: A 1198 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9212 (mm)
REVERT: A 1214 LEU cc_start: 0.9516 (mp) cc_final: 0.9160 (mt)
REVERT: A 1228 LEU cc_start: 0.8867 (tp) cc_final: 0.8658 (tp)
  outliers start: 24
  outliers final: 15
  residues processed: 95
  average time/residue: 0.0966
  time to fit residues: 13.5702
Evaluate side-chains
  86 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  364 ASP
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  943 TYR
Chi-restraints excluded: chain A residue 1192 LYS
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1226 LEU
Chi-restraints excluded: chain A residue 1260 GLU
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1349 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 81 optimal weight:    4.9990
   chunk 16 optimal weight:    9.9990
   chunk 99 optimal weight:    9.9990
   chunk 102 optimal weight:   10.0000
   chunk 107 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 78 optimal weight:   10.0000
   chunk 75 optimal weight:    6.9990
   chunk 98 optimal weight:    9.9990
   chunk 105 optimal weight:   20.0000
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 595 HIS
** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 739 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.038081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2661 r_free = 0.2661 target = 0.027414 restraints weight = 105210.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2690 r_free = 0.2690 target = 0.028366 restraints weight = 57655.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.028998 restraints weight = 39248.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.029378 restraints weight = 30470.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.029672 restraints weight = 25987.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.2691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.6784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  12062  Z= 0.215
  Angle     :  0.623  12.205  16948  Z= 0.333
  Chirality :  0.038   0.227   1959
  Planarity :  0.004   0.062   1601
  Dihedral  : 20.100 155.001   3176
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 14.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 11.60 %
    Favored  : 85.45 %
  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:  0.40 (0.26), residues: 1007
  helix:  1.04 (0.22), residues: 521
  sheet:  1.37 (0.67), residues: 55
  loop : -0.81 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A1359 
 TYR   0.024   0.002   TYR A1237 
 PHE   0.021   0.002   PHE A 575 
 TRP   0.011   0.001   TRP A 659 
 HIS   0.006   0.002   HIS A1297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 (12062)
  covalent geometry    : angle       0.62329 (16948)
  hydrogen bonds       : bond        0.05037 (  515)
  hydrogen bonds       : angle       4.67378 ( 1368)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 66
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7715 (tmm) cc_final: 0.7388 (tmm)
REVERT: A   60 GLU cc_start: 0.9629 (pm20) cc_final: 0.9332 (pm20)
REVERT: A  125 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8010 (mm-30)
REVERT: A  161 MET cc_start: 0.9507 (mmm) cc_final: 0.9095 (mmt)
REVERT: A  524 LEU cc_start: 0.9652 (OUTLIER) cc_final: 0.9328 (pp)
REVERT: A  629 ARG cc_start: 0.9326 (mtt180) cc_final: 0.8910 (mmt180)
REVERT: A  631 MET cc_start: 0.9378 (tpt) cc_final: 0.9133 (mtt)
REVERT: A  652 LYS cc_start: 0.9616 (tttt) cc_final: 0.8860 (tttm)
REVERT: A  949 LEU cc_start: 0.9096 (mt) cc_final: 0.8877 (mm)
REVERT: A  951 ARG cc_start: 0.9599 (mpp-170) cc_final: 0.9303 (mmt90)
REVERT: A 1198 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9120 (mm)
REVERT: A 1213 MET cc_start: 0.9661 (tpp) cc_final: 0.9454 (tpp)
REVERT: A 1214 LEU cc_start: 0.9585 (mp) cc_final: 0.9155 (mp)
  outliers start: 27
  outliers final: 21
  residues processed: 85
  average time/residue: 0.0955
  time to fit residues: 11.8907
Evaluate side-chains
  83 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 59
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  500 LYS
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  575 PHE
Chi-restraints excluded: chain A residue  645 ASP
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  694 MET
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  943 TYR
Chi-restraints excluded: chain A residue 1192 LYS
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1226 LEU
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1337 THR
Chi-restraints excluded: chain A residue 1349 HIS
Chi-restraints excluded: chain A residue 1353 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 75 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 99 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 32 optimal weight:    9.9990
   chunk 45 optimal weight:    8.9990
   chunk 98 optimal weight:    7.9990
   chunk 109 optimal weight:   20.0000
   chunk 26 optimal weight:    8.9990
   chunk 97 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  99 HIS
A 402 GLN
** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.038232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.027515 restraints weight = 104309.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.028473 restraints weight = 56978.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.029087 restraints weight = 38917.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.029551 restraints weight = 30305.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.029893 restraints weight = 25380.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.2702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.7165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  12062  Z= 0.161
  Angle     :  0.565  15.578  16948  Z= 0.298
  Chirality :  0.036   0.155   1959
  Planarity :  0.003   0.057   1601
  Dihedral  : 19.974 156.254   3176
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 12.69 %
    Favored  : 85.23 %
  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:  0.62 (0.26), residues: 1007
  helix:  1.26 (0.23), residues: 523
  sheet:  0.90 (0.59), residues: 68
  loop : -0.74 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1171 
 TYR   0.012   0.001   TYR A 973 
 PHE   0.019   0.002   PHE A1204 
 TRP   0.004   0.001   TRP A 464 
 HIS   0.004   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (12062)
  covalent geometry    : angle       0.56502 (16948)
  hydrogen bonds       : bond        0.04508 (  515)
  hydrogen bonds       : angle       4.43717 ( 1368)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7576 (tmm) cc_final: 0.7234 (tmm)
REVERT: A   60 GLU cc_start: 0.9618 (pm20) cc_final: 0.9291 (pm20)
REVERT: A  125 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8024 (mm-30)
REVERT: A  161 MET cc_start: 0.9474 (mmm) cc_final: 0.9055 (mmt)
REVERT: A  383 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7140 (mmm)
REVERT: A  495 MET cc_start: 0.9133 (pmm) cc_final: 0.8813 (pmm)
REVERT: A  524 LEU cc_start: 0.9677 (OUTLIER) cc_final: 0.9374 (pp)
REVERT: A  629 ARG cc_start: 0.9347 (mtt180) cc_final: 0.8943 (mmt180)
REVERT: A  631 MET cc_start: 0.9403 (tpt) cc_final: 0.9167 (mtt)
REVERT: A  652 LYS cc_start: 0.9622 (tttt) cc_final: 0.8820 (tttm)
REVERT: A 1198 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9152 (mm)
REVERT: A 1214 LEU cc_start: 0.9493 (mp) cc_final: 0.9100 (mp)
  outliers start: 19
  outliers final: 12
  residues processed: 79
  average time/residue: 0.1007
  time to fit residues: 11.4663
Evaluate side-chains
  76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  500 LYS
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue 1192 LYS
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1349 HIS
Chi-restraints excluded: chain A residue 1353 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 76 optimal weight:    9.9990
   chunk 75 optimal weight:    8.9990
   chunk 6 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 71 optimal weight:   20.0000
   chunk 90 optimal weight:    9.9990
   chunk 68 optimal weight:    9.9990
   chunk 52 optimal weight:    7.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 723 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.038212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.027580 restraints weight = 104492.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.028555 restraints weight = 56704.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.029200 restraints weight = 38382.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2735 r_free = 0.2735 target = 0.029632 restraints weight = 29797.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.029906 restraints weight = 25094.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start:          0.7471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12062  Z= 0.143
  Angle     :  0.559  14.322  16948  Z= 0.289
  Chirality :  0.035   0.157   1959
  Planarity :  0.003   0.051   1601
  Dihedral  : 19.954 156.540   3176
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 12.58 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.26), residues: 1007
  helix:  1.31 (0.23), residues: 522
  sheet:  1.06 (0.55), residues: 78
  loop : -0.74 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 425 
 TYR   0.009   0.001   TYR A 973 
 PHE   0.019   0.001   PHE A 575 
 TRP   0.004   0.001   TRP A 659 
 HIS   0.004   0.001   HIS A1297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (12062)
  covalent geometry    : angle       0.55874 (16948)
  hydrogen bonds       : bond        0.04250 (  515)
  hydrogen bonds       : angle       4.36175 ( 1368)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 61
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7588 (tmm) cc_final: 0.7243 (tmm)
REVERT: A   60 GLU cc_start: 0.9620 (pm20) cc_final: 0.9299 (pm20)
REVERT: A   90 MET cc_start: 0.9391 (tpt) cc_final: 0.9052 (tpt)
REVERT: A  125 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8020 (mm-30)
REVERT: A  161 MET cc_start: 0.9470 (mmm) cc_final: 0.9010 (mmt)
REVERT: A  383 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7194 (mmm)
REVERT: A  524 LEU cc_start: 0.9680 (OUTLIER) cc_final: 0.9343 (pp)
REVERT: A  629 ARG cc_start: 0.9330 (mtt180) cc_final: 0.8867 (mmt-90)
REVERT: A  631 MET cc_start: 0.9417 (tpt) cc_final: 0.9165 (mtt)
REVERT: A  652 LYS cc_start: 0.9618 (tttt) cc_final: 0.8796 (tttm)
REVERT: A 1198 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9181 (mm)
REVERT: A 1214 LEU cc_start: 0.9408 (mp) cc_final: 0.9003 (mp)
  outliers start: 25
  outliers final: 16
  residues processed: 82
  average time/residue: 0.1093
  time to fit residues: 12.9721
Evaluate side-chains
  81 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 61
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  500 LYS
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  943 TYR
Chi-restraints excluded: chain A residue  990 ASN
Chi-restraints excluded: chain A residue 1192 LYS
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1353 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 97 optimal weight:    7.9990
   chunk 74 optimal weight:   10.0000
   chunk 68 optimal weight:    9.9990
   chunk 102 optimal weight:   10.0000
   chunk 43 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 78 optimal weight:   20.0000
   chunk 103 optimal weight:   10.0000
   chunk 3 optimal weight:   20.0000
   chunk 16 optimal weight:    8.9990
   chunk 14 optimal weight:    7.9990
   overall best weight:    8.9992

-------------------------------------------------------------------------------
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 = 0.2918 r_free = 0.2918 target = 0.035452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2565 r_free = 0.2565 target = 0.025127 restraints weight = 112186.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2597 r_free = 0.2597 target = 0.026019 restraints weight = 61710.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2616 r_free = 0.2616 target = 0.026571 restraints weight = 42253.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.2631 r_free = 0.2631 target = 0.026988 restraints weight = 33244.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.027232 restraints weight = 28233.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.2605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8735
moved from start:          0.8323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  12062  Z= 0.295
  Angle     :  0.720  14.046  16948  Z= 0.383
  Chirality :  0.040   0.154   1959
  Planarity :  0.005   0.058   1601
  Dihedral  : 20.432 155.940   3176
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 19.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 13.46 %
    Favored  : 83.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.18 (0.25), residues: 1007
  helix:  0.50 (0.22), residues: 519
  sheet:  0.59 (0.62), residues: 68
  loop : -0.95 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 494 
 TYR   0.034   0.002   TYR A1356 
 PHE   0.026   0.003   PHE A 575 
 TRP   0.016   0.002   TRP A 464 
 HIS   0.010   0.002   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00580 (12062)
  covalent geometry    : angle       0.71973 (16948)
  hydrogen bonds       : bond        0.06212 (  515)
  hydrogen bonds       : angle       4.97669 ( 1368)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 59
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7726 (tmm) cc_final: 0.7389 (tmm)
REVERT: A   60 GLU cc_start: 0.9647 (pm20) cc_final: 0.9296 (pm20)
REVERT: A  125 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8313 (mm-30)
REVERT: A  161 MET cc_start: 0.9500 (mmm) cc_final: 0.9032 (mmm)
REVERT: A  383 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7347 (mmm)
REVERT: A  629 ARG cc_start: 0.9280 (mtt180) cc_final: 0.8892 (mmt180)
REVERT: A  631 MET cc_start: 0.9427 (tpt) cc_final: 0.9184 (mtp)
REVERT: A  652 LYS cc_start: 0.9621 (tttt) cc_final: 0.8815 (tttm)
REVERT: A 1198 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9103 (mm)
REVERT: A 1214 LEU cc_start: 0.9483 (mp) cc_final: 0.9202 (mp)
  outliers start: 25
  outliers final: 20
  residues processed: 79
  average time/residue: 0.0991
  time to fit residues: 11.5368
Evaluate side-chains
  78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 55
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  364 ASP
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  500 LYS
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  575 PHE
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  943 TYR
Chi-restraints excluded: chain A residue  990 ASN
Chi-restraints excluded: chain A residue 1192 LYS
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1260 GLU
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1337 THR
Chi-restraints excluded: chain A residue 1353 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 86 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 64 optimal weight:   30.0000
   chunk 14 optimal weight:    8.9990
   chunk 4 optimal weight:   20.0000
   chunk 55 optimal weight:    1.9990
   chunk 111 optimal weight:   20.0000
   chunk 78 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A1224 ASN ** 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 = 0.2985 r_free = 0.2985 target = 0.037442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.026900 restraints weight = 102785.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.027832 restraints weight = 56522.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.028433 restraints weight = 38678.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.028886 restraints weight = 30210.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.029152 restraints weight = 25484.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.8219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12062  Z= 0.122
  Angle     :  0.574  15.554  16948  Z= 0.294
  Chirality :  0.036   0.172   1959
  Planarity :  0.003   0.051   1601
  Dihedral  : 20.082 159.629   3176
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 13.79 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.26), residues: 1007
  helix:  1.16 (0.23), residues: 521
  sheet:  0.55 (0.56), residues: 82
  loop : -0.84 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 691 
 TYR   0.009   0.001   TYR A 973 
 PHE   0.019   0.001   PHE A 575 
 TRP   0.006   0.001   TRP A 464 
 HIS   0.005   0.001   HIS A1297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (12062)
  covalent geometry    : angle       0.57440 (16948)
  hydrogen bonds       : bond        0.04207 (  515)
  hydrogen bonds       : angle       4.39905 ( 1368)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 66
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7547 (tmm) cc_final: 0.7219 (tmm)
REVERT: A   90 MET cc_start: 0.9363 (tpt) cc_final: 0.8885 (tpp)
REVERT: A  125 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8075 (mm-30)
REVERT: A  161 MET cc_start: 0.9499 (mmm) cc_final: 0.9044 (mmt)
REVERT: A  383 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7368 (mmm)
REVERT: A  516 GLU cc_start: 0.9330 (mt-10) cc_final: 0.8954 (mt-10)
REVERT: A  629 ARG cc_start: 0.9267 (mtt180) cc_final: 0.8814 (mmt-90)
REVERT: A  631 MET cc_start: 0.9446 (tpt) cc_final: 0.9211 (mtt)
REVERT: A 1169 MET cc_start: 0.9602 (mmm) cc_final: 0.9348 (tpt)
REVERT: A 1198 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9150 (mm)
  outliers start: 19
  outliers final: 15
  residues processed: 81
  average time/residue: 0.0985
  time to fit residues: 11.4593
Evaluate side-chains
  79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 61
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  324 ARG
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  500 LYS
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  927 ILE
Chi-restraints excluded: chain A residue  943 TYR
Chi-restraints excluded: chain A residue  990 ASN
Chi-restraints excluded: chain A residue 1192 LYS
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1353 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 95 optimal weight:    2.9990
   chunk 3 optimal weight:   20.0000
   chunk 37 optimal weight:    8.9990
   chunk 86 optimal weight:    5.9990
   chunk 57 optimal weight:    7.9990
   chunk 2 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 71 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
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 = 0.2988 r_free = 0.2988 target = 0.037229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.026842 restraints weight = 105031.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.027804 restraints weight = 56335.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.028443 restraints weight = 37963.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.028859 restraints weight = 29305.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.029149 restraints weight = 24709.370|
|-----------------------------------------------------------------------------|
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8679
moved from start:          0.8421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12062  Z= 0.147
  Angle     :  0.592  15.821  16948  Z= 0.304
  Chirality :  0.036   0.170   1959
  Planarity :  0.003   0.049   1601
  Dihedral  : 20.050 158.153   3176
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 14.55 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.49 (0.26), residues: 1007
  helix:  1.15 (0.23), residues: 522
  sheet:  0.77 (0.57), residues: 78
  loop : -0.81 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 691 
 TYR   0.013   0.001   TYR A1356 
 PHE   0.024   0.002   PHE A1204 
 TRP   0.006   0.001   TRP A 464 
 HIS   0.005   0.001   HIS A1297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (12062)
  covalent geometry    : angle       0.59220 (16948)
  hydrogen bonds       : bond        0.04330 (  515)
  hydrogen bonds       : angle       4.44722 ( 1368)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7587 (tmm) cc_final: 0.7263 (tmm)
REVERT: A   90 MET cc_start: 0.9363 (tpt) cc_final: 0.8874 (tpp)
REVERT: A  125 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8104 (mm-30)
REVERT: A  161 MET cc_start: 0.9507 (mmm) cc_final: 0.9054 (mmt)
REVERT: A  383 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7443 (mmm)
REVERT: A  629 ARG cc_start: 0.9264 (mtt180) cc_final: 0.8832 (mmt-90)
REVERT: A  631 MET cc_start: 0.9454 (tpt) cc_final: 0.9208 (mtt)
REVERT: A 1198 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9176 (mm)
  outliers start: 18
  outliers final: 15
  residues processed: 74
  average time/residue: 0.1065
  time to fit residues: 11.4193
Evaluate side-chains
  74 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 56
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  324 ARG
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  500 LYS
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  927 ILE
Chi-restraints excluded: chain A residue  943 TYR
Chi-restraints excluded: chain A residue  990 ASN
Chi-restraints excluded: chain A residue 1192 LYS
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1353 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 86 optimal weight:    7.9990
   chunk 79 optimal weight:   30.0000
   chunk 50 optimal weight:    4.9990
   chunk 75 optimal weight:   20.0000
   chunk 16 optimal weight:    9.9990
   chunk 23 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 37 optimal weight:    8.9990
   chunk 22 optimal weight:    5.9990
   chunk 43 optimal weight:   20.0000
   chunk 20 optimal weight:   10.0000
   overall best weight:    7.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 985 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.035759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2610 r_free = 0.2610 target = 0.025749 restraints weight = 110381.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.026644 restraints weight = 59483.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.027247 restraints weight = 40285.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.027619 restraints weight = 31166.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.027907 restraints weight = 26469.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8739
moved from start:          0.8873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  12062  Z= 0.254
  Angle     :  0.690  15.398  16948  Z= 0.359
  Chirality :  0.039   0.207   1959
  Planarity :  0.004   0.049   1601
  Dihedral  : 20.288 159.110   3176
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 17.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 14.22 %
    Favored  : 83.59 %
  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:  0.00 (0.26), residues: 1007
  helix:  0.67 (0.22), residues: 519
  sheet:  0.55 (0.57), residues: 80
  loop : -0.92 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1171 
 TYR   0.023   0.002   TYR A1356 
 PHE   0.025   0.002   PHE A 575 
 TRP   0.015   0.002   TRP A 464 
 HIS   0.007   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 (12062)
  covalent geometry    : angle       0.69025 (16948)
  hydrogen bonds       : bond        0.05372 (  515)
  hydrogen bonds       : angle       4.88061 ( 1368)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1692.48 seconds
wall clock time: 30 minutes 10.59 seconds (1810.59 seconds total)