Starting phenix.real_space_refine
on Wed Feb  4 15:24:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k4d_62055/02_2026/9k4d_62055.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k4d_62055/02_2026/9k4d_62055.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k4d_62055/02_2026/9k4d_62055.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k4d_62055/02_2026/9k4d_62055.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k4d_62055/02_2026/9k4d_62055.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k4d_62055/02_2026/9k4d_62055.map"
  }
  resolution = 3.53
  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=   0.006 sd=   0.090
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     146      5.49       5
     S      19      5.16       5
     C    6745      2.51       5
     N    2024      2.21       5
     O    2524      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: 11458
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8325
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1017, 8325
          Classifications: {'peptide': 1017}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 27, 'TRANS': 989}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 719
          Classifications: {'DNA': 35}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 34}
    Chain: "C"
      Number of atoms: 325
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 325
          Classifications: {'DNA': 16}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 15}
    Chain: "D"
      Number of atoms: 2089
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 2089
          Classifications: {'RNA': 98}
          Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 48, 'rna3p_pyr': 39}
          Link IDs: {'rna2p': 11, 'rna3p': 86}
  Time building chain proxies: 2.77, per 1000 atoms: 0.24
  Number of scatterers: 11458
  At special positions: 0
  Unit cell: (119.658, 104.566, 143.374, 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      19     16.00
     P     146     15.00
     O    2524      8.00
     N    2024      7.00
     C    6745      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: 0.95
  Conformation dependent library (CDL) restraints added in 400.6 milliseconds
  

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1934

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 7 sheets defined
      54.7% alpha, 11.3% beta
      58 base pairs and 95 stacking pairs defined.
    Time for finding SS restraints: 1.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 94
      removed outlier: 4.771A  pdb=" N   ASN A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 5.357A  pdb=" N   GLU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   LYS A  92 " --> pdb=" O   ASN A  88 " (cutoff:3.500A)
      removed outlier: 3.539A  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: 3.646A  pdb=" N   LEU A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 164
    Processing helix  chain 'A' and resid 293 through 306
      removed outlier: 3.904A  pdb=" N   ASP A 304 " --> pdb=" O   ILE A 300 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ILE A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 343
      removed outlier: 3.696A  pdb=" N   ALA A 319 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 352
    Processing helix  chain 'A' and resid 358 through 364
    Processing helix  chain 'A' and resid 368 through 382
      Proline residue:  A 378  - end of helix
    Processing helix  chain 'A' and resid 386 through 395
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.809A  pdb=" N   GLY A 408 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 426
      removed outlier: 4.281A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 436
      removed outlier: 3.786A  pdb=" N   LYS A 434 " --> pdb=" O   TYR A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 446
    Processing helix  chain 'A' and resid 474 through 476
      No H-bonds generated for 'chain 'A' and resid 474 through 476'
    Processing helix  chain 'A' and resid 477 through 482
      removed outlier: 3.561A  pdb=" N   VAL A 481 " --> pdb=" O   ASN A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 496
      removed outlier: 4.422A  pdb=" N   MET A 495 " --> pdb=" O   PHE A 491 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   THR A 496 " --> pdb=" O   ILE A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 526
      removed outlier: 3.995A  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
      removed outlier: 3.533A  pdb=" N   LEU A 607 " --> pdb=" O   ASP A 603 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 626
    Processing helix  chain 'A' and resid 628 through 637
    Processing helix  chain 'A' and resid 638 through 640
      No H-bonds generated for 'chain 'A' and resid 638 through 640'
    Processing helix  chain 'A' and resid 644 through 652
    Processing helix  chain 'A' and resid 663 through 669
    Processing helix  chain 'A' and resid 678 through 685
    Processing helix  chain 'A' and resid 692 through 698
    Processing helix  chain 'A' and resid 702 through 712
      removed outlier: 4.470A  pdb=" N   GLU A 706 " --> pdb=" O   LEU A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 727
    Processing helix  chain 'A' and resid 730 through 751
      removed outlier: 3.645A  pdb=" N   LYS A 734 " --> pdb=" O   SER A 730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 926 through 940
    Processing helix  chain 'A' and resid 959 through 970
      removed outlier: 4.028A  pdb=" N   VAL A 963 " --> pdb=" O   LYS A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 980 through 999
      removed outlier: 4.557A  pdb=" N   ALA A 984 " --> pdb=" O   ASN A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1078 through 1088
    Processing helix  chain 'A' and resid 1127 through 1132
    Processing helix  chain 'A' and resid 1170 through 1177
    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
    Processing helix  chain 'A' and resid 1264 through 1281
      removed outlier: 3.587A  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: 3.518A  pdb=" N   PHE A1313 " --> pdb=" O   ILE A1309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1340 through 1344
      removed outlier: 3.718A  pdb=" N   ASP A1344 " --> pdb=" O   GLU A1341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1363 through 1365
      No H-bonds generated for 'chain 'A' and resid 1363 through 1365'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957
      removed outlier: 6.583A  pdb=" N   ILE A 759 " --> pdb=" O   ILE A 956 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   ASN A 758 " --> pdb=" O   TYR A   5 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46
      removed outlier: 10.369A  pdb=" N   GLU A1357 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   LYS A  33 " --> pdb=" O   GLU A1357 " (cutoff:3.500A)
      removed outlier: 8.205A  pdb=" N   ARG A1359 " --> pdb=" O   LYS A  33 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   LEU A  35 " --> pdb=" O   ARG A1359 " (cutoff:3.500A)
      removed outlier: 7.856A  pdb=" N   ASP A1361 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   SER A1202 " --> pdb=" O   LEU A1214 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539
      removed outlier: 3.672A  pdb=" N   LYS A 528 " --> pdb=" O   SER A 581 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1120 through 1121
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 3.586A  pdb=" N   TYR A1141 " --> pdb=" O   ILE A1166 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 3.586A  pdb=" N   TYR A1141 " --> pdb=" O   ILE A1166 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ILE A1196 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1324 through 1326
      removed outlier: 3.578A  pdb=" N   PHE A1324 " --> pdb=" O   ILE A1331 " (cutoff:3.500A)

    411 hydrogen bonds defined for protein.
    1194 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      146 hydrogen bonds
      284 hydrogen bond angles
      0 basepair planarities
      58 basepair parallelities
      95 stacking parallelities
  Total time for adding SS restraints: 2.71

  Time building geometry restraints manager: 1.23 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3089
        1.34 -     1.46: 2808
        1.46 -     1.58: 5761
        1.58 -     1.69: 292
        1.69 -     1.81: 36
  Bond restraints: 11986
  Sorted by residual:
  bond pdb=" C3'  DG B   7 "
       pdb=" O3'  DG B   7 "
    ideal  model  delta    sigma   weight residual
    1.422  1.458 -0.036 3.00e-02 1.11e+03 1.41e+00
  bond pdb=" CA  ASP A  94 "
       pdb=" C   ASP A  94 "
    ideal  model  delta    sigma   weight residual
    1.522  1.533 -0.011 1.08e-02 8.57e+03 1.07e+00
  bond pdb=" N   PHE A1327 "
       pdb=" CA  PHE A1327 "
    ideal  model  delta    sigma   weight residual
    1.457  1.470 -0.013 1.29e-02 6.01e+03 1.00e+00
  bond pdb=" C3'  DC C  10 "
       pdb=" C2'  DC C  10 "
    ideal  model  delta    sigma   weight residual
    1.525  1.542 -0.017 2.00e-02 2.50e+03 7.00e-01
  bond pdb=" C3'  DC B  14 "
       pdb=" C2'  DC B  14 "
    ideal  model  delta    sigma   weight residual
    1.525  1.541 -0.016 2.00e-02 2.50e+03 6.79e-01
  ... (remaining 11981 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 16466
        1.37 -     2.74: 319
        2.74 -     4.12: 40
        4.12 -     5.49: 5
        5.49 -     6.86: 1
  Bond angle restraints: 16831
  Sorted by residual:
  angle pdb=" C   PHE A1327 "
        pdb=" CA  PHE A1327 "
        pdb=" CB  PHE A1327 "
      ideal   model   delta    sigma   weight residual
     110.42  115.33   -4.91 1.99e+00 2.53e-01 6.09e+00
  angle pdb=" N   ASP A 585 "
        pdb=" CA  ASP A 585 "
        pdb=" CB  ASP A 585 "
      ideal   model   delta    sigma   weight residual
     113.65  110.20    3.45 1.47e+00 4.63e-01 5.51e+00
  angle pdb=" CB  MET A 939 "
        pdb=" CG  MET A 939 "
        pdb=" SD  MET A 939 "
      ideal   model   delta    sigma   weight residual
     112.70  119.56   -6.86 3.00e+00 1.11e-01 5.23e+00
  angle pdb=" N   LEU A 551 "
        pdb=" CA  LEU A 551 "
        pdb=" C   LEU A 551 "
      ideal   model   delta    sigma   weight residual
     111.36  113.50   -2.14 1.09e+00 8.42e-01 3.86e+00
  angle pdb=" C3'  DG B   7 "
        pdb=" O3'  DG B   7 "
        pdb=" P    DA B   8 "
      ideal   model   delta    sigma   weight residual
     120.20  123.14   -2.94 1.50e+00 4.44e-01 3.84e+00
  ... (remaining 16826 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.55: 6883
       35.55 -    71.10: 332
       71.10 -   106.65: 24
      106.65 -   142.20: 0
      142.20 -   177.76: 1
  Dihedral angle restraints: 7240
    sinusoidal: 4253
      harmonic: 2987
  Sorted by residual:
  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   42.24  177.76     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" CA  PHE A 446 "
           pdb=" C   PHE A 446 "
           pdb=" N   ARG A 447 "
           pdb=" CA  ARG A 447 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.17   16.83     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CG  ARG A1359 "
           pdb=" CD  ARG A1359 "
           pdb=" NE  ARG A1359 "
           pdb=" CZ  ARG A1359 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -136.60  -43.40     2      1.50e+01 4.44e-03 1.01e+01
  ... (remaining 7237 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1307
       0.026 -    0.052: 412
       0.052 -    0.078: 148
       0.078 -    0.104: 50
       0.104 -    0.130: 27
  Chirality restraints: 1944
  Sorted by residual:
  chirality pdb=" CA  ILE A 956 "
            pdb=" N   ILE A 956 "
            pdb=" C   ILE A 956 "
            pdb=" CB  ILE A 956 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.25e-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    2.56   -0.12 2.00e-01 2.50e+01 3.83e-01
  chirality pdb=" C1'   A D  42 "
            pdb=" O4'   A D  42 "
            pdb=" C2'   A D  42 "
            pdb=" N9    A D  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.33    0.12 2.00e-01 2.50e+01 3.81e-01
  ... (remaining 1941 not shown)

  Planarity restraints: 1601
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  42 "    0.022 2.00e-02 2.50e+03   1.01e-02 2.79e+00
        pdb=" N9    A D  42 "   -0.024 2.00e-02 2.50e+03
        pdb=" C8    A D  42 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    A D  42 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    A D  42 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    A D  42 "    0.002 2.00e-02 2.50e+03
        pdb=" N6    A D  42 "    0.006 2.00e-02 2.50e+03
        pdb=" N1    A D  42 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    A D  42 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A D  42 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    A D  42 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G D  54 "    0.018 2.00e-02 2.50e+03   8.10e-03 1.97e+00
        pdb=" N9    G D  54 "   -0.020 2.00e-02 2.50e+03
        pdb=" C8    G D  54 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    G D  54 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5    G D  54 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G D  54 "   -0.000 2.00e-02 2.50e+03
        pdb=" O6    G D  54 "    0.006 2.00e-02 2.50e+03
        pdb=" N1    G D  54 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    G D  54 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G D  54 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    G D  54 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    G D  54 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 315 "    0.022 5.00e-02 4.00e+02   3.40e-02 1.85e+00
        pdb=" N   PRO A 316 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 316 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 316 "    0.019 5.00e-02 4.00e+02
  ... (remaining 1598 not shown)

  Histogram of nonbonded interaction distances:
        1.30 -     2.02: 4
        2.02 -     2.74: 880
        2.74 -     3.46: 15390
        3.46 -     4.18: 29092
        4.18 -     4.90: 46980
  Nonbonded interactions: 92346
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 510 "
            pdb=" OP1   G D   6 "
     model   vdw
     1.297 3.120
  nonbonded pdb=" NZ  LYS A  44 "
            pdb=" O6    G D  92 "
     model   vdw
     1.298 3.120
  nonbonded pdb=" ND2 ASN A  77 "
            pdb=" O2    U D  59 "
     model   vdw
     1.298 3.120
  nonbonded pdb=" NH1 ARG A  71 "
            pdb=" C5    C D  18 "
     model   vdw
     1.431 3.420
  nonbonded pdb=" N2   DG B   9 "
            pdb=" O2   DC C   8 "
     model   vdw
     2.126 2.496
  ... (remaining 92341 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:             0.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     13.240
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
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   0.036  11986  Z= 0.117
  Angle     :  0.477   6.861  16831  Z= 0.281
  Chirality :  0.033   0.130   1944
  Planarity :  0.003   0.034   1601
  Dihedral  : 16.931 177.755   5306
  Min Nonbonded Distance : 1.297

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.68 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  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:  1.57 (0.26), residues: 1009
  helix:  1.76 (0.24), residues: 506
  sheet:  1.12 (0.53), residues: 105
  loop :  0.17 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 494 
 TYR   0.009   0.001   TYR A  72 
 PHE   0.009   0.001   PHE A 432 
 TRP   0.010   0.001   TRP A1126 
 HIS   0.004   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (11986)
  covalent geometry    : angle       0.47745 (16831)
  hydrogen bonds       : bond        0.14550 (  546)
  hydrogen bonds       : angle       5.64256 ( 1478)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  441 GLU cc_start: 0.8216 (mt-10) cc_final: 0.8013 (mt-10)
REVERT: A  511 HIS cc_start: 0.7288 (m90) cc_final: 0.6204 (m-70)
REVERT: A  534 MET cc_start: -0.0525 (mtt) cc_final: -0.2080 (tpt)
REVERT: A  618 ASP cc_start: 0.8720 (t70) cc_final: 0.8348 (t0)
REVERT: A  623 LEU cc_start: 0.9401 (mt) cc_final: 0.9166 (mt)
REVERT: A  630 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8546 (mt-10)
REVERT: A  653 ARG cc_start: 0.8049 (mtt180) cc_final: 0.7734 (mtm-85)
REVERT: A  654 ARG cc_start: 0.7393 (tpt170) cc_final: 0.6702 (ttm170)
REVERT: A  656 TYR cc_start: 0.8101 (m-80) cc_final: 0.7861 (m-10)
REVERT: A  709 GLN cc_start: 0.7939 (mt0) cc_final: 0.7613 (mt0)
REVERT: A  762 GLU cc_start: 0.7669 (pp20) cc_final: 0.7038 (tm-30)
REVERT: A  954 LYS cc_start: 0.8294 (mttt) cc_final: 0.8054 (mttm)
REVERT: A  962 LEU cc_start: 0.8939 (mt) cc_final: 0.8243 (tp)
REVERT: A  979 ASN cc_start: 0.8427 (p0) cc_final: 0.8109 (p0)
REVERT: A 1148 LYS cc_start: 0.8270 (mttt) cc_final: 0.7791 (mtpp)
REVERT: A 1169 MET cc_start: 0.8891 (ttp) cc_final: 0.8617 (ttm)
REVERT: A 1230 SER cc_start: 0.7697 (m) cc_final: 0.7447 (t)
REVERT: A 1261 GLN cc_start: 0.9029 (mt0) cc_final: 0.8728 (mt0)
REVERT: A 1325 LYS cc_start: 0.8858 (mttt) cc_final: 0.8443 (ttmm)
REVERT: A 1326 TYR cc_start: 0.8507 (t80) cc_final: 0.7942 (t80)
REVERT: A 1339 THR cc_start: 0.9245 (p) cc_final: 0.8948 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 223
  average time/residue: 0.1344
  time to fit residues: 39.6197
Evaluate side-chains
  111 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 97 optimal weight:   10.0000
   chunk 113 optimal weight:   10.0000
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    5.9990
   overall best weight:    4.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 178 ASN
A 595 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.163580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.105579 restraints weight = 19222.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.109325 restraints weight = 9140.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.111589 restraints weight = 6377.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.112758 restraints weight = 5348.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.113245 restraints weight = 4905.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  11986  Z= 0.281
  Angle     :  0.633   6.560  16831  Z= 0.343
  Chirality :  0.041   0.144   1944
  Planarity :  0.005   0.053   1601
  Dihedral  : 19.509 177.864   3143
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.07 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  :  8.00 %
    Favored  : 89.49 %
  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:  1.23 (0.26), residues: 1009
  helix:  1.51 (0.23), residues: 515
  sheet:  0.84 (0.51), residues: 104
  loop : -0.02 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  71 
 TYR   0.020   0.002   TYR A   5 
 PHE   0.020   0.002   PHE A1313 
 TRP   0.011   0.002   TRP A1126 
 HIS   0.008   0.002   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00634 (11986)
  covalent geometry    : angle       0.63260 (16831)
  hydrogen bonds       : bond        0.06461 (  546)
  hydrogen bonds       : angle       4.50978 ( 1478)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASP cc_start: 0.7978 (m-30) cc_final: 0.7369 (m-30)
REVERT: A  304 ASP cc_start: 0.8687 (m-30) cc_final: 0.8380 (p0)
REVERT: A  465 MET cc_start: 0.8370 (ttp) cc_final: 0.8133 (tmm)
REVERT: A  508 LEU cc_start: 0.8522 (mm) cc_final: 0.8308 (mp)
REVERT: A  618 ASP cc_start: 0.8818 (t70) cc_final: 0.8273 (t0)
REVERT: A  630 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8308 (mt-10)
REVERT: A  653 ARG cc_start: 0.8041 (mtt180) cc_final: 0.7730 (mtm-85)
REVERT: A  654 ARG cc_start: 0.7593 (tpt170) cc_final: 0.7099 (ttm170)
REVERT: A  709 GLN cc_start: 0.8018 (mt0) cc_final: 0.7816 (mp10)
REVERT: A  762 GLU cc_start: 0.7878 (pp20) cc_final: 0.7011 (tm-30)
REVERT: A  942 LYS cc_start: 0.8234 (mmmt) cc_final: 0.7414 (mtpt)
REVERT: A  954 LYS cc_start: 0.8436 (mttt) cc_final: 0.8010 (ttmm)
REVERT: A 1148 LYS cc_start: 0.8533 (mttt) cc_final: 0.8145 (mtpp)
REVERT: A 1180 ASP cc_start: 0.8577 (m-30) cc_final: 0.8370 (m-30)
REVERT: A 1261 GLN cc_start: 0.8906 (mt0) cc_final: 0.8634 (mt0)
REVERT: A 1339 THR cc_start: 0.9251 (p) cc_final: 0.8987 (t)
  outliers start: 23
  outliers final: 17
  residues processed: 130
  average time/residue: 0.0911
  time to fit residues: 17.1424
Evaluate side-chains
  107 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  645 ASP
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1106 SER
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1240 SER
Chi-restraints excluded: chain A residue 1259 VAL
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 67 optimal weight:    8.9990
   chunk 28 optimal weight:    2.9990
   chunk 10 optimal weight:    0.3980
   chunk 33 optimal weight:    0.7980
   chunk 85 optimal weight:    6.9990
   chunk 12 optimal weight:    6.9990
   chunk 74 optimal weight:    2.9990
   chunk 48 optimal weight:   20.0000
   chunk 90 optimal weight:   10.0000
   chunk 112 optimal weight:   10.0000
   overall best weight:    2.2386

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

Flipped N/Q/H residues before XYZ refinement:
A 116 HIS
A 511 HIS
A1256 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.157571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.099374 restraints weight = 19082.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.103224 restraints weight = 8903.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.105580 restraints weight = 6141.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.106893 restraints weight = 5099.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.107438 restraints weight = 4652.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.2616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11986  Z= 0.162
  Angle     :  0.504   9.372  16831  Z= 0.279
  Chirality :  0.036   0.141   1944
  Planarity :  0.004   0.052   1601
  Dihedral  : 19.469 179.207   3143
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.58 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  9.86 %
    Favored  : 88.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.26), residues: 1009
  helix:  1.66 (0.23), residues: 515
  sheet:  0.51 (0.48), residues: 112
  loop : -0.08 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  71 
 TYR   0.024   0.001   TYR A 988 
 PHE   0.010   0.001   PHE A 429 
 TRP   0.005   0.001   TRP A1126 
 HIS   0.005   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (11986)
  covalent geometry    : angle       0.50368 (16831)
  hydrogen bonds       : bond        0.05036 (  546)
  hydrogen bonds       : angle       4.11180 ( 1478)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 ASP cc_start: 0.7911 (m-30) cc_final: 0.7251 (m-30)
REVERT: A  304 ASP cc_start: 0.8505 (m-30) cc_final: 0.8264 (p0)
REVERT: A  321 MET cc_start: 0.9022 (mmt) cc_final: 0.8708 (mmt)
REVERT: A  465 MET cc_start: 0.8294 (ttp) cc_final: 0.8048 (tmm)
REVERT: A  618 ASP cc_start: 0.8825 (t70) cc_final: 0.8255 (t0)
REVERT: A  630 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8292 (mt-10)
REVERT: A  631 MET cc_start: 0.8514 (mmm) cc_final: 0.7879 (mmm)
REVERT: A  653 ARG cc_start: 0.8038 (mtt180) cc_final: 0.7697 (mtm-85)
REVERT: A  654 ARG cc_start: 0.7453 (tpt170) cc_final: 0.7179 (ttm170)
REVERT: A  709 GLN cc_start: 0.8125 (mt0) cc_final: 0.7876 (mp10)
REVERT: A  762 GLU cc_start: 0.7937 (pp20) cc_final: 0.7207 (tp30)
REVERT: A  954 LYS cc_start: 0.8481 (mttt) cc_final: 0.8133 (ttmm)
REVERT: A 1148 LYS cc_start: 0.8468 (mttt) cc_final: 0.8012 (mtpp)
REVERT: A 1180 ASP cc_start: 0.8646 (m-30) cc_final: 0.8403 (m-30)
REVERT: A 1261 GLN cc_start: 0.8920 (mt0) cc_final: 0.8662 (mt0)
REVERT: A 1268 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7940 (mp0)
REVERT: A 1325 LYS cc_start: 0.8835 (tttt) cc_final: 0.8368 (ttmm)
REVERT: A 1339 THR cc_start: 0.9231 (p) cc_final: 0.8966 (t)
  outliers start: 15
  outliers final: 9
  residues processed: 111
  average time/residue: 0.1157
  time to fit residues: 18.2301
Evaluate side-chains
  94 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  645 ASP
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1240 SER
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 43 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 52 optimal weight:   10.0000
   chunk 106 optimal weight:    7.9990
   chunk 93 optimal weight:    2.9990
   chunk 60 optimal weight:    6.9990
   chunk 67 optimal weight:    0.2980
   chunk 96 optimal weight:    7.9990
   chunk 3 optimal weight:    7.9990
   chunk 64 optimal weight:    6.9990
   chunk 111 optimal weight:    7.9990
   overall best weight:    4.6588

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 511 HIS
A1234 ASN
** A1308 ASN ** 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 = 0.3842 r_free = 0.3842 target = 0.149580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.099099 restraints weight = 18353.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.098981 restraints weight = 11465.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.101391 restraints weight = 8550.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.101173 restraints weight = 6638.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.101329 restraints weight = 6278.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.3317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.041  11986  Z= 0.296
  Angle     :  0.643   8.223  16831  Z= 0.346
  Chirality :  0.041   0.152   1944
  Planarity :  0.005   0.053   1601
  Dihedral  : 19.695 178.965   3143
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.16 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 11.72 %
    Favored  : 85.98 %
  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: 1009
  helix:  1.29 (0.23), residues: 514
  sheet:  0.24 (0.47), residues: 113
  loop : -0.37 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1333 
 TYR   0.024   0.002   TYR A   5 
 PHE   0.019   0.002   PHE A1080 
 TRP   0.007   0.002   TRP A1126 
 HIS   0.005   0.002   HIS A 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00664 (11986)
  covalent geometry    : angle       0.64301 (16831)
  hydrogen bonds       : bond        0.06527 (  546)
  hydrogen bonds       : angle       4.39191 ( 1478)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 ASN cc_start: 0.6019 (m-40) cc_final: 0.5697 (m110)
REVERT: A  307 ARG cc_start: 0.7971 (tpp80) cc_final: 0.7731 (ttm110)
REVERT: A  321 MET cc_start: 0.9042 (mmt) cc_final: 0.8366 (mmt)
REVERT: A  534 MET cc_start: -0.0636 (mtt) cc_final: -0.0920 (mpp)
REVERT: A  618 ASP cc_start: 0.8694 (t70) cc_final: 0.8202 (t0)
REVERT: A  630 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8234 (mt-10)
REVERT: A  653 ARG cc_start: 0.7920 (mtt180) cc_final: 0.7444 (ttm-80)
REVERT: A  762 GLU cc_start: 0.8061 (pp20) cc_final: 0.7149 (tm-30)
REVERT: A  954 LYS cc_start: 0.8490 (mttt) cc_final: 0.8188 (ttmm)
REVERT: A 1148 LYS cc_start: 0.8507 (mttt) cc_final: 0.8187 (mtpp)
REVERT: A 1261 GLN cc_start: 0.8993 (mt0) cc_final: 0.8709 (mt0)
REVERT: A 1325 LYS cc_start: 0.8848 (tttt) cc_final: 0.8387 (ttmm)
REVERT: A 1339 THR cc_start: 0.9267 (p) cc_final: 0.8966 (t)
  outliers start: 21
  outliers final: 15
  residues processed: 112
  average time/residue: 0.1127
  time to fit residues: 17.8378
Evaluate side-chains
  96 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  517 TYR
Chi-restraints excluded: chain A residue  645 ASP
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1087 LEU
Chi-restraints excluded: chain A residue 1106 SER
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 19 optimal weight:    0.5980
   chunk 107 optimal weight:    5.9990
   chunk 17 optimal weight:    0.0030
   chunk 110 optimal weight:    5.9990
   chunk 66 optimal weight:    6.9990
   chunk 73 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 63 optimal weight:    0.6980
   chunk 27 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   overall best weight:    0.6190

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

Flipped N/Q/H residues before XYZ refinement:
** A  77 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 = 0.4051 r_free = 0.4051 target = 0.159551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.101926 restraints weight = 19063.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.105870 restraints weight = 8982.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.108332 restraints weight = 6202.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.109571 restraints weight = 5135.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.109954 restraints weight = 4680.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.3299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  11986  Z= 0.106
  Angle     :  0.473   8.342  16831  Z= 0.262
  Chirality :  0.034   0.140   1944
  Planarity :  0.003   0.050   1601
  Dihedral  : 19.426 179.255   3143
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.08 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 12.71 %
    Favored  : 85.98 %
  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:  1.19 (0.26), residues: 1009
  helix:  1.72 (0.24), residues: 513
  sheet:  0.33 (0.48), residues: 113
  loop : -0.28 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 951 
 TYR   0.022   0.001   TYR A   5 
 PHE   0.012   0.001   PHE A 429 
 TRP   0.006   0.001   TRP A 464 
 HIS   0.004   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 (11986)
  covalent geometry    : angle       0.47292 (16831)
  hydrogen bonds       : bond        0.04288 (  546)
  hydrogen bonds       : angle       3.88868 ( 1478)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.386 
Fit side-chains
REVERT: A  178 ASN cc_start: 0.6045 (m-40) cc_final: 0.5837 (m110)
REVERT: A  307 ARG cc_start: 0.7778 (tpp80) cc_final: 0.7474 (mmm-85)
REVERT: A  534 MET cc_start: -0.1110 (mtt) cc_final: -0.1457 (mpp)
REVERT: A  618 ASP cc_start: 0.8814 (t70) cc_final: 0.8318 (t0)
REVERT: A  630 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8270 (mt-10)
REVERT: A  631 MET cc_start: 0.8494 (mmm) cc_final: 0.8196 (mmm)
REVERT: A  653 ARG cc_start: 0.7978 (mtt180) cc_final: 0.7536 (mtm-85)
REVERT: A  762 GLU cc_start: 0.7970 (pp20) cc_final: 0.7006 (tm-30)
REVERT: A  954 LYS cc_start: 0.8433 (mttt) cc_final: 0.8107 (ttmm)
REVERT: A 1261 GLN cc_start: 0.8984 (mt0) cc_final: 0.8657 (mt0)
REVERT: A 1268 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7792 (mt-10)
REVERT: A 1303 ARG cc_start: 0.7583 (ptm-80) cc_final: 0.7380 (ptm-80)
REVERT: A 1317 ASN cc_start: 0.8521 (t0) cc_final: 0.8263 (t0)
REVERT: A 1325 LYS cc_start: 0.8797 (tttt) cc_final: 0.8340 (ttmm)
REVERT: A 1339 THR cc_start: 0.9233 (p) cc_final: 0.8897 (t)
  outliers start: 12
  outliers final: 4
  residues processed: 110
  average time/residue: 0.1273
  time to fit residues: 19.6144
Evaluate side-chains
  90 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1240 SER
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 22 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 112 optimal weight:   10.0000
   chunk 89 optimal weight:    8.9990
   chunk 36 optimal weight:    0.8980
   chunk 6 optimal weight:    4.9990
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    9.9990
   chunk 7 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** A  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1308 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.156070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.104563 restraints weight = 18071.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.104242 restraints weight = 10476.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.107197 restraints weight = 8149.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.106770 restraints weight = 6293.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.107000 restraints weight = 5947.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.3442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11986  Z= 0.129
  Angle     :  0.486   8.489  16831  Z= 0.265
  Chirality :  0.035   0.145   1944
  Planarity :  0.003   0.050   1601
  Dihedral  : 19.330 179.917   3143
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.97 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 12.71 %
    Favored  : 85.76 %
  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:  1.16 (0.26), residues: 1009
  helix:  1.70 (0.23), residues: 513
  sheet:  0.36 (0.48), residues: 114
  loop : -0.31 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 654 
 TYR   0.027   0.001   TYR A   5 
 PHE   0.013   0.001   PHE A1327 
 TRP   0.003   0.001   TRP A 476 
 HIS   0.004   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (11986)
  covalent geometry    : angle       0.48562 (16831)
  hydrogen bonds       : bond        0.04507 (  546)
  hydrogen bonds       : angle       3.85103 ( 1478)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: A  307 ARG cc_start: 0.7808 (tpp80) cc_final: 0.7544 (mmm-85)
REVERT: A  534 MET cc_start: -0.0609 (mtt) cc_final: -0.1001 (mpp)
REVERT: A  618 ASP cc_start: 0.8795 (t70) cc_final: 0.8293 (t0)
REVERT: A  630 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8241 (pt0)
REVERT: A  631 MET cc_start: 0.8365 (mmm) cc_final: 0.7751 (mmm)
REVERT: A  639 TYR cc_start: 0.7314 (m-80) cc_final: 0.7079 (m-10)
REVERT: A  954 LYS cc_start: 0.8411 (mttt) cc_final: 0.8079 (ttmm)
REVERT: A 1261 GLN cc_start: 0.8992 (mt0) cc_final: 0.8671 (mt0)
REVERT: A 1268 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7892 (mt-10)
REVERT: A 1317 ASN cc_start: 0.8432 (t0) cc_final: 0.8196 (t0)
REVERT: A 1325 LYS cc_start: 0.8829 (tttt) cc_final: 0.8432 (ttmm)
REVERT: A 1339 THR cc_start: 0.9281 (p) cc_final: 0.8933 (t)
  outliers start: 14
  outliers final: 9
  residues processed: 104
  average time/residue: 0.1102
  time to fit residues: 16.5097
Evaluate side-chains
  94 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 GLU
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  517 TYR
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue 1087 LEU
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1240 SER
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 69 optimal weight:    9.9990
   chunk 102 optimal weight:    7.9990
   chunk 81 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 52 optimal weight:   10.0000
   chunk 3 optimal weight:    8.9990
   chunk 77 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 17 optimal weight:   10.0000
   chunk 82 optimal weight:    0.8980
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 309 ASN
A 726 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.154267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.103240 restraints weight = 18316.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.102862 restraints weight = 11254.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.105870 restraints weight = 8591.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.105496 restraints weight = 6598.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.105596 restraints weight = 6324.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.3596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11986  Z= 0.146
  Angle     :  0.497   8.811  16831  Z= 0.271
  Chirality :  0.035   0.138   1944
  Planarity :  0.003   0.049   1601
  Dihedral  : 19.260 179.794   3143
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.97 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 13.36 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.26), residues: 1009
  helix:  1.77 (0.23), residues: 506
  sheet:  0.46 (0.48), residues: 112
  loop : -0.32 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 951 
 TYR   0.027   0.001   TYR A   5 
 PHE   0.008   0.001   PHE A 478 
 TRP   0.004   0.001   TRP A 659 
 HIS   0.004   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (11986)
  covalent geometry    : angle       0.49665 (16831)
  hydrogen bonds       : bond        0.04665 (  546)
  hydrogen bonds       : angle       3.85149 ( 1478)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  307 ARG cc_start: 0.7801 (tpp80) cc_final: 0.7564 (mmm-85)
REVERT: A  534 MET cc_start: -0.0644 (mtt) cc_final: -0.1031 (mpp)
REVERT: A  618 ASP cc_start: 0.8751 (t70) cc_final: 0.8263 (t0)
REVERT: A  630 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8296 (pt0)
REVERT: A  631 MET cc_start: 0.8292 (mmm) cc_final: 0.7714 (mmm)
REVERT: A  639 TYR cc_start: 0.7204 (m-80) cc_final: 0.6985 (m-10)
REVERT: A  762 GLU cc_start: 0.7966 (pp20) cc_final: 0.7303 (tp30)
REVERT: A  954 LYS cc_start: 0.8392 (mttt) cc_final: 0.8138 (ttmm)
REVERT: A 1261 GLN cc_start: 0.9036 (mt0) cc_final: 0.8747 (mt0)
REVERT: A 1268 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7809 (mt-10)
REVERT: A 1325 LYS cc_start: 0.8816 (tttt) cc_final: 0.8446 (ttmm)
REVERT: A 1339 THR cc_start: 0.9256 (p) cc_final: 0.8911 (t)
  outliers start: 16
  outliers final: 10
  residues processed: 99
  average time/residue: 0.1250
  time to fit residues: 17.3894
Evaluate side-chains
  94 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  517 TYR
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue 1087 LEU
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1240 SER
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 72 optimal weight:    9.9990
   chunk 93 optimal weight:    0.8980
   chunk 92 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:   10.0000
   chunk 74 optimal weight:    5.9990
   chunk 11 optimal weight:    0.5980
   chunk 48 optimal weight:    6.9990
   chunk 68 optimal weight:    9.9990
   chunk 69 optimal weight:    6.9990
   chunk 77 optimal weight:    0.8980
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
** A  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1308 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.155359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.106604 restraints weight = 18076.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.103696 restraints weight = 11125.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.107019 restraints weight = 9400.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.106409 restraints weight = 6944.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.106522 restraints weight = 6819.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.3712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11986  Z= 0.117
  Angle     :  0.468   8.900  16831  Z= 0.259
  Chirality :  0.034   0.137   1944
  Planarity :  0.003   0.048   1601
  Dihedral  : 19.209 179.342   3143
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.68 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 13.58 %
    Favored  : 85.10 %
  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:  1.31 (0.27), residues: 1009
  helix:  1.83 (0.24), residues: 506
  sheet:  0.54 (0.49), residues: 112
  loop : -0.25 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 951 
 TYR   0.017   0.001   TYR A   5 
 PHE   0.009   0.001   PHE A 164 
 TRP   0.002   0.001   TRP A 659 
 HIS   0.004   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (11986)
  covalent geometry    : angle       0.46760 (16831)
  hydrogen bonds       : bond        0.04258 (  546)
  hydrogen bonds       : angle       3.80076 ( 1478)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  534 MET cc_start: -0.0623 (mtt) cc_final: -0.1041 (mpp)
REVERT: A  618 ASP cc_start: 0.8790 (t70) cc_final: 0.8298 (t0)
REVERT: A  630 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8349 (pt0)
REVERT: A  639 TYR cc_start: 0.7166 (m-80) cc_final: 0.6959 (m-10)
REVERT: A  762 GLU cc_start: 0.8007 (pp20) cc_final: 0.7348 (tp30)
REVERT: A  954 LYS cc_start: 0.8400 (mttt) cc_final: 0.8127 (ttmm)
REVERT: A 1234 ASN cc_start: 0.8884 (m-40) cc_final: 0.8401 (m110)
REVERT: A 1261 GLN cc_start: 0.9044 (mt0) cc_final: 0.8719 (mt0)
REVERT: A 1268 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7765 (mt-10)
REVERT: A 1325 LYS cc_start: 0.8780 (tttt) cc_final: 0.8238 (ttmm)
REVERT: A 1339 THR cc_start: 0.9211 (p) cc_final: 0.8886 (t)
  outliers start: 12
  outliers final: 10
  residues processed: 99
  average time/residue: 0.1321
  time to fit residues: 18.4491
Evaluate side-chains
  95 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  517 TYR
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1087 LEU
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1240 SER
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 68 optimal weight:    9.9990
   chunk 84 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 97 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 70 optimal weight:    0.3980
   chunk 11 optimal weight:    5.9990
   chunk 86 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    2.0786

-------------------------------------------------------------------------------
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 = 0.3881 r_free = 0.3881 target = 0.153253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.103656 restraints weight = 18079.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.100673 restraints weight = 10968.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.104312 restraints weight = 9068.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.103541 restraints weight = 6691.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.103676 restraints weight = 6494.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.3861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11986  Z= 0.155
  Angle     :  0.508   8.589  16831  Z= 0.277
  Chirality :  0.035   0.148   1944
  Planarity :  0.003   0.048   1601
  Dihedral  : 19.265 179.487   3143
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.07 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 13.14 %
    Favored  : 85.10 %
  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:  1.23 (0.26), residues: 1009
  helix:  1.77 (0.24), residues: 506
  sheet:  0.51 (0.48), residues: 112
  loop : -0.29 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 400 
 TYR   0.012   0.001   TYR A 155 
 PHE   0.009   0.001   PHE A 478 
 TRP   0.004   0.001   TRP A 476 
 HIS   0.004   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (11986)
  covalent geometry    : angle       0.50831 (16831)
  hydrogen bonds       : bond        0.04779 (  546)
  hydrogen bonds       : angle       3.87731 ( 1478)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  402 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.7840 (mp10)
REVERT: A  534 MET cc_start: -0.0661 (mtt) cc_final: -0.1084 (mpp)
REVERT: A  618 ASP cc_start: 0.8830 (t70) cc_final: 0.8337 (t0)
REVERT: A  630 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8478 (pt0)
REVERT: A  639 TYR cc_start: 0.7048 (m-80) cc_final: 0.6826 (m-10)
REVERT: A  762 GLU cc_start: 0.7982 (pp20) cc_final: 0.7260 (tp30)
REVERT: A  954 LYS cc_start: 0.8362 (mttt) cc_final: 0.8082 (ttmm)
REVERT: A 1261 GLN cc_start: 0.9054 (mt0) cc_final: 0.8748 (mt0)
REVERT: A 1268 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7951 (mt-10)
REVERT: A 1325 LYS cc_start: 0.8817 (tttt) cc_final: 0.8257 (ttmm)
REVERT: A 1339 THR cc_start: 0.9267 (p) cc_final: 0.8934 (t)
  outliers start: 16
  outliers final: 12
  residues processed: 99
  average time/residue: 0.1187
  time to fit residues: 16.9425
Evaluate side-chains
  98 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  402 GLN
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  517 TYR
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1087 LEU
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1240 SER
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 111 optimal weight:    7.9990
   chunk 32 optimal weight:    2.9990
   chunk 36 optimal weight:    0.3980
   chunk 56 optimal weight:    3.9990
   chunk 112 optimal weight:   10.0000
   chunk 65 optimal weight:   10.0000
   chunk 46 optimal weight:   30.0000
   chunk 80 optimal weight:   10.0000
   chunk 8 optimal weight:    0.8980
   chunk 113 optimal weight:   10.0000
   overall best weight:    2.4586

-------------------------------------------------------------------------------
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 = 0.3871 r_free = 0.3871 target = 0.152322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.101873 restraints weight = 18255.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.101114 restraints weight = 11132.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.104095 restraints weight = 8722.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.103633 restraints weight = 6691.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.103866 restraints weight = 6293.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.4002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  11986  Z= 0.174
  Angle     :  0.527   8.468  16831  Z= 0.286
  Chirality :  0.036   0.144   1944
  Planarity :  0.003   0.050   1601
  Dihedral  : 19.310 179.290   3143
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.17 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 13.58 %
    Favored  : 84.78 %
  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:  1.04 (0.27), residues: 1009
  helix:  1.62 (0.23), residues: 512
  sheet:  0.33 (0.48), residues: 113
  loop : -0.42 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 400 
 TYR   0.016   0.001   TYR A   5 
 PHE   0.010   0.001   PHE A1080 
 TRP   0.004   0.001   TRP A 659 
 HIS   0.004   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (11986)
  covalent geometry    : angle       0.52662 (16831)
  hydrogen bonds       : bond        0.04989 (  546)
  hydrogen bonds       : angle       3.92212 ( 1478)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
REVERT: A  402 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.7984 (mp10)
REVERT: A  534 MET cc_start: -0.0592 (mtt) cc_final: -0.1053 (mpp)
REVERT: A  571 LYS cc_start: 0.7767 (mttt) cc_final: 0.7305 (mtmm)
REVERT: A  618 ASP cc_start: 0.8752 (t70) cc_final: 0.8271 (t0)
REVERT: A  631 MET cc_start: 0.8238 (mmm) cc_final: 0.7618 (mmm)
REVERT: A  639 TYR cc_start: 0.6931 (m-80) cc_final: 0.6715 (m-10)
REVERT: A  726 ASN cc_start: 0.7938 (m110) cc_final: 0.7624 (p0)
REVERT: A  762 GLU cc_start: 0.7967 (pp20) cc_final: 0.7302 (tp30)
REVERT: A  954 LYS cc_start: 0.8316 (mttt) cc_final: 0.8060 (ttmm)
REVERT: A 1261 GLN cc_start: 0.9040 (mt0) cc_final: 0.8746 (mt0)
REVERT: A 1268 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7956 (mt-10)
REVERT: A 1325 LYS cc_start: 0.8839 (tttt) cc_final: 0.8456 (ttmm)
REVERT: A 1339 THR cc_start: 0.9235 (p) cc_final: 0.8919 (t)
  outliers start: 15
  outliers final: 12
  residues processed: 96
  average time/residue: 0.1164
  time to fit residues: 15.9936
Evaluate side-chains
  95 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  402 GLN
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  517 TYR
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1087 LEU
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1240 SER
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 72 optimal weight:    9.9990
   chunk 65 optimal weight:    0.9980
   chunk 61 optimal weight:    7.9990
   chunk 47 optimal weight:    8.9990
   chunk 41 optimal weight:    8.9990
   chunk 55 optimal weight:   20.0000
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 95 optimal weight:    1.9990
   chunk 105 optimal weight:   40.0000
   chunk 63 optimal weight:    2.9990
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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 = 0.3879 r_free = 0.3879 target = 0.152973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.105040 restraints weight = 18178.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.101952 restraints weight = 12399.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.105143 restraints weight = 10030.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.104621 restraints weight = 6962.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.105108 restraints weight = 6663.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.4085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11986  Z= 0.149
  Angle     :  0.509   8.283  16831  Z= 0.278
  Chirality :  0.035   0.146   1944
  Planarity :  0.003   0.048   1601
  Dihedral  : 19.289 178.876   3143
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.07 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 13.25 %
    Favored  : 84.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.26), residues: 1009
  helix:  1.72 (0.24), residues: 506
  sheet:  0.47 (0.49), residues: 111
  loop : -0.41 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 400 
 TYR   0.030   0.001   TYR A   5 
 PHE   0.008   0.001   PHE A1080 
 TRP   0.004   0.001   TRP A 659 
 HIS   0.004   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (11986)
  covalent geometry    : angle       0.50935 (16831)
  hydrogen bonds       : bond        0.04708 (  546)
  hydrogen bonds       : angle       3.86347 ( 1478)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1907.05 seconds
wall clock time: 33 minutes 42.29 seconds (2022.29 seconds total)