Starting phenix.real_space_refine
on Wed Mar  4 09:14:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7trd_26086/03_2026/7trd_26086.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7trd_26086/03_2026/7trd_26086.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7trd_26086/03_2026/7trd_26086.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7trd_26086/03_2026/7trd_26086.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7trd_26086/03_2026/7trd_26086.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7trd_26086/03_2026/7trd_26086.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     224      5.49       5
     S      36      5.16       5
     C    6931      2.51       5
     N    2219      2.21       5
     O    2830      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 59 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12240
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 4605
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 4605
          Classifications: {'RNA': 217}
          Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 21, 'rna3p_pur': 86, 'rna3p_pyr': 96}
          Link IDs: {'rna2p': 35, 'rna3p': 181}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 7488
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 934, 7488
          Classifications: {'peptide': 934}
          Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 877}
          Chain breaks: 4
    Chain: "N"
      Number of atoms: 147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 147
          Classifications: {'DNA': 7}
          Link IDs: {'rna3p': 6}
  Time building chain proxies: 3.07, per 1000 atoms: 0.25
  Number of scatterers: 12240
  At special positions: 0
  Unit cell: (108.9, 122.1, 108.9, 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      36     16.00
     P     224     15.00
     O    2830      8.00
     N    2219      7.00
     C    6931      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  Conformation dependent library (CDL) restraints added in 446.6 milliseconds
  

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1766

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 8 sheets defined
      55.4% alpha, 15.2% beta
      64 base pairs and 96 stacking pairs defined.
    Time for finding SS restraints: 1.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 18
      removed outlier: 3.604A  pdb=" N   ARG A  11 " --> pdb=" O   CYS A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 24 through 32
    Processing helix  chain 'A' and resid 44 through 53
    Processing helix  chain 'A' and resid 76 through 92
    Processing helix  chain 'A' and resid 125 through 134
    Processing helix  chain 'A' and resid 134 through 145
    Processing helix  chain 'A' and resid 146 through 156
    Processing helix  chain 'A' and resid 174 through 178
      removed outlier: 3.839A  pdb=" N   LEU A 178 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 332
      removed outlier: 3.999A  pdb=" N   LEU A 332 " --> pdb=" O   LYS A 329 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 329 through 332'
    Processing helix  chain 'A' and resid 345 through 350
    Processing helix  chain 'A' and resid 353 through 366
      removed outlier: 3.574A  pdb=" N   ALA A 357 " --> pdb=" O   SER A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 388
    Processing helix  chain 'A' and resid 389 through 401
      removed outlier: 4.037A  pdb=" N   PHE A 393 " --> pdb=" O   MET A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 413
      removed outlier: 3.782A  pdb=" N   LEU A 408 " --> pdb=" O   PRO A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 454
      removed outlier: 3.781A  pdb=" N   GLN A 454 " --> pdb=" O   GLN A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 471
      removed outlier: 3.716A  pdb=" N   ARG A 471 " --> pdb=" O   ALA A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 479
    Processing helix  chain 'A' and resid 480 through 496
      removed outlier: 3.506A  pdb=" N   GLU A 484 " --> pdb=" O   SER A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 505 through 509
    Processing helix  chain 'A' and resid 517 through 521
      removed outlier: 3.655A  pdb=" N   LEU A 520 " --> pdb=" O   CYS A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 560
      removed outlier: 3.764A  pdb=" N   HIS A 534 " --> pdb=" O   PRO A 530 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   VAL A 553 " --> pdb=" O   MET A 549 " (cutoff:3.500A)
      removed outlier: 5.266A  pdb=" N   VAL A 554 " --> pdb=" O   SER A 550 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   PHE A 560 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 596
      removed outlier: 4.387A  pdb=" N   ILE A 587 " --> pdb=" O   LYS A 583 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   GLY A 588 " --> pdb=" O   LEU A 584 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL A 596 " --> pdb=" O   HIS A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 612
      removed outlier: 3.515A  pdb=" N   GLU A 611 " --> pdb=" O   ARG A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 672
      removed outlier: 3.531A  pdb=" N   SER A 656 " --> pdb=" O   GLU A 652 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ARG A 672 " --> pdb=" O   GLU A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 677
      removed outlier: 3.651A  pdb=" N   LEU A 676 " --> pdb=" O   PRO A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 698
      removed outlier: 3.762A  pdb=" N   ILE A 686 " --> pdb=" O   GLY A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 733
    Processing helix  chain 'A' and resid 765 through 769
      removed outlier: 4.006A  pdb=" N   LEU A 769 " --> pdb=" O   LEU A 766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 784
      removed outlier: 3.582A  pdb=" N   PHE A 776 " --> pdb=" O   TYR A 772 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 815
    Processing helix  chain 'A' and resid 837 through 854
    Processing helix  chain 'A' and resid 876 through 890
    Processing helix  chain 'A' and resid 946 through 950
      removed outlier: 3.789A  pdb=" N   ALA A 950 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 958
      removed outlier: 4.052A  pdb=" N   LEU A 958 " --> pdb=" O   ARG A 955 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 965 through 982
    Processing helix  chain 'A' and resid 983 through 988
    Processing helix  chain 'A' and resid 993 through 1017
    Processing helix  chain 'A' and resid 1024 through 1027
    Processing helix  chain 'A' and resid 1028 through 1051
      removed outlier: 4.120A  pdb=" N   PHE A1032 " --> pdb=" O   ASN A1028 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   TYR A1044 " --> pdb=" O   ALA A1040 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ASN A1051 " --> pdb=" O   LEU A1047 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1082
      removed outlier: 4.323A  pdb=" N   VAL A1070 " --> pdb=" O   PRO A1066 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLN A1071 " --> pdb=" O   SER A1067 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   TRP A1072 " --> pdb=" O   GLU A1068 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1085 through 1107
      removed outlier: 3.651A  pdb=" N   TYR A1089 " --> pdb=" O   HIS A1085 " (cutoff:3.500A)
      Proline residue:  A1091  - end of helix
      removed outlier: 4.508A  pdb=" N   GLY A1094 " --> pdb=" O   VAL A1090 " (cutoff:3.500A)
      removed outlier: 5.654A  pdb=" N   SER A1095 " --> pdb=" O   PRO A1091 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ARG A1105 " --> pdb=" O   THR A1101 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LYS A1106 " --> pdb=" O   GLN A1102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1108 through 1119
      removed outlier: 3.712A  pdb=" N   ALA A1119 " --> pdb=" O   LEU A1115 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 23
      removed outlier: 6.418A  pdb=" N   LEU A 158 " --> pdb=" O   VAL A 170 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL A 160 " --> pdb=" O   TYR A 168 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR A 168 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 5.715A  pdb=" N   ALA A 167 " --> pdb=" O   VAL A 791 " (cutoff:3.500A)
      removed outlier: 7.472A  pdb=" N   GLU A 793 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   GLN A 169 " --> pdb=" O   GLU A 793 " (cutoff:3.500A)
      removed outlier: 10.472A  pdb=" N   SER A 795 " --> pdb=" O   GLN A 169 " (cutoff:3.500A)
      removed outlier: 14.579A  pdb=" N   CYS A 171 " --> pdb=" O   SER A 795 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ARG A 743 " --> pdb=" O   GLN A 794 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TYR A 744 " --> pdb=" O   LYS A 760 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23
      removed outlier: 6.418A  pdb=" N   LEU A 158 " --> pdb=" O   VAL A 170 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL A 160 " --> pdb=" O   TYR A 168 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR A 168 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 5.715A  pdb=" N   ALA A 167 " --> pdb=" O   VAL A 791 " (cutoff:3.500A)
      removed outlier: 7.472A  pdb=" N   GLU A 793 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   GLN A 169 " --> pdb=" O   GLU A 793 " (cutoff:3.500A)
      removed outlier: 10.472A  pdb=" N   SER A 795 " --> pdb=" O   GLN A 169 " (cutoff:3.500A)
      removed outlier: 14.579A  pdb=" N   CYS A 171 " --> pdb=" O   SER A 795 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ARG A 743 " --> pdb=" O   GLN A 794 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103
    Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 327
    Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 564
    Processing sheet with id=AA6, first strand: chain 'A' and resid 598 through 600
      removed outlier: 6.601A  pdb=" N   SER A 619 " --> pdb=" O   ARG A 819 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 862 through 865
      removed outlier: 3.640A  pdb=" N   VAL A 904 " --> pdb=" O   LYS A 710 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   ASP A 712 " --> pdb=" O   LYS A 902 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   LYS A 902 " --> pdb=" O   ASP A 712 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 927 through 930

    396 hydrogen bonds defined for protein.
    1131 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      174 hydrogen bonds
      332 hydrogen bond angles
      0 basepair planarities
      64 basepair parallelities
      96 stacking parallelities
  Total time for adding SS restraints: 2.79

  Time building geometry restraints manager: 1.42 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2612
        1.33 -     1.45: 3958
        1.45 -     1.57: 5907
        1.57 -     1.69: 444
        1.69 -     1.81: 47
  Bond restraints: 12968
  Sorted by residual:
  bond pdb=" C   LYS A 973 "
       pdb=" N   LEU A 974 "
    ideal  model  delta    sigma   weight residual
    1.334  1.384 -0.049 1.27e-02 6.20e+03 1.50e+01
  bond pdb=" N   VAL A 697 "
       pdb=" CA  VAL A 697 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.037 1.21e-02 6.83e+03 9.11e+00
  bond pdb=" N   VAL A 127 "
       pdb=" CA  VAL A 127 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.17e-02 7.31e+03 7.97e+00
  bond pdb=" N   ASN A 125 "
       pdb=" CA  ASN A 125 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.031 1.22e-02 6.72e+03 6.26e+00
  bond pdb=" N   GLU A 705 "
       pdb=" CA  GLU A 705 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.031 1.28e-02 6.10e+03 6.06e+00
  ... (remaining 12963 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 17958
        1.52 -     3.05: 595
        3.05 -     4.57: 76
        4.57 -     6.09: 14
        6.09 -     7.61: 1
  Bond angle restraints: 18644
  Sorted by residual:
  angle pdb=" O   LYS A 973 "
        pdb=" C   LYS A 973 "
        pdb=" N   LEU A 974 "
      ideal   model   delta    sigma   weight residual
     122.07  117.19    4.88 1.03e+00 9.43e-01 2.25e+01
  angle pdb=" N   VAL A 596 "
        pdb=" CA  VAL A 596 "
        pdb=" C   VAL A 596 "
      ideal   model   delta    sigma   weight residual
     112.43  108.61    3.82 9.20e-01 1.18e+00 1.73e+01
  angle pdb=" CA  LYS A 973 "
        pdb=" C   LYS A 973 "
        pdb=" N   LEU A 974 "
      ideal   model   delta    sigma   weight residual
     117.07  121.64   -4.57 1.14e+00 7.69e-01 1.61e+01
  angle pdb=" C   LYS A 973 "
        pdb=" N   LEU A 974 "
        pdb=" CA  LEU A 974 "
      ideal   model   delta    sigma   weight residual
     120.44  125.62   -5.18 1.30e+00 5.92e-01 1.59e+01
  angle pdb=" N   ASP A1038 "
        pdb=" CA  ASP A1038 "
        pdb=" C   ASP A1038 "
      ideal   model   delta    sigma   weight residual
     113.28  109.10    4.18 1.22e+00 6.72e-01 1.18e+01
  ... (remaining 18639 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.85: 7444
       35.85 -    71.70: 614
       71.70 -   107.56: 96
      107.56 -   143.41: 4
      143.41 -   179.26: 3
  Dihedral angle restraints: 8161
    sinusoidal: 5438
      harmonic: 2723
  Sorted by residual:
  dihedral pdb=" O4'   U B  43 "
           pdb=" C1'   U B  43 "
           pdb=" N1    U B  43 "
           pdb=" C2    U B  43 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   52.74  179.26     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U B 133 "
           pdb=" C1'   U B 133 "
           pdb=" N1    U B 133 "
           pdb=" C2    U B 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   48.74 -176.74     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U B 291 "
           pdb=" C1'   U B 291 "
           pdb=" N1    U B 291 "
           pdb=" C2    U B 291 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   40.41 -168.41     1      1.70e+01 3.46e-03 6.58e+01
  ... (remaining 8158 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1913
       0.048 -    0.095: 287
       0.095 -    0.143: 61
       0.143 -    0.190: 22
       0.190 -    0.238: 2
  Chirality restraints: 2285
  Sorted by residual:
  chirality pdb=" P     G B 130 "
            pdb=" OP1   G B 130 "
            pdb=" OP2   G B 130 "
            pdb=" O5'   G B 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.65   -0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" C1'   A B 174 "
            pdb=" O4'   A B 174 "
            pdb=" C2'   A B 174 "
            pdb=" N9    A B 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.24    0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" C3'   G B 130 "
            pdb=" C4'   G B 130 "
            pdb=" O3'   G B 130 "
            pdb=" C2'   G B 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.67    0.19 2.00e-01 2.50e+01 8.80e-01
  ... (remaining 2282 not shown)

  Planarity restraints: 1542
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B 130 "   -0.001 2.00e-02 2.50e+03   4.15e-02 5.17e+01
        pdb=" N9    G B 130 "    0.002 2.00e-02 2.50e+03
        pdb=" C8    G B 130 "   -0.010 2.00e-02 2.50e+03
        pdb=" N7    G B 130 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    G B 130 "    0.036 2.00e-02 2.50e+03
        pdb=" C6    G B 130 "   -0.105 2.00e-02 2.50e+03
        pdb=" O6    G B 130 "    0.069 2.00e-02 2.50e+03
        pdb=" N1    G B 130 "   -0.039 2.00e-02 2.50e+03
        pdb=" C2    G B 130 "    0.046 2.00e-02 2.50e+03
        pdb=" N2    G B 130 "    0.000 2.00e-02 2.50e+03
        pdb=" N3    G B 130 "   -0.000 2.00e-02 2.50e+03
        pdb=" C4    G B 130 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B 129 "    0.003 2.00e-02 2.50e+03   3.20e-02 2.82e+01
        pdb=" N9    A B 129 "   -0.003 2.00e-02 2.50e+03
        pdb=" C8    A B 129 "   -0.008 2.00e-02 2.50e+03
        pdb=" N7    A B 129 "   -0.015 2.00e-02 2.50e+03
        pdb=" C5    A B 129 "    0.075 2.00e-02 2.50e+03
        pdb=" C6    A B 129 "    0.020 2.00e-02 2.50e+03
        pdb=" N6    A B 129 "   -0.014 2.00e-02 2.50e+03
        pdb=" N1    A B 129 "   -0.045 2.00e-02 2.50e+03
        pdb=" C2    A B 129 "    0.031 2.00e-02 2.50e+03
        pdb=" N3    A B 129 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    A B 129 "   -0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B 131 "   -0.015 2.00e-02 2.50e+03   3.41e-02 2.62e+01
        pdb=" N1    C B 131 "   -0.012 2.00e-02 2.50e+03
        pdb=" C2    C B 131 "    0.001 2.00e-02 2.50e+03
        pdb=" O2    C B 131 "   -0.000 2.00e-02 2.50e+03
        pdb=" N3    C B 131 "    0.007 2.00e-02 2.50e+03
        pdb=" C4    C B 131 "    0.077 2.00e-02 2.50e+03
        pdb=" N4    C B 131 "   -0.064 2.00e-02 2.50e+03
        pdb=" C5    C B 131 "    0.005 2.00e-02 2.50e+03
        pdb=" C6    C B 131 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1539 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 1470
        2.74 -     3.28: 11066
        3.28 -     3.82: 21444
        3.82 -     4.36: 24209
        4.36 -     4.90: 37863
  Nonbonded interactions: 96052
  Sorted by model distance:
  nonbonded pdb=" O   LEU A1079 "
            pdb=" OG1 THR A1083 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O2'   G B  71 "
            pdb=" OP1   C B  72 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OG  SER A 619 "
            pdb=" O   ASN A 635 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O2'   A B 175 "
            pdb=" OP1   A B 176 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" O2'   U B 314 "
            pdb=" OE2 GLU A 538 "
     model   vdw
     2.293 3.040
  ... (remaining 96047 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.480
  Find NCS groups from input model:        0.050
  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:             0.010
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
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   0.049  12968  Z= 0.213
  Angle     :  0.636   7.614  18644  Z= 0.378
  Chirality :  0.039   0.238   2285
  Planarity :  0.005   0.042   1542
  Dihedral  : 21.934 179.261   6395
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.86 %
    Favored  : 99.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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: -0.10 (0.28), residues: 924
  helix:  1.00 (0.26), residues: 443
  sheet: -0.29 (0.51), residues: 93
  loop : -1.25 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 470 
 TYR   0.009   0.001   TYR A 168 
 PHE   0.026   0.002   PHE A1021 
 TRP   0.016   0.001   TRP A 581 
 HIS   0.011   0.001   HIS A 779 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (12968)
  covalent geometry    : angle       0.63569 (18644)
  hydrogen bonds       : bond        0.13344 (  556)
  hydrogen bonds       : angle       5.61174 ( 1463)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A  372 MET cc_start: 0.4197 (mmp) cc_final: 0.3919 (mmm)
REVERT: A  700 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7503 (mt0)
REVERT: A 1059 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8219 (ttmm)
  outliers start: 1
  outliers final: 0
  residues processed: 49
  average time/residue: 0.1820
  time to fit residues: 11.8007
Evaluate side-chains
  32 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 31
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  700 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    0.8980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.7980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 779 HIS
** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1023 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.144835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.088525 restraints weight = 23341.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 2.24
r_work: 0.3032 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.0979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12968  Z= 0.125
  Angle     :  0.561   8.826  18644  Z= 0.283
  Chirality :  0.033   0.168   2285
  Planarity :  0.004   0.037   1542
  Dihedral  : 23.387 179.982   4579
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  5.67 %
    Favored  : 93.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  0.38 (0.29), residues: 924
  helix:  1.38 (0.25), residues: 452
  sheet: -0.17 (0.48), residues: 103
  loop : -1.04 (0.34), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 132 
 TYR   0.008   0.001   TYR A 122 
 PHE   0.014   0.001   PHE A1021 
 TRP   0.010   0.001   TRP A 581 
 HIS   0.009   0.001   HIS A 779 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (12968)
  covalent geometry    : angle       0.56100 (18644)
  hydrogen bonds       : bond        0.04676 (  556)
  hydrogen bonds       : angle       4.17919 ( 1463)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.311 
Fit side-chains
REVERT: A  372 MET cc_start: 0.4916 (mmp) cc_final: 0.4676 (mmm)
REVERT: A 1059 LYS cc_start: 0.8692 (ttmt) cc_final: 0.8309 (ttmm)
  outliers start: 3
  outliers final: 2
  residues processed: 43
  average time/residue: 0.1073
  time to fit residues: 7.1619
Evaluate side-chains
  37 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 35
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 17 optimal weight:   20.0000
   chunk 89 optimal weight:    4.9990
   chunk 92 optimal weight:    5.9990
   chunk 87 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 14 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 64 optimal weight:    0.9980
   chunk 68 optimal weight:    0.8980
   chunk 29 optimal weight:    4.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    1.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 779 HIS
A1085 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.143111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.086255 restraints weight = 23504.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 2.25
r_work: 0.2996 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.1208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12968  Z= 0.179
  Angle     :  0.572   8.099  18644  Z= 0.289
  Chirality :  0.034   0.177   2285
  Planarity :  0.004   0.034   1542
  Dihedral  : 23.328 179.120   4576
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  7.88 %
    Favored  : 91.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.29), residues: 924
  helix:  1.43 (0.25), residues: 454
  sheet: -0.12 (0.48), residues: 103
  loop : -0.98 (0.34), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 132 
 TYR   0.019   0.001   TYR A 168 
 PHE   0.020   0.002   PHE A1021 
 TRP   0.011   0.001   TRP A 581 
 HIS   0.011   0.001   HIS A 779 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (12968)
  covalent geometry    : angle       0.57231 (18644)
  hydrogen bonds       : bond        0.05005 (  556)
  hydrogen bonds       : angle       4.06890 ( 1463)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.399 
Fit side-chains
REVERT: A  372 MET cc_start: 0.4815 (mmp) cc_final: 0.4535 (mmm)
REVERT: A 1059 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8370 (ttmm)
  outliers start: 3
  outliers final: 3
  residues processed: 37
  average time/residue: 0.1006
  time to fit residues: 5.7585
Evaluate side-chains
  36 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 37 optimal weight:    0.0270
   chunk 4 optimal weight:   20.0000
   chunk 26 optimal weight:    3.9990
   chunk 75 optimal weight:    7.9990
   chunk 104 optimal weight:    1.9990
   chunk 63 optimal weight:    6.9990
   chunk 74 optimal weight:    0.8980
   chunk 90 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    1.3844

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

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN
A 779 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.144143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.087600 restraints weight = 23522.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 2.24
r_work: 0.3011 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.1386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12968  Z= 0.139
  Angle     :  0.537   8.621  18644  Z= 0.270
  Chirality :  0.033   0.184   2285
  Planarity :  0.004   0.044   1542
  Dihedral  : 23.271 178.887   4576
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  9.24 %
    Favored  : 89.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  0.64 (0.29), residues: 924
  helix:  1.63 (0.25), residues: 453
  sheet: -0.06 (0.48), residues: 103
  loop : -0.96 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 132 
 TYR   0.016   0.001   TYR A 168 
 PHE   0.016   0.001   PHE A 331 
 TRP   0.011   0.001   TRP A 581 
 HIS   0.004   0.001   HIS A 609 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (12968)
  covalent geometry    : angle       0.53696 (18644)
  hydrogen bonds       : bond        0.04480 (  556)
  hydrogen bonds       : angle       3.91896 ( 1463)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 35
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A  372 MET cc_start: 0.4808 (mmp) cc_final: 0.4520 (mmm)
REVERT: A 1059 LYS cc_start: 0.8785 (ttmt) cc_final: 0.8438 (ttmt)
  outliers start: 8
  outliers final: 5
  residues processed: 41
  average time/residue: 0.0976
  time to fit residues: 6.3566
Evaluate side-chains
  39 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1088 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 94 optimal weight:    2.9990
   chunk 13 optimal weight:    6.9990
   chunk 59 optimal weight:    2.9990
   chunk 3 optimal weight:   30.0000
   chunk 75 optimal weight:    0.9990
   chunk 76 optimal weight:    3.9990
   chunk 88 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 779 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.143651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.087045 restraints weight = 23307.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 2.23
r_work: 0.3001 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.1492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12968  Z= 0.151
  Angle     :  0.539   8.700  18644  Z= 0.272
  Chirality :  0.033   0.188   2285
  Planarity :  0.004   0.035   1542
  Dihedral  : 23.234 178.708   4576
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 10.47 %
    Favored  : 88.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.29), residues: 924
  helix:  1.66 (0.25), residues: 453
  sheet:  0.03 (0.49), residues: 103
  loop : -0.91 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 132 
 TYR   0.012   0.001   TYR A 168 
 PHE   0.018   0.001   PHE A 331 
 TRP   0.010   0.001   TRP A 581 
 HIS   0.004   0.001   HIS A1075 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (12968)
  covalent geometry    : angle       0.53941 (18644)
  hydrogen bonds       : bond        0.04529 (  556)
  hydrogen bonds       : angle       3.87312 ( 1463)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 37
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A  372 MET cc_start: 0.4933 (mmp) cc_final: 0.4638 (mmm)
REVERT: A 1059 LYS cc_start: 0.8829 (ttmt) cc_final: 0.8462 (ttmm)
  outliers start: 5
  outliers final: 5
  residues processed: 41
  average time/residue: 0.0878
  time to fit residues: 5.9138
Evaluate side-chains
  39 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1088 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 87 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9980
   chunk 18 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9990
   chunk 105 optimal weight:    0.3980
   chunk 58 optimal weight:    2.9990
   chunk 13 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 37 optimal weight:    0.4980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN
A 779 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.145302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.088787 restraints weight = 23289.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 2.25
r_work: 0.3034 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.1650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  12968  Z= 0.106
  Angle     :  0.511   8.877  18644  Z= 0.256
  Chirality :  0.031   0.189   2285
  Planarity :  0.004   0.034   1542
  Dihedral  : 23.179 178.332   4576
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 11.70 %
    Favored  : 87.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  0.90 (0.29), residues: 924
  helix:  1.85 (0.25), residues: 453
  sheet:  0.23 (0.51), residues: 96
  loop : -0.86 (0.34), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 132 
 TYR   0.013   0.001   TYR A 168 
 PHE   0.012   0.001   PHE A 331 
 TRP   0.013   0.001   TRP A 581 
 HIS   0.004   0.001   HIS A 779 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 (12968)
  covalent geometry    : angle       0.51146 (18644)
  hydrogen bonds       : bond        0.04026 (  556)
  hydrogen bonds       : angle       3.73722 ( 1463)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.317 
Fit side-chains
REVERT: A  372 MET cc_start: 0.5031 (mmp) cc_final: 0.4728 (mmm)
REVERT: A 1059 LYS cc_start: 0.8910 (ttmt) cc_final: 0.8521 (ttmm)
  outliers start: 8
  outliers final: 6
  residues processed: 46
  average time/residue: 0.0899
  time to fit residues: 6.6425
Evaluate side-chains
  42 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1088 THR
Chi-restraints excluded: chain A residue 1090 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   chunk 51 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 3 optimal weight:   30.0000
   chunk 108 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 89 optimal weight:    4.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 779 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.144651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.087998 restraints weight = 23355.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 2.24
r_work: 0.3021 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.1721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12968  Z= 0.132
  Angle     :  0.522   8.838  18644  Z= 0.262
  Chirality :  0.032   0.192   2285
  Planarity :  0.004   0.034   1542
  Dihedral  : 23.140 178.025   4576
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 12.81 %
    Favored  : 86.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  0.89 (0.29), residues: 924
  helix:  1.85 (0.25), residues: 453
  sheet:  0.25 (0.51), residues: 96
  loop : -0.89 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 132 
 TYR   0.011   0.001   TYR A 168 
 PHE   0.016   0.001   PHE A 331 
 TRP   0.010   0.001   TRP A 581 
 HIS   0.007   0.001   HIS A 779 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (12968)
  covalent geometry    : angle       0.52201 (18644)
  hydrogen bonds       : bond        0.04200 (  556)
  hydrogen bonds       : angle       3.73534 ( 1463)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A  372 MET cc_start: 0.4919 (mmp) cc_final: 0.4623 (mmm)
REVERT: A  472 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9034 (tp)
REVERT: A 1059 LYS cc_start: 0.8944 (ttmt) cc_final: 0.8550 (ttmm)
  outliers start: 8
  outliers final: 6
  residues processed: 44
  average time/residue: 0.0855
  time to fit residues: 6.2525
Evaluate side-chains
  44 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1088 THR
Chi-restraints excluded: chain A residue 1090 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 0 optimal weight:   30.0000
   chunk 22 optimal weight:    9.9990
   chunk 65 optimal weight:    2.9990
   chunk 112 optimal weight:    0.6980
   chunk 102 optimal weight:    0.0670
   chunk 9 optimal weight:   20.0000
   chunk 89 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 70 optimal weight:    4.9990
   chunk 110 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    1.1524

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

Flipped N/Q/H residues before XYZ refinement:
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 779 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.144911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.091999 restraints weight = 23203.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 2.25
r_work: 0.3005 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12968  Z= 0.123
  Angle     :  0.513   8.907  18644  Z= 0.258
  Chirality :  0.032   0.194   2285
  Planarity :  0.004   0.034   1542
  Dihedral  : 23.090 177.997   4576
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 13.18 %
    Favored  : 85.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.29), residues: 924
  helix:  1.90 (0.25), residues: 454
  sheet:  0.31 (0.51), residues: 96
  loop : -0.87 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 620 
 TYR   0.011   0.001   TYR A 168 
 PHE   0.014   0.001   PHE A 331 
 TRP   0.010   0.001   TRP A 581 
 HIS   0.004   0.001   HIS A 609 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (12968)
  covalent geometry    : angle       0.51258 (18644)
  hydrogen bonds       : bond        0.04099 (  556)
  hydrogen bonds       : angle       3.71398 ( 1463)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A  472 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9065 (tp)
REVERT: A 1059 LYS cc_start: 0.8925 (ttmt) cc_final: 0.8502 (ttmm)
  outliers start: 8
  outliers final: 6
  residues processed: 44
  average time/residue: 0.0868
  time to fit residues: 6.3083
Evaluate side-chains
  45 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1088 THR
Chi-restraints excluded: chain A residue 1090 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 113 optimal weight:    0.0170
   chunk 65 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 11 optimal weight:   30.0000
   chunk 25 optimal weight:   20.0000
   chunk 107 optimal weight:    0.8980
   chunk 76 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9980
   chunk 33 optimal weight:    7.9990
   chunk 46 optimal weight:    0.5980
   chunk 20 optimal weight:    4.9990
   overall best weight:    1.1020

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

Flipped N/Q/H residues before XYZ refinement:
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 779 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.145168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.091341 restraints weight = 23284.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 2.33
r_work: 0.3006 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12968  Z= 0.120
  Angle     :  0.516   9.917  18644  Z= 0.257
  Chirality :  0.032   0.196   2285
  Planarity :  0.004   0.033   1542
  Dihedral  : 23.047 177.907   4576
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 14.16 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  1.00 (0.29), residues: 924
  helix:  1.95 (0.25), residues: 454
  sheet:  0.29 (0.51), residues: 96
  loop : -0.87 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 865 
 TYR   0.011   0.001   TYR A 168 
 PHE   0.014   0.001   PHE A 331 
 TRP   0.010   0.001   TRP A 581 
 HIS   0.009   0.001   HIS A 779 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (12968)
  covalent geometry    : angle       0.51579 (18644)
  hydrogen bonds       : bond        0.04048 (  556)
  hydrogen bonds       : angle       3.68021 ( 1463)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A  472 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9054 (tp)
REVERT: A 1059 LYS cc_start: 0.8984 (ttmt) cc_final: 0.8623 (ttmm)
  outliers start: 7
  outliers final: 6
  residues processed: 44
  average time/residue: 0.0886
  time to fit residues: 6.4508
Evaluate side-chains
  45 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1088 THR
Chi-restraints excluded: chain A residue 1090 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 7 optimal weight:    6.9990
   chunk 36 optimal weight:    7.9990
   chunk 10 optimal weight:   20.0000
   chunk 112 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 43 optimal weight:    0.1980
   chunk 82 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   chunk 2 optimal weight:    8.9990
   chunk 81 optimal weight:    0.5980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 779 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.145967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.092451 restraints weight = 23296.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 2.28
r_work: 0.3037 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  12968  Z= 0.100
  Angle     :  0.503   8.971  18644  Z= 0.250
  Chirality :  0.031   0.195   2285
  Planarity :  0.004   0.034   1542
  Dihedral  : 23.006 177.726   4576
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 13.79 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  1.09 (0.29), residues: 924
  helix:  2.06 (0.25), residues: 453
  sheet:  0.29 (0.51), residues: 96
  loop : -0.86 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 132 
 TYR   0.012   0.001   TYR A 168 
 PHE   0.011   0.001   PHE A 331 
 TRP   0.011   0.001   TRP A 581 
 HIS   0.006   0.001   HIS A 779 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 (12968)
  covalent geometry    : angle       0.50302 (18644)
  hydrogen bonds       : bond        0.03817 (  556)
  hydrogen bonds       : angle       3.61908 ( 1463)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.333 
Fit side-chains
REVERT: A  472 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9038 (tp)
REVERT: A  536 LEU cc_start: 0.9123 (tp) cc_final: 0.8797 (tp)
REVERT: A 1059 LYS cc_start: 0.8974 (ttmt) cc_final: 0.8609 (ttmm)
  outliers start: 7
  outliers final: 6
  residues processed: 45
  average time/residue: 0.0885
  time to fit residues: 6.5132
Evaluate side-chains
  47 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1088 THR
Chi-restraints excluded: chain A residue 1090 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 25 optimal weight:    7.9990
   chunk 68 optimal weight:    0.0870
   chunk 101 optimal weight:    1.9990
   chunk 6 optimal weight:   10.0000
   chunk 63 optimal weight:    7.9990
   chunk 45 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 83 optimal weight:    4.9990
   chunk 30 optimal weight:   10.0000
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.9362

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

Flipped N/Q/H residues before XYZ refinement:
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 779 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.145903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.089806 restraints weight = 22891.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 2.19
r_work: 0.3051 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  12968  Z= 0.111
  Angle     :  0.500   8.930  18644  Z= 0.250
  Chirality :  0.031   0.197   2285
  Planarity :  0.004   0.033   1542
  Dihedral  : 22.971 177.469   4576
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 13.79 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  1.12 (0.29), residues: 924
  helix:  2.08 (0.25), residues: 454
  sheet:  0.32 (0.51), residues: 96
  loop : -0.85 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 865 
 TYR   0.010   0.001   TYR A 168 
 PHE   0.013   0.001   PHE A 331 
 TRP   0.010   0.001   TRP A 581 
 HIS   0.007   0.001   HIS A 779 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (12968)
  covalent geometry    : angle       0.50045 (18644)
  hydrogen bonds       : bond        0.03870 (  556)
  hydrogen bonds       : angle       3.61984 ( 1463)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2915.21 seconds
wall clock time: 50 minutes 35.09 seconds (3035.09 seconds total)