Starting phenix.real_space_refine
on Thu Sep 18 21:46:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dz6_47325/09_2025/9dz6_47325_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dz6_47325/09_2025/9dz6_47325.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dz6_47325/09_2025/9dz6_47325.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dz6_47325/09_2025/9dz6_47325.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dz6_47325/09_2025/9dz6_47325_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dz6_47325/09_2025/9dz6_47325_trim.cif"
  }
  resolution = 3.1
  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=   0.001 sd=   0.015
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: 7
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      1      5.21       5
     S      52      5.16       5
     C    6532      2.51       5
     N    1645      2.21       5
     O    1846      1.98       5
     H   10125      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 20204
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 17384
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1056, 17384
          Classifications: {'peptide': 1056}
          Link IDs: {'PTRANS': 40, 'TRANS': 1015}
          Chain breaks: 6
    Chain: "B"
      Number of atoms: 2787
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 170, 2787
          Classifications: {'peptide': 170}
          Link IDs: {'PTRANS': 6, 'TRANS': 163}
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 3.49, per 1000 atoms: 0.17
  Number of scatterers: 20204
  At special positions: 0
  Unit cell: (85.078, 109.858, 129.682, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      52     16.00
     P       3     15.00
     Mg      1     11.99
     O    1846      8.00
     N    1645      7.00
     C    6532      6.00
     H   10125      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.74
  Conformation dependent library (CDL) restraints added in 605.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2372

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 1 sheets defined
      78.2% alpha, 3.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 18
    Processing helix  chain 'A' and resid 22 through 38
    Processing helix  chain 'A' and resid 41 through 53
    Processing helix  chain 'A' and resid 56 through 74
    Processing helix  chain 'A' and resid 79 through 96
    Processing helix  chain 'A' and resid 102 through 121
      removed outlier: 3.686A  pdb=" N   ARG A 119 " --> pdb=" O   GLU A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 127
    Processing helix  chain 'A' and resid 131 through 138
    Processing helix  chain 'A' and resid 141 through 150
    Processing helix  chain 'A' and resid 153 through 172
    Processing helix  chain 'A' and resid 176 through 195
      removed outlier: 5.768A  pdb=" N   THR A 184 " --> pdb=" O   LEU A 180 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   VAL A 185 " --> pdb=" O   LYS A 181 " (cutoff:3.500A)
      Proline residue:  A 188  - end of helix
      removed outlier: 3.548A  pdb=" N   VAL A 194 " --> pdb=" O   CYS A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 204
      removed outlier: 3.739A  pdb=" N   LYS A 203 " --> pdb=" O   VAL A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 214
      removed outlier: 3.670A  pdb=" N   TRP A 210 " --> pdb=" O   SER A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 235
      Proline residue:  A 226  - end of helix
    Processing helix  chain 'A' and resid 236 through 249
      removed outlier: 3.958A  pdb=" N   THR A 249 " --> pdb=" O   GLU A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 262
      removed outlier: 3.816A  pdb=" N   ILE A 259 " --> pdb=" O   LEU A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 274
      removed outlier: 3.820A  pdb=" N   SER A 267 " --> pdb=" O   ASP A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 293
    Processing helix  chain 'A' and resid 297 through 310
      removed outlier: 3.711A  pdb=" N   TYR A 301 " --> pdb=" O   ASN A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 323
    Processing helix  chain 'A' and resid 334 through 347
      removed outlier: 3.606A  pdb=" N   CYS A 347 " --> pdb=" O   ASP A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 355
      Proline residue:  A 353  - end of helix
    Processing helix  chain 'A' and resid 360 through 374
    Processing helix  chain 'A' and resid 377 through 394
      removed outlier: 4.153A  pdb=" N   THR A 384 " --> pdb=" O   VAL A 380 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ASP A 386 " --> pdb=" O   GLY A 382 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   LEU A 387 " --> pdb=" O   LEU A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 405
      removed outlier: 3.832A  pdb=" N   LYS A 403 " --> pdb=" O   PRO A 399 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   TYR A 404 " --> pdb=" O   LYS A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 416
      removed outlier: 3.662A  pdb=" N   GLN A 411 " --> pdb=" O   PRO A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 436
      removed outlier: 4.010A  pdb=" N   LYS A 430 " --> pdb=" O   HIS A 426 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   PHE A 431 " --> pdb=" O   ILE A 427 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLU A 433 " --> pdb=" O   LYS A 429 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ILE A 434 " --> pdb=" O   LYS A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 464
    Processing helix  chain 'A' and resid 464 through 482
    Processing helix  chain 'A' and resid 482 through 491
    Processing helix  chain 'A' and resid 498 through 525
      removed outlier: 3.650A  pdb=" N   LYS A 522 " --> pdb=" O   CYS A 518 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ILE A 523 " --> pdb=" O   ILE A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 552
      removed outlier: 3.624A  pdb=" N   LEU A 552 " --> pdb=" O   GLN A 548 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 556 through 572
      removed outlier: 3.842A  pdb=" N   THR A 572 " --> pdb=" O   ALA A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 591
      removed outlier: 3.551A  pdb=" N   LYS A 585 " --> pdb=" O   THR A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 627
      removed outlier: 3.758A  pdb=" N   ALA A 608 " --> pdb=" O   ALA A 604 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   VAL A 609 " --> pdb=" O   GLU A 605 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLY A 617 " --> pdb=" O   ARG A 613 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 633
      removed outlier: 4.426A  pdb=" N   LYS A 633 " --> pdb=" O   GLU A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 634 through 646
      removed outlier: 3.737A  pdb=" N   SER A 640 " --> pdb=" O   PRO A 636 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 649
      No H-bonds generated for 'chain 'A' and resid 647 through 649'
    Processing helix  chain 'A' and resid 650 through 668
      removed outlier: 3.594A  pdb=" N   SER A 656 " --> pdb=" O   HIS A 652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 686
      Proline residue:  A 683  - end of helix
    Processing helix  chain 'A' and resid 690 through 697
    Processing helix  chain 'A' and resid 699 through 708
    Processing helix  chain 'A' and resid 708 through 719
    Processing helix  chain 'A' and resid 733 through 751
      removed outlier: 3.688A  pdb=" N   SER A 749 " --> pdb=" O   LYS A 745 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 752 through 764
    Processing helix  chain 'A' and resid 769 through 785
      Proline residue:  A 782  - end of helix
      removed outlier: 3.550A  pdb=" N   VAL A 785 " --> pdb=" O   ARG A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 802
      removed outlier: 4.049A  pdb=" N   HIS A 802 " --> pdb=" O   LEU A 798 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 803 through 810
      removed outlier: 4.098A  pdb=" N   GLY A 809 " --> pdb=" O   ASN A 806 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 811 through 823
      removed outlier: 4.402A  pdb=" N   SER A 816 " --> pdb=" O   THR A 812 " (cutoff:3.500A)
      removed outlier: 4.807A  pdb=" N   PHE A 817 " --> pdb=" O   VAL A 813 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 849 through 878
    Processing helix  chain 'A' and resid 879 through 884
    Processing helix  chain 'A' and resid 887 through 898
      removed outlier: 4.038A  pdb=" N   ILE A 898 " --> pdb=" O   ASN A 894 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 911 through 929
      removed outlier: 4.401A  pdb=" N   ARG A 924 " --> pdb=" O   ASN A 920 " (cutoff:3.500A)
      Proline residue:  A 925  - end of helix
    Processing helix  chain 'A' and resid 938 through 941
    Processing helix  chain 'A' and resid 942 through 960
      removed outlier: 3.761A  pdb=" N   SER A 960 " --> pdb=" O   GLN A 956 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 979 through 1002
    Processing helix  chain 'A' and resid 1018 through 1029
      removed outlier: 3.822A  pdb=" N   GLU A1022 " --> pdb=" O   ASN A1018 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LYS A1025 " --> pdb=" O   MET A1021 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1030 through 1046
      Proline residue:  A1036  - end of helix
      removed outlier: 3.617A  pdb=" N   SER A1046 " --> pdb=" O   ASN A1042 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1049 through 1068
      removed outlier: 5.121A  pdb=" N   THR A1065 " --> pdb=" O   LYS A1061 " (cutoff:3.500A)
      removed outlier: 5.884A  pdb=" N   SER A1066 " --> pdb=" O   CYS A1062 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1074 through 1081
    Processing helix  chain 'A' and resid 1081 through 1087
    Processing helix  chain 'A' and resid 1100 through 1115
      removed outlier: 3.847A  pdb=" N   THR A1113 " --> pdb=" O   VAL A1109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1121 through 1127
    Processing helix  chain 'B' and resid 24 through 34
    Processing helix  chain 'B' and resid 79 through 83
    Processing helix  chain 'B' and resid 96 through 102
      removed outlier: 4.053A  pdb=" N   TYR B 100 " --> pdb=" O   SER B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 112
    Processing helix  chain 'B' and resid 134 through 138
    Processing helix  chain 'B' and resid 139 through 144
    Processing helix  chain 'B' and resid 160 through 172
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 56
      removed outlier: 7.009A  pdb=" N   PHE B  13 " --> pdb=" O   ASP B  64 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   TRP B  66 " --> pdb=" O   PHE B  13 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   LEU B  15 " --> pdb=" O   TRP B  66 " (cutoff:3.500A)
      removed outlier: 7.191A  pdb=" N   THR B  68 " --> pdb=" O   LEU B  15 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   LEU B  17 " --> pdb=" O   THR B  68 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   GLN B 147 " --> pdb=" O   ILE B 119 " (cutoff:3.500A)

    641 hydrogen bonds defined for protein.
    1863 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.14

  Time building geometry restraints manager: 2.53 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 10100
        1.03 -     1.23: 29
        1.23 -     1.42: 4275
        1.42 -     1.61: 5945
        1.61 -     1.81: 79
  Bond restraints: 20428
  Sorted by residual:
  bond pdb=" C   LEU A 870 "
       pdb=" O   LEU A 870 "
    ideal  model  delta    sigma   weight residual
    1.236  1.202  0.034 1.26e-02 6.30e+03 7.23e+00
  bond pdb=" C   ARG A 757 "
       pdb=" O   ARG A 757 "
    ideal  model  delta    sigma   weight residual
    1.236  1.205  0.032 1.26e-02 6.30e+03 6.33e+00
  bond pdb=" N   PHE A 899 "
       pdb=" CA  PHE A 899 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.030 1.23e-02 6.61e+03 6.05e+00
  bond pdb=" N   PHE B 159 "
       pdb=" CA  PHE B 159 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.030 1.29e-02 6.01e+03 5.54e+00
  bond pdb=" N   LEU A 952 "
       pdb=" CA  LEU A 952 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.027 1.21e-02 6.83e+03 5.15e+00
  ... (remaining 20423 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.20: 35569
        1.20 -     2.40: 1313
        2.40 -     3.59: 74
        3.59 -     4.79: 29
        4.79 -     5.99: 6
  Bond angle restraints: 36991
  Sorted by residual:
  angle pdb=" CA  ASN A 230 "
        pdb=" C   ASN A 230 "
        pdb=" O   ASN A 230 "
      ideal   model   delta    sigma   weight residual
     120.42  116.21    4.21 1.06e+00 8.90e-01 1.58e+01
  angle pdb=" N   ASP A 263 "
        pdb=" CA  ASP A 263 "
        pdb=" C   ASP A 263 "
      ideal   model   delta    sigma   weight residual
     111.24  106.10    5.14 1.38e+00 5.25e-01 1.39e+01
  angle pdb=" CA  ASP A 263 "
        pdb=" CB  ASP A 263 "
        pdb=" CG  ASP A 263 "
      ideal   model   delta    sigma   weight residual
     112.60  116.23   -3.63 1.00e+00 1.00e+00 1.32e+01
  angle pdb=" CA  ASP B 150 "
        pdb=" CB  ASP B 150 "
        pdb=" CG  ASP B 150 "
      ideal   model   delta    sigma   weight residual
     112.60  115.97   -3.37 1.00e+00 1.00e+00 1.14e+01
  angle pdb=" CA  ASP B 150 "
        pdb=" C   ASP B 150 "
        pdb=" O   ASP B 150 "
      ideal   model   delta    sigma   weight residual
     120.46  117.10    3.36 1.07e+00 8.73e-01 9.89e+00
  ... (remaining 36986 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.89: 9313
       31.89 -    63.78: 210
       63.78 -    95.67: 35
       95.67 -   127.56: 1
      127.56 -   159.46: 2
  Dihedral angle restraints: 9561
    sinusoidal: 5186
      harmonic: 4375
  Sorted by residual:
  dihedral pdb=" C8  GTP B 201 "
           pdb=" C1' GTP B 201 "
           pdb=" N9  GTP B 201 "
           pdb=" O4' GTP B 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -54.86  159.46     1      2.00e+01 2.50e-03 4.65e+01
  dihedral pdb=" O5' GTP B 201 "
           pdb=" O3A GTP B 201 "
           pdb=" PA  GTP B 201 "
           pdb=" PB  GTP B 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     274.12  136.96  137.16     1      2.00e+01 2.50e-03 4.16e+01
  dihedral pdb=" O3B GTP B 201 "
           pdb=" O3A GTP B 201 "
           pdb=" PB  GTP B 201 "
           pdb=" PA  GTP B 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     291.08  175.97  115.11     1      2.00e+01 2.50e-03 3.42e+01
  ... (remaining 9558 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1063
       0.030 -    0.061: 381
       0.061 -    0.091: 97
       0.091 -    0.121: 40
       0.121 -    0.152: 7
  Chirality restraints: 1588
  Sorted by residual:
  chirality pdb=" CA  LEU A 952 "
            pdb=" N   LEU A 952 "
            pdb=" C   LEU A 952 "
            pdb=" CB  LEU A 952 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.76e-01
  chirality pdb=" CA  VAL B  10 "
            pdb=" N   VAL B  10 "
            pdb=" C   VAL B  10 "
            pdb=" CB  VAL B  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.51e-01
  chirality pdb=" CA  LYS A 937 "
            pdb=" N   LYS A 937 "
            pdb=" C   LYS A 937 "
            pdb=" CB  LYS A 937 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.41e-01
  ... (remaining 1585 not shown)

  Planarity restraints: 2903
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 757 "   -0.589 9.50e-02 1.11e+02   5.44e-01 5.82e+03
        pdb=" NE  ARG A 757 "   -0.126 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 757 "   -0.027 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 757 "    0.027 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 757 "    0.013 2.00e-02 2.50e+03
        pdb="HH11 ARG A 757 "   -0.716 2.00e-02 2.50e+03
        pdb="HH12 ARG A 757 "    0.804 2.00e-02 2.50e+03
        pdb="HH21 ARG A 757 "    0.779 2.00e-02 2.50e+03
        pdb="HH22 ARG A 757 "   -0.727 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 230 "   -0.032 2.00e-02 2.50e+03   4.44e-01 2.95e+03
        pdb=" CG  ASN A 230 "    0.003 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 230 "    0.031 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 230 "    0.002 2.00e-02 2.50e+03
        pdb="HD21 ASN A 230 "    0.766 2.00e-02 2.50e+03
        pdb="HD22 ASN A 230 "   -0.770 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 159 "   -0.014 2.00e-02 2.50e+03   2.59e-02 6.72e+00
        pdb=" N   GLU B 160 "    0.045 2.00e-02 2.50e+03
        pdb=" CA  GLU B 160 "   -0.011 2.00e-02 2.50e+03
        pdb=" H   GLU B 160 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 2900 not shown)

  Histogram of nonbonded interaction distances:
        1.43 -     2.07: 264
        2.07 -     2.70: 33165
        2.70 -     3.33: 61841
        3.33 -     3.97: 75991
        3.97 -     4.60: 122052
  Nonbonded interactions: 293313
  Sorted by model distance:
  nonbonded pdb=" O   TRP A 121 "
            pdb="HH22 ARG A 182 "
     model   vdw
     1.433 2.450
  nonbonded pdb=" OE1 GLU A 596 "
            pdb=" H   GLU A 596 "
     model   vdw
     1.592 2.450
  nonbonded pdb=" HG  SER A 650 "
            pdb=" OE1 GLU A 653 "
     model   vdw
     1.597 2.450
  nonbonded pdb=" OE1 GLU A 198 "
            pdb=" H   GLU A 198 "
     model   vdw
     1.616 2.450
  nonbonded pdb=" O   LYS A1025 "
            pdb="HD21 ASN A1029 "
     model   vdw
     1.626 2.450
  ... (remaining 293308 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=0.25 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.880
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.080
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     19.520
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
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      :  0.004   0.036  10303  Z= 0.188
  Angle     :  0.487   5.988  13963  Z= 0.275
  Chirality :  0.036   0.152   1588
  Planarity :  0.005   0.166   1735
  Dihedral  : 11.847 159.455   3831
  Min Nonbonded Distance : 1.821

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.31 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  5.38 %
    Favored  : 94.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.01 (0.25), residues: 1210
  helix:  1.89 (0.18), residues: 852
  sheet:  1.31 (0.88), residues: 35
  loop : -0.08 (0.36), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 182 
 TYR   0.010   0.001   TYR A 796 
 PHE   0.019   0.001   PHE A 570 
 TRP   0.011   0.001   TRP A 807 
 HIS   0.002   0.001   HIS A 859 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 (10303)
  covalent geometry    : angle       0.48693 (13963)
  hydrogen bonds       : bond        0.14673 (  641)
  hydrogen bonds       : angle       5.82799 ( 1863)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  627 MET cc_start: 0.8037 (mtm) cc_final: 0.7456 (ptp)
REVERT: A  717 GLN cc_start: 0.9484 (tt0) cc_final: 0.9260 (tm-30)
REVERT: A  896 ILE cc_start: 0.8940 (mt) cc_final: 0.8556 (tp)
REVERT: A  952 LEU cc_start: 0.8114 (mt) cc_final: 0.7737 (mm)
REVERT: A 1064 LEU cc_start: 0.9129 (tt) cc_final: 0.8808 (tt)
REVERT: A 1083 MET cc_start: 0.8689 (mtp) cc_final: 0.8239 (mmt)
REVERT: B   55 TYR cc_start: 0.8838 (m-80) cc_final: 0.8154 (m-80)
  outliers start: 3
  outliers final: 1
  residues processed: 82
  average time/residue: 0.2112
  time to fit residues: 24.7374
Evaluate side-chains
  58 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    0.4980
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.6980
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 117 optimal weight:    0.0980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  53 ASN
A 300 HIS
A 917 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.073688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.050277 restraints weight = 78432.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.2837 rms_B_bonded: 3.07
r_work: 0.2699 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2708
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2708 r_free = 0.2708    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2708 r_free = 0.2708    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2708
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.1017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  10303  Z= 0.119
  Angle     :  0.492   5.930  13963  Z= 0.262
  Chirality :  0.037   0.143   1588
  Planarity :  0.004   0.049   1735
  Dihedral  :  8.056 156.906   1335
  Min Nonbonded Distance : 1.804

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.57 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  7.05 %
    Favored  : 92.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.40 (0.25), residues: 1210
  helix:  2.09 (0.18), residues: 872
  sheet:  1.49 (0.84), residues: 40
  loop :  0.17 (0.39), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  26 
 TYR   0.010   0.001   TYR A 796 
 PHE   0.015   0.001   PHE B 159 
 TRP   0.009   0.001   TRP A 747 
 HIS   0.003   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (10303)
  covalent geometry    : angle       0.49249 (13963)
  hydrogen bonds       : bond        0.04345 (  641)
  hydrogen bonds       : angle       4.42030 ( 1863)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 62
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  627 MET cc_start: 0.8036 (mtm) cc_final: 0.7481 (ptp)
REVERT: A  717 GLN cc_start: 0.9477 (tt0) cc_final: 0.9262 (tm-30)
REVERT: A  896 ILE cc_start: 0.9007 (mt) cc_final: 0.8629 (tp)
  outliers start: 4
  outliers final: 1
  residues processed: 66
  average time/residue: 0.1866
  time to fit residues: 18.7188
Evaluate side-chains
  54 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  815 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 101 optimal weight:    9.9990
   chunk 35 optimal weight:    0.5980
   chunk 93 optimal weight:    9.9990
   chunk 65 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0570
   overall best weight:    1.1300

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

Flipped N/Q/H residues before XYZ refinement:
A 815 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.073289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.049865 restraints weight = 78674.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.2827 rms_B_bonded: 3.06
r_work: 0.2685 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2696
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2696 r_free = 0.2696    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2696 r_free = 0.2696    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2696
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.1176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10303  Z= 0.135
  Angle     :  0.463   5.831  13963  Z= 0.246
  Chirality :  0.036   0.135   1588
  Planarity :  0.004   0.046   1735
  Dihedral  :  7.993 157.430   1334
  Min Nonbonded Distance : 1.784

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.82 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  8.20 %
    Favored  : 91.53 %
  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 aren not related in a simple way.
  whole:  2.50 (0.25), residues: 1210
  helix:  2.15 (0.18), residues: 874
  sheet:  1.60 (0.86), residues: 40
  loop :  0.23 (0.39), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 865 
 TYR   0.011   0.001   TYR A 104 
 PHE   0.016   0.001   PHE A 570 
 TRP   0.009   0.001   TRP A 807 
 HIS   0.003   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (10303)
  covalent geometry    : angle       0.46325 (13963)
  hydrogen bonds       : bond        0.03875 (  641)
  hydrogen bonds       : angle       4.26279 ( 1863)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  509 MET cc_start: 0.8687 (mtp) cc_final: 0.8469 (mtm)
REVERT: A  627 MET cc_start: 0.8086 (mtm) cc_final: 0.7194 (ptp)
REVERT: A  717 GLN cc_start: 0.9471 (tt0) cc_final: 0.9253 (tm-30)
REVERT: A  896 ILE cc_start: 0.8992 (mt) cc_final: 0.8632 (tp)
  outliers start: 3
  outliers final: 3
  residues processed: 58
  average time/residue: 0.1598
  time to fit residues: 14.7121
Evaluate side-chains
  55 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  815 GLN
Chi-restraints excluded: chain A residue  917 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 109 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 97 optimal weight:    6.9990
   chunk 60 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 88 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9980
   chunk 103 optimal weight:   10.0000
   overall best weight:    1.3984

-------------------------------------------------------------------------------
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 = 0.3397 r_free = 0.3397 target = 0.073026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.049525 restraints weight = 78712.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.2824 rms_B_bonded: 3.08
r_work: 0.2684 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2691
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2691 r_free = 0.2691    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2691 r_free = 0.2691    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2691
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.1286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10303  Z= 0.155
  Angle     :  0.468   5.830  13963  Z= 0.249
  Chirality :  0.036   0.135   1588
  Planarity :  0.004   0.057   1735
  Dihedral  :  7.999 158.159   1334
  Min Nonbonded Distance : 1.770

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.74 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  8.29 %
    Favored  : 90.92 %
  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 aren not related in a simple way.
  whole:  2.49 (0.25), residues: 1210
  helix:  2.16 (0.18), residues: 874
  sheet:  1.32 (0.84), residues: 40
  loop :  0.22 (0.39), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  26 
 TYR   0.012   0.001   TYR A 104 
 PHE   0.016   0.001   PHE A 570 
 TRP   0.009   0.001   TRP A 807 
 HIS   0.003   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (10303)
  covalent geometry    : angle       0.46845 (13963)
  hydrogen bonds       : bond        0.03669 (  641)
  hydrogen bonds       : angle       4.20025 ( 1863)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  509 MET cc_start: 0.8732 (mtp) cc_final: 0.8500 (mtm)
REVERT: A  627 MET cc_start: 0.8108 (mtm) cc_final: 0.7263 (ptp)
REVERT: A  717 GLN cc_start: 0.9468 (tt0) cc_final: 0.9248 (tm-30)
REVERT: A  896 ILE cc_start: 0.9001 (mt) cc_final: 0.8651 (tp)
  outliers start: 9
  outliers final: 3
  residues processed: 62
  average time/residue: 0.1769
  time to fit residues: 17.4073
Evaluate side-chains
  56 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 53
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  815 GLN
Chi-restraints excluded: chain A residue  917 HIS
Chi-restraints excluded: chain A residue 1054 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 111 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 71 optimal weight:    7.9990
   chunk 6 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9990
   overall best weight:    1.5588

-------------------------------------------------------------------------------
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 = 0.3390 r_free = 0.3390 target = 0.072664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.049024 restraints weight = 78673.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.2808 rms_B_bonded: 3.08
r_work: 0.2669 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2681
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2681 r_free = 0.2681    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2681 r_free = 0.2681    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2681
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.1370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10303  Z= 0.168
  Angle     :  0.469   5.825  13963  Z= 0.249
  Chirality :  0.037   0.135   1588
  Planarity :  0.004   0.048   1735
  Dihedral  :  8.033 159.292   1334
  Min Nonbonded Distance : 1.758

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.74 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  8.82 %
    Favored  : 90.30 %
  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 aren not related in a simple way.
  whole:  2.49 (0.25), residues: 1210
  helix:  2.19 (0.18), residues: 871
  sheet:  1.09 (0.83), residues: 40
  loop :  0.19 (0.39), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 865 
 TYR   0.012   0.001   TYR A 104 
 PHE   0.017   0.001   PHE A 570 
 TRP   0.012   0.001   TRP A 807 
 HIS   0.004   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (10303)
  covalent geometry    : angle       0.46913 (13963)
  hydrogen bonds       : bond        0.03567 (  641)
  hydrogen bonds       : angle       4.15180 ( 1863)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  509 MET cc_start: 0.8709 (mtp) cc_final: 0.8480 (mtm)
REVERT: A  627 MET cc_start: 0.8085 (mtm) cc_final: 0.7513 (ptp)
REVERT: A  717 GLN cc_start: 0.9478 (tt0) cc_final: 0.9248 (tm-30)
REVERT: A  896 ILE cc_start: 0.8999 (mt) cc_final: 0.8683 (tp)
  outliers start: 10
  outliers final: 6
  residues processed: 62
  average time/residue: 0.1730
  time to fit residues: 17.0842
Evaluate side-chains
  59 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  792 THR
Chi-restraints excluded: chain A residue  815 GLN
Chi-restraints excluded: chain A residue  917 HIS
Chi-restraints excluded: chain A residue 1054 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 81 optimal weight:    4.9990
   chunk 111 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 102 optimal weight:   10.0000
   chunk 32 optimal weight:    0.0470
   overall best weight:    1.1284

-------------------------------------------------------------------------------
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 = 0.3402 r_free = 0.3402 target = 0.073227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.049709 restraints weight = 78361.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.2829 rms_B_bonded: 3.08
r_work: 0.2690 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2696
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2696 r_free = 0.2696    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2696 r_free = 0.2696    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2696
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.1491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10303  Z= 0.131
  Angle     :  0.451   5.872  13963  Z= 0.237
  Chirality :  0.036   0.136   1588
  Planarity :  0.004   0.043   1735
  Dihedral  :  8.010 158.598   1334
  Min Nonbonded Distance : 1.765

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.65 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  9.17 %
    Favored  : 90.04 %
  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 aren not related in a simple way.
  whole:  2.59 (0.25), residues: 1210
  helix:  2.28 (0.18), residues: 869
  sheet:  1.03 (0.82), residues: 40
  loop :  0.20 (0.39), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  26 
 TYR   0.011   0.001   TYR A 104 
 PHE   0.014   0.001   PHE A 570 
 TRP   0.010   0.001   TRP A 807 
 HIS   0.003   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (10303)
  covalent geometry    : angle       0.45059 (13963)
  hydrogen bonds       : bond        0.03334 (  641)
  hydrogen bonds       : angle       4.02916 ( 1863)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  509 MET cc_start: 0.8726 (mtp) cc_final: 0.8504 (mtm)
REVERT: A  627 MET cc_start: 0.8052 (mtm) cc_final: 0.7185 (ptp)
REVERT: A  717 GLN cc_start: 0.9470 (tt0) cc_final: 0.9242 (tm-30)
REVERT: A  896 ILE cc_start: 0.8985 (mt) cc_final: 0.8687 (tp)
  outliers start: 9
  outliers final: 8
  residues processed: 68
  average time/residue: 0.2033
  time to fit residues: 20.5925
Evaluate side-chains
  62 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  618 ILE
Chi-restraints excluded: chain A residue  792 THR
Chi-restraints excluded: chain A residue  815 GLN
Chi-restraints excluded: chain A residue  917 HIS
Chi-restraints excluded: chain A residue 1054 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 84 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   chunk 97 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 112 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 = 0.3395 r_free = 0.3395 target = 0.072897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.049580 restraints weight = 78932.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.2825 rms_B_bonded: 3.06
r_work: 0.2684 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2690
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2690 r_free = 0.2690    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2690 r_free = 0.2690    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2690
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10303  Z= 0.149
  Angle     :  0.460   5.822  13963  Z= 0.241
  Chirality :  0.036   0.136   1588
  Planarity :  0.004   0.043   1735
  Dihedral  :  8.021 158.969   1334
  Min Nonbonded Distance : 1.762

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.57 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  9.61 %
    Favored  : 89.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.61 (0.25), residues: 1210
  helix:  2.29 (0.18), residues: 870
  sheet:  0.99 (0.81), residues: 40
  loop :  0.21 (0.39), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  31 
 TYR   0.012   0.001   TYR A 104 
 PHE   0.016   0.001   PHE A 570 
 TRP   0.009   0.001   TRP A 807 
 HIS   0.003   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (10303)
  covalent geometry    : angle       0.45952 (13963)
  hydrogen bonds       : bond        0.03338 (  641)
  hydrogen bonds       : angle       4.03422 ( 1863)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  509 MET cc_start: 0.8728 (mtp) cc_final: 0.8504 (mtm)
REVERT: A  717 GLN cc_start: 0.9464 (tt0) cc_final: 0.9238 (tm-30)
REVERT: A  820 TYR cc_start: 0.8752 (m-10) cc_final: 0.8551 (m-10)
REVERT: A  896 ILE cc_start: 0.8982 (mt) cc_final: 0.8693 (tp)
  outliers start: 8
  outliers final: 7
  residues processed: 61
  average time/residue: 0.1663
  time to fit residues: 16.1308
Evaluate side-chains
  60 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  618 ILE
Chi-restraints excluded: chain A residue  792 THR
Chi-restraints excluded: chain A residue  815 GLN
Chi-restraints excluded: chain A residue  917 HIS
Chi-restraints excluded: chain A residue 1054 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 94 optimal weight:    6.9990
   chunk 76 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 96 optimal weight:    3.9990
   chunk 71 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9980
   chunk 118 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.3407 r_free = 0.3407 target = 0.073538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.049743 restraints weight = 78004.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.2832 rms_B_bonded: 3.12
r_work: 0.2695 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2703
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2703 r_free = 0.2703    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2703 r_free = 0.2703    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2703
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10303  Z= 0.115
  Angle     :  0.446   5.883  13963  Z= 0.233
  Chirality :  0.036   0.137   1588
  Planarity :  0.003   0.042   1735
  Dihedral  :  7.991 157.922   1334
  Min Nonbonded Distance : 1.773

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.57 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  9.70 %
    Favored  : 89.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.74 (0.25), residues: 1210
  helix:  2.40 (0.18), residues: 869
  sheet:  0.96 (0.81), residues: 40
  loop :  0.22 (0.39), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  26 
 TYR   0.010   0.001   TYR A 104 
 PHE   0.013   0.001   PHE A 570 
 TRP   0.009   0.001   TRP A 807 
 HIS   0.003   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (10303)
  covalent geometry    : angle       0.44581 (13963)
  hydrogen bonds       : bond        0.03174 (  641)
  hydrogen bonds       : angle       3.93490 ( 1863)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  509 MET cc_start: 0.8641 (mtp) cc_final: 0.8435 (mtm)
REVERT: A  717 GLN cc_start: 0.9469 (tt0) cc_final: 0.9232 (tm-30)
REVERT: A  820 TYR cc_start: 0.8760 (m-10) cc_final: 0.8549 (m-10)
REVERT: A  896 ILE cc_start: 0.8918 (mt) cc_final: 0.8651 (tp)
  outliers start: 8
  outliers final: 8
  residues processed: 62
  average time/residue: 0.1748
  time to fit residues: 16.0961
Evaluate side-chains
  63 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  618 ILE
Chi-restraints excluded: chain A residue  792 THR
Chi-restraints excluded: chain A residue  815 GLN
Chi-restraints excluded: chain A residue  917 HIS
Chi-restraints excluded: chain A residue 1054 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 121 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 7 optimal weight:    0.4980
   chunk 8 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3437 r_free = 0.3437 target = 0.073741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.050548 restraints weight = 79068.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.2871 rms_B_bonded: 3.08
r_work: 0.2734 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2743
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2743 r_free = 0.2743    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2743 r_free = 0.2743    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2743
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10303  Z= 0.111
  Angle     :  0.441   5.851  13963  Z= 0.229
  Chirality :  0.035   0.137   1588
  Planarity :  0.003   0.043   1735
  Dihedral  :  7.963 157.135   1334
  Min Nonbonded Distance : 1.785

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.49 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  9.88 %
    Favored  : 89.42 %
  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 aren not related in a simple way.
  whole:  2.81 (0.25), residues: 1210
  helix:  2.47 (0.18), residues: 869
  sheet:  0.93 (0.81), residues: 40
  loop :  0.21 (0.39), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  26 
 TYR   0.010   0.001   TYR A 104 
 PHE   0.013   0.001   PHE A 570 
 TRP   0.009   0.001   TRP A 747 
 HIS   0.003   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (10303)
  covalent geometry    : angle       0.44077 (13963)
  hydrogen bonds       : bond        0.03083 (  641)
  hydrogen bonds       : angle       3.88470 ( 1863)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  509 MET cc_start: 0.8771 (mtp) cc_final: 0.8558 (mtm)
REVERT: A  717 GLN cc_start: 0.9446 (tt0) cc_final: 0.9222 (tm-30)
REVERT: A  820 TYR cc_start: 0.8749 (m-10) cc_final: 0.8527 (m-10)
REVERT: A  896 ILE cc_start: 0.8908 (mt) cc_final: 0.8654 (tp)
  outliers start: 8
  outliers final: 7
  residues processed: 63
  average time/residue: 0.1920
  time to fit residues: 18.1164
Evaluate side-chains
  61 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  618 ILE
Chi-restraints excluded: chain A residue  792 THR
Chi-restraints excluded: chain A residue  815 GLN
Chi-restraints excluded: chain A residue  917 HIS
Chi-restraints excluded: chain A residue 1054 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 111 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 105 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 70 optimal weight:    2.9990
   chunk 93 optimal weight:   10.0000
   chunk 58 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A1069 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.073141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.049964 restraints weight = 79376.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.2856 rms_B_bonded: 3.08
r_work: 0.2719 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2728
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2728 r_free = 0.2728    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2728 r_free = 0.2728    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2728
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10303  Z= 0.147
  Angle     :  0.454   5.823  13963  Z= 0.238
  Chirality :  0.036   0.137   1588
  Planarity :  0.004   0.043   1735
  Dihedral  :  7.989 157.990   1334
  Min Nonbonded Distance : 1.765

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.74 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 10.05 %
    Favored  : 89.24 %
  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 aren not related in a simple way.
  whole:  2.76 (0.25), residues: 1210
  helix:  2.43 (0.18), residues: 869
  sheet:  0.95 (0.81), residues: 40
  loop :  0.18 (0.39), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  26 
 TYR   0.011   0.001   TYR A 104 
 PHE   0.016   0.001   PHE A 570 
 TRP   0.009   0.001   TRP A 807 
 HIS   0.003   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (10303)
  covalent geometry    : angle       0.45447 (13963)
  hydrogen bonds       : bond        0.03189 (  641)
  hydrogen bonds       : angle       3.92724 ( 1863)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  509 MET cc_start: 0.8777 (mtp) cc_final: 0.8571 (mtm)
REVERT: A  717 GLN cc_start: 0.9444 (tt0) cc_final: 0.9221 (tm-30)
REVERT: A  820 TYR cc_start: 0.8756 (m-10) cc_final: 0.8529 (m-10)
REVERT: A  896 ILE cc_start: 0.8914 (mt) cc_final: 0.8651 (tp)
  outliers start: 8
  outliers final: 7
  residues processed: 63
  average time/residue: 0.2009
  time to fit residues: 18.9966
Evaluate side-chains
  61 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  618 ILE
Chi-restraints excluded: chain A residue  792 THR
Chi-restraints excluded: chain A residue  815 GLN
Chi-restraints excluded: chain A residue  917 HIS
Chi-restraints excluded: chain A residue 1054 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 88 optimal weight:    5.9990
   chunk 94 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 40 optimal weight:    0.5980
   chunk 35 optimal weight:    0.7980
   chunk 90 optimal weight:    0.6980
   chunk 118 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 81 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 234 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.074094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.050758 restraints weight = 78758.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 3.09
r_work: 0.2738 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2746
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2746 r_free = 0.2746    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2746 r_free = 0.2746    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2746
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  10303  Z= 0.103
  Angle     :  0.439   5.915  13963  Z= 0.228
  Chirality :  0.035   0.138   1588
  Planarity :  0.003   0.045   1735
  Dihedral  :  7.962 156.693   1334
  Min Nonbonded Distance : 1.780

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.49 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 10.14 %
    Favored  : 89.15 %
  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 aren not related in a simple way.
  whole:  2.88 (0.25), residues: 1210
  helix:  2.52 (0.18), residues: 869
  sheet:  0.88 (0.80), residues: 40
  loop :  0.24 (0.39), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  26 
 TYR   0.010   0.001   TYR A 104 
 PHE   0.018   0.001   PHE A 570 
 TRP   0.009   0.001   TRP A 747 
 HIS   0.003   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (10303)
  covalent geometry    : angle       0.43941 (13963)
  hydrogen bonds       : bond        0.03027 (  641)
  hydrogen bonds       : angle       3.83532 ( 1863)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3731.98 seconds
wall clock time: 64 minutes 6.80 seconds (3846.80 seconds total)