Starting phenix.real_space_refine
on Tue Jun 10 11:34:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wb1_32392/06_2025/7wb1_32392.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wb1_32392/06_2025/7wb1_32392.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wb1_32392/06_2025/7wb1_32392.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wb1_32392/06_2025/7wb1_32392.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wb1_32392/06_2025/7wb1_32392.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wb1_32392/06_2025/7wb1_32392.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.002
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     178      5.49       5
     S      28      5.16       5
     C    6661      2.51       5
     N    2059      2.21       5
     O    2598      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 11524
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 614
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 614
          Classifications: {'DNA': 30}
          Link IDs: {'rna3p': 29}
    Chain: "C"
      Number of atoms: 547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 547
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
    Chain: "D"
      Number of atoms: 2577
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 2577
          Classifications: {'RNA': 121}
          Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 59, 'rna3p_pyr': 48}
          Link IDs: {'rna2p': 14, 'rna3p': 106}
    Chain: "A"
      Number of atoms: 7786
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 960, 7786
          Classifications: {'peptide': 960}
          Link IDs: {'PTRANS': 37, 'TRANS': 922}
          Chain breaks: 2
  Time building chain proxies: 7.54, per 1000 atoms: 0.65
  Number of scatterers: 11524
  At special positions: 0
  Unit cell: (101.52, 141, 121.26, 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      28     16.00
     P     178     15.00
     O    2598      8.00
     N    2059      7.00
     C    6661      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: 3.08
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1810

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 12 sheets defined
      49.4% alpha, 13.1% beta
      62 base pairs and 95 stacking pairs defined.
    Time for finding SS restraints: 4.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 17
    Processing helix  chain 'A' and resid 38 through 47
    Processing helix  chain 'A' and resid 60 through 92
      removed outlier: 3.735A  pdb=" N   ARG A  64 " --> pdb=" O   SER A  60 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ALA A  65 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ASN A  66 " --> pdb=" O   THR A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 100
    Processing helix  chain 'A' and resid 161 through 165
    Processing helix  chain 'A' and resid 195 through 201
      removed outlier: 3.552A  pdb=" N   ILE A 199 " --> pdb=" O   ASP A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 215
    Processing helix  chain 'A' and resid 222 through 271
      removed outlier: 3.577A  pdb=" N   ASP A 231 " --> pdb=" O   LYS A 227 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ALA A 236 " --> pdb=" O   ALA A 232 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   LEU A 249 " --> pdb=" O   GLN A 245 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   GLU A 250 " --> pdb=" O   ASP A 246 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   GLN A 252 " --> pdb=" O   ILE A 248 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   LYS A 260 " --> pdb=" O   LYS A 256 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ARG A 261 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LEU A 262 " --> pdb=" O   ASN A 258 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   ALA A 263 " --> pdb=" O   GLU A 259 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ASN A 264 " --> pdb=" O   LYS A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 309
    Processing helix  chain 'A' and resid 343 through 358
      removed outlier: 3.605A  pdb=" N   GLU A 357 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   LYS A 358 " --> pdb=" O   LEU A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 368
      removed outlier: 3.748A  pdb=" N   GLY A 362 " --> pdb=" O   LYS A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 378
      removed outlier: 3.755A  pdb=" N   GLU A 376 " --> pdb=" O   TYR A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 382
    Processing helix  chain 'A' and resid 384 through 390
      removed outlier: 3.807A  pdb=" N   LYS A 390 " --> pdb=" O   GLU A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 411
    Processing helix  chain 'A' and resid 413 through 443
      removed outlier: 4.041A  pdb=" N   VAL A 417 " --> pdb=" O   ASP A 413 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   TYR A 418 " --> pdb=" O   TRP A 414 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   ASP A 419 " --> pdb=" O   GLY A 415 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   ARG A 442 " --> pdb=" O   LEU A 438 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   ARG A 443 " --> pdb=" O   GLU A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 466
      removed outlier: 4.200A  pdb=" N   LYS A 450 " --> pdb=" O   ASP A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 469
      No H-bonds generated for 'chain 'A' and resid 467 through 469'
    Processing helix  chain 'A' and resid 472 through 493
    Processing helix  chain 'A' and resid 494 through 496
      No H-bonds generated for 'chain 'A' and resid 494 through 496'
    Processing helix  chain 'A' and resid 589 through 596
    Processing helix  chain 'A' and resid 697 through 717
      removed outlier: 3.602A  pdb=" N   LYS A 701 " --> pdb=" O   SER A 697 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ARG A 715 " --> pdb=" O   VAL A 711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 720 through 724
    Processing helix  chain 'A' and resid 725 through 750
    Processing helix  chain 'A' and resid 770 through 774
    Processing helix  chain 'A' and resid 776 through 789
    Processing helix  chain 'A' and resid 793 through 798
      removed outlier: 4.163A  pdb=" N   TYR A 797 " --> pdb=" O   PRO A 793 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 818 through 829
      removed outlier: 3.504A  pdb=" N   LYS A 828 " --> pdb=" O   ARG A 824 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 866 through 874
    Processing helix  chain 'A' and resid 875 through 877
      No H-bonds generated for 'chain 'A' and resid 875 through 877'
    Processing helix  chain 'A' and resid 881 through 885
    Processing helix  chain 'A' and resid 886 through 901
      removed outlier: 3.754A  pdb=" N   GLU A 892 " --> pdb=" O   GLY A 888 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 920 through 937
      removed outlier: 3.835A  pdb=" N   GLN A 924 " --> pdb=" O   HIS A 920 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA A 930 " --> pdb=" O   ALA A 926 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ARG A 937 " --> pdb=" O   TRP A 933 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 939 through 949
    Processing helix  chain 'A' and resid 954 through 971
      removed outlier: 3.805A  pdb=" N   PHE A 958 " --> pdb=" O   ASP A 954 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22
    Processing sheet with id=AA2, first strand: chain 'A' and resid 502 through 506
      removed outlier: 3.505A  pdb=" N   SER A 502 " --> pdb=" O   GLU A 618 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   GLY A 614 " --> pdb=" O   ILE A 506 " (cutoff:3.500A)
      removed outlier: 5.291A  pdb=" N   LEU A 611 " --> pdb=" O   GLU A 640 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   GLU A 640 " --> pdb=" O   LEU A 611 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ASN A 613 " --> pdb=" O   THR A 638 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   LEU A 633 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   VAL A  36 " --> pdb=" O   LEU A 633 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 587 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 115
      removed outlier: 4.525A  pdb=" N   ILE A 114 " --> pdb=" O   LYS A 141 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   GLN A 135 " --> pdb=" O   CYS A 130 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   PHE A 128 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 115
      removed outlier: 4.525A  pdb=" N   ILE A 114 " --> pdb=" O   LYS A 141 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   TYR A 155 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 145
      removed outlier: 3.629A  pdb=" N   GLN A 144 " --> pdb=" O   HIS A 152 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   HIS A 152 " --> pdb=" O   GLN A 144 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 542 through 545
      removed outlier: 3.504A  pdb=" N   ARG A 542 " --> pdb=" O   ASN A 573 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ASN A 573 " --> pdb=" O   ARG A 542 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   VAL A 572 " --> pdb=" O   PHE A 556 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   PHE A 556 " --> pdb=" O   VAL A 572 " (cutoff:3.500A)
      removed outlier: 5.393A  pdb=" N   VAL A 559 " --> pdb=" O   PHE A 517 " (cutoff:3.500A)
      removed outlier: 7.260A  pdb=" N   PHE A 517 " --> pdb=" O   VAL A 559 " (cutoff:3.500A)
      removed outlier: 10.291A  pdb=" N   ASN A 561 " --> pdb=" O   CYS A 515 " (cutoff:3.500A)
      removed outlier: 12.651A  pdb=" N   CYS A 515 " --> pdb=" O   ASN A 561 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 622 through 623
    Processing sheet with id=AA8, first strand: chain 'A' and resid 691 through 694
      removed outlier: 4.777A  pdb=" N   ALA A 756 " --> pdb=" O   ILE A 658 " (cutoff:3.500A)
      removed outlier: 7.691A  pdb=" N   THR A 801 " --> pdb=" O   LEU A 753 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   PHE A 755 " --> pdb=" O   THR A 801 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 681 through 682
    Processing sheet with id=AB1, first strand: chain 'A' and resid 830 through 831
      removed outlier: 3.513A  pdb=" N   LYS A 830 " --> pdb=" O   MET A 837 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 850 through 853
      removed outlier: 4.192A  pdb=" N   TYR A 853 " --> pdb=" O   VAL A 862 " (cutoff:3.500A)
      removed outlier: 4.731A  pdb=" N   VAL A 862 " --> pdb=" O   TYR A 853 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 910 through 911

    382 hydrogen bonds defined for protein.
    1095 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      150 hydrogen bonds
      276 hydrogen bond angles
      0 basepair planarities
      62 basepair parallelities
      95 stacking parallelities
  Total time for adding SS restraints: 5.92

  Time building geometry restraints manager: 3.67 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2385
        1.33 -     1.45: 3515
        1.45 -     1.57: 5830
        1.57 -     1.69: 353
        1.69 -     1.81: 41
  Bond restraints: 12124
  Sorted by residual:
  bond pdb=" CG  LEU A  70 "
       pdb=" CD2 LEU A  70 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.69e+00
  bond pdb=" N1    C D 103 "
       pdb=" C2    C D 103 "
    ideal  model  delta    sigma   weight residual
    1.397  1.422 -0.025 2.00e-02 2.50e+03 1.59e+00
  bond pdb=" C2    C D 104 "
       pdb=" O2    C D 104 "
    ideal  model  delta    sigma   weight residual
    1.240  1.216  0.024 2.00e-02 2.50e+03 1.50e+00
  bond pdb=" O4'  DG B  19 "
       pdb=" C1'  DG B  19 "
    ideal  model  delta    sigma   weight residual
    1.414  1.395  0.019 2.00e-02 2.50e+03 9.34e-01
  bond pdb=" CG  ARG A 967 "
       pdb=" CD  ARG A 967 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.98e-01
  ... (remaining 12119 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 16501
        1.32 -     2.64: 542
        2.64 -     3.96: 102
        3.96 -     5.28: 15
        5.28 -     6.60: 11
  Bond angle restraints: 17171
  Sorted by residual:
  angle pdb=" N   TYR A 854 "
        pdb=" CA  TYR A 854 "
        pdb=" C   TYR A 854 "
      ideal   model   delta    sigma   weight residual
     107.32  112.15   -4.83 1.65e+00 3.67e-01 8.57e+00
  angle pdb=" C   GLU A 439 "
        pdb=" N   GLU A 440 "
        pdb=" CA  GLU A 440 "
      ideal   model   delta    sigma   weight residual
     121.94  116.41    5.53 2.00e+00 2.50e-01 7.63e+00
  angle pdb=" C2'   G D  73 "
        pdb=" C1'   G D  73 "
        pdb=" N9    G D  73 "
      ideal   model   delta    sigma   weight residual
     112.00  115.74   -3.74 1.50e+00 4.44e-01 6.23e+00
  angle pdb=" C   TYR A 966 "
        pdb=" N   ARG A 967 "
        pdb=" CA  ARG A 967 "
      ideal   model   delta    sigma   weight residual
     121.14  116.80    4.34 1.75e+00 3.27e-01 6.14e+00
  angle pdb=" O3'   G D  45 "
        pdb=" C3'   G D  45 "
        pdb=" C2'   G D  45 "
      ideal   model   delta    sigma   weight residual
     113.70  117.36   -3.66 1.50e+00 4.44e-01 5.95e+00
  ... (remaining 17166 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.91: 6686
       35.91 -    71.82: 558
       71.82 -   107.73: 49
      107.73 -   143.64: 3
      143.64 -   179.55: 6
  Dihedral angle restraints: 7302
    sinusoidal: 4500
      harmonic: 2802
  Sorted by residual:
  dihedral pdb=" O4'   U D  11 "
           pdb=" C1'   U D  11 "
           pdb=" N1    U D  11 "
           pdb=" C2    U D  11 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   51.55 -179.55     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U D  17 "
           pdb=" C1'   U D  17 "
           pdb=" N1    U D  17 "
           pdb=" C2    U D  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   50.22 -178.22     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U D   9 "
           pdb=" C1'   U D   9 "
           pdb=" N1    U D   9 "
           pdb=" C2    U D   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00 -100.01  -59.99     1      1.50e+01 4.44e-03 2.13e+01
  ... (remaining 7299 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1634
       0.045 -    0.089: 268
       0.089 -    0.134: 68
       0.134 -    0.178: 8
       0.178 -    0.223: 1
  Chirality restraints: 1979
  Sorted by residual:
  chirality pdb=" C1'   G D  73 "
            pdb=" O4'   G D  73 "
            pdb=" C2'   G D  73 "
            pdb=" N9    G D  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.23    0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" C3'   C D  41 "
            pdb=" C4'   C D  41 "
            pdb=" O3'   C D  41 "
            pdb=" C2'   C D  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.30   -0.18 2.00e-01 2.50e+01 7.72e-01
  chirality pdb=" C3'   G D  45 "
            pdb=" C4'   G D  45 "
            pdb=" O3'   G D  45 "
            pdb=" C2'   G D  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.30   -0.17 2.00e-01 2.50e+01 7.50e-01
  ... (remaining 1976 not shown)

  Planarity restraints: 1546
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C D 104 "    0.009 2.00e-02 2.50e+03   2.56e-02 1.47e+01
        pdb=" N1    C D 104 "   -0.006 2.00e-02 2.50e+03
        pdb=" C2    C D 104 "   -0.063 2.00e-02 2.50e+03
        pdb=" O2    C D 104 "    0.039 2.00e-02 2.50e+03
        pdb=" N3    C D 104 "    0.001 2.00e-02 2.50e+03
        pdb=" C4    C D 104 "   -0.005 2.00e-02 2.50e+03
        pdb=" N4    C D 104 "    0.010 2.00e-02 2.50e+03
        pdb=" C5    C D 104 "    0.010 2.00e-02 2.50e+03
        pdb=" C6    C D 104 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C D 118 "    0.022 2.00e-02 2.50e+03   1.66e-02 6.17e+00
        pdb=" N1    C D 118 "   -0.033 2.00e-02 2.50e+03
        pdb=" C2    C D 118 "    0.007 2.00e-02 2.50e+03
        pdb=" O2    C D 118 "   -0.006 2.00e-02 2.50e+03
        pdb=" N3    C D 118 "   -0.000 2.00e-02 2.50e+03
        pdb=" C4    C D 118 "    0.025 2.00e-02 2.50e+03
        pdb=" N4    C D 118 "   -0.010 2.00e-02 2.50e+03
        pdb=" C5    C D 118 "    0.004 2.00e-02 2.50e+03
        pdb=" C6    C D 118 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  56 "   -0.006 2.00e-02 2.50e+03   1.42e-02 5.57e+00
        pdb=" N9    A D  56 "   -0.000 2.00e-02 2.50e+03
        pdb=" C8    A D  56 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    A D  56 "    0.004 2.00e-02 2.50e+03
        pdb=" C5    A D  56 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    A D  56 "    0.007 2.00e-02 2.50e+03
        pdb=" N6    A D  56 "    0.000 2.00e-02 2.50e+03
        pdb=" N1    A D  56 "   -0.033 2.00e-02 2.50e+03
        pdb=" C2    A D  56 "    0.031 2.00e-02 2.50e+03
        pdb=" N3    A D  56 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4    A D  56 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1543 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 183
        2.62 -     3.19: 9664
        3.19 -     3.76: 19864
        3.76 -     4.33: 25399
        4.33 -     4.90: 38127
  Nonbonded interactions: 93237
  Sorted by model distance:
  nonbonded pdb=" N2    G D  59 "
            pdb=" O2    C D  94 "
     model   vdw
     2.046 2.496
  nonbonded pdb=" OP2   G D 101 "
            pdb=" NH2 ARG A 591 "
     model   vdw
     2.182 3.120
  nonbonded pdb=" NZ  LYS A 521 "
            pdb=" OE2 GLU A 605 "
     model   vdw
     2.227 3.120
  nonbonded pdb=" O6   DG B  22 "
            pdb=" NZ  LYS A 227 "
     model   vdw
     2.236 3.120
  nonbonded pdb=" OG1 THR A 202 "
            pdb=" OE1 GLU A 204 "
     model   vdw
     2.263 3.040
  ... (remaining 93232 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.500
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     34.860
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
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      :  0.003   0.043  12124  Z= 0.139
  Angle     :  0.590   6.604  17171  Z= 0.317
  Chirality :  0.037   0.223   1979
  Planarity :  0.004   0.044   1546
  Dihedral  : 22.125 179.554   5492
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.72 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.28), residues: 954
  helix:  1.86 (0.26), residues: 412
  sheet: -0.69 (0.45), residues: 140
  loop : -0.80 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 962 
 HIS   0.015   0.002   HIS A 435 
 PHE   0.016   0.001   PHE A 332 
 TYR   0.017   0.001   TYR A 857 
 ARG   0.003   0.000   ARG A 764 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17607 (  531)
  hydrogen bonds       : angle       5.88496 ( 1371)
  covalent geometry    : bond        0.00282 (12124)
  covalent geometry    : angle       0.59037 (17171)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.998 
Fit side-chains
REVERT: A   29 MET cc_start: 0.6906 (ppp) cc_final: 0.5886 (ppp)
REVERT: A  375 GLN cc_start: 0.7736 (mm110) cc_final: 0.7534 (tp40)
REVERT: A  570 MET cc_start: 0.7668 (tpt) cc_final: 0.7458 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.2360
  time to fit residues: 29.5104
Evaluate side-chains
  58 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    9.9990
   chunk 85 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 29 optimal weight:    3.9990
   chunk 57 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 34 optimal weight:    7.9990
   chunk 53 optimal weight:    0.7980
   chunk 65 optimal weight:    8.9990
   chunk 102 optimal weight:    3.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 251 HIS
A 729 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.095327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.069539 restraints weight = 43640.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.071670 restraints weight = 23563.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.073018 restraints weight = 16498.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.1225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12124  Z= 0.132
  Angle     :  0.586   8.144  17171  Z= 0.311
  Chirality :  0.037   0.222   1979
  Planarity :  0.004   0.046   1546
  Dihedral  : 24.688 179.190   3482
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  7.39 %
    Favored  : 91.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.28), residues: 954
  helix:  2.06 (0.26), residues: 420
  sheet: -0.82 (0.42), residues: 154
  loop : -0.66 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 366 
 HIS   0.006   0.001   HIS A 435 
 PHE   0.024   0.001   PHE A 399 
 TYR   0.015   0.001   TYR A 857 
 ARG   0.003   0.000   ARG A 740 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06977 (  531)
  hydrogen bonds       : angle       4.47603 ( 1371)
  covalent geometry    : bond        0.00274 (12124)
  covalent geometry    : angle       0.58606 (17171)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  486 TRP cc_start: 0.6989 (m-10) cc_final: 0.6773 (m-10)
REVERT: A  570 MET cc_start: 0.8009 (tpt) cc_final: 0.7642 (mmm)
  outliers start: 6
  outliers final: 2
  residues processed: 74
  average time/residue: 0.2061
  time to fit residues: 24.1392
Evaluate side-chains
  62 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 60
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  630 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 64 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 93 optimal weight:    3.9990
   chunk 65 optimal weight:   10.0000
   chunk 102 optimal weight:    7.9990
   chunk 27 optimal weight:    0.6980
   chunk 31 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9980
   chunk 52 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    3.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 152 HIS
A 160 ASN
A 306 ASN
A 375 GLN
A 520 GLN
** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.091955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.065949 restraints weight = 44257.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.068041 restraints weight = 23855.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.069338 restraints weight = 16766.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  12124  Z= 0.219
  Angle     :  0.672  10.289  17171  Z= 0.354
  Chirality :  0.041   0.220   1979
  Planarity :  0.005   0.047   1546
  Dihedral  : 24.766 178.814   3482
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 10.73 %
    Favored  : 87.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.27), residues: 954
  helix:  1.52 (0.25), residues: 420
  sheet: -1.00 (0.45), residues: 133
  loop : -0.99 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 782 
 HIS   0.008   0.002   HIS A 435 
 PHE   0.020   0.002   PHE A 399 
 TYR   0.018   0.002   TYR A 857 
 ARG   0.004   0.001   ARG A 642 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07307 (  531)
  hydrogen bonds       : angle       4.55143 ( 1371)
  covalent geometry    : bond        0.00466 (12124)
  covalent geometry    : angle       0.67246 (17171)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 63
  time to evaluate  : 1.127 
Fit side-chains
   revert: symmetry clash
REVERT: A  341 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6491 (tp30)
REVERT: A  486 TRP cc_start: 0.7053 (m-10) cc_final: 0.6828 (m-10)
REVERT: A  570 MET cc_start: 0.7905 (tpt) cc_final: 0.7588 (mmm)
REVERT: A  744 TYR cc_start: 0.8569 (t80) cc_final: 0.8353 (t80)
REVERT: A  781 ASP cc_start: 0.7074 (m-30) cc_final: 0.6874 (m-30)
  outliers start: 16
  outliers final: 13
  residues processed: 71
  average time/residue: 0.1899
  time to fit residues: 22.2214
Evaluate side-chains
  68 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  134 CYS
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  152 HIS
Chi-restraints excluded: chain A residue  233 CYS
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  630 GLU
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  934 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 8 optimal weight:   10.0000
   chunk 28 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   chunk 77 optimal weight:    5.9990
   overall best weight:    1.1788

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.094558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.068644 restraints weight = 43533.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.070768 restraints weight = 23495.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.072086 restraints weight = 16501.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  12124  Z= 0.127
  Angle     :  0.568   8.671  17171  Z= 0.301
  Chirality :  0.037   0.220   1979
  Planarity :  0.004   0.051   1546
  Dihedral  : 24.587 179.710   3482
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 11.08 %
    Favored  : 87.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.28), residues: 954
  helix:  1.96 (0.26), residues: 420
  sheet: -0.88 (0.44), residues: 146
  loop : -0.74 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 598 
 HIS   0.012   0.001   HIS A 152 
 PHE   0.012   0.001   PHE A 399 
 TYR   0.009   0.001   TYR A 822 
 ARG   0.003   0.000   ARG A 740 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05998 (  531)
  hydrogen bonds       : angle       4.17206 ( 1371)
  covalent geometry    : bond        0.00261 (12124)
  covalent geometry    : angle       0.56780 (17171)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 1.136 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.6491 (ppp) cc_final: 0.5807 (ppp)
REVERT: A  341 GLU cc_start: 0.6717 (mm-30) cc_final: 0.6412 (tp30)
REVERT: A  489 ASP cc_start: 0.7754 (m-30) cc_final: 0.7459 (m-30)
REVERT: A  570 MET cc_start: 0.7891 (tpt) cc_final: 0.7644 (mmm)
  outliers start: 16
  outliers final: 7
  residues processed: 78
  average time/residue: 0.1827
  time to fit residues: 23.1475
Evaluate side-chains
  67 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  630 GLU
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  732 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 3 optimal weight:    7.9990
   chunk 70 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 59 optimal weight:    7.9990
   chunk 90 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 81 optimal weight:    0.0020
   chunk 96 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   chunk 32 optimal weight:    0.1980
   chunk 11 optimal weight:   10.0000
   overall best weight:    3.0394

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

Flipped N/Q/H residues before XYZ refinement:
A 306 ASN
** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.092283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.066594 restraints weight = 43741.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 71)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.068623 restraints weight = 24291.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.069887 restraints weight = 17281.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.2149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12124  Z= 0.200
  Angle     :  0.634   8.654  17171  Z= 0.335
  Chirality :  0.039   0.218   1979
  Planarity :  0.005   0.052   1546
  Dihedral  : 24.690 179.567   3482
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 12.75 %
    Favored  : 84.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.28), residues: 954
  helix:  1.60 (0.25), residues: 417
  sheet: -0.89 (0.44), residues: 143
  loop : -0.95 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 344 
 HIS   0.005   0.001   HIS A 251 
 PHE   0.029   0.002   PHE A 399 
 TYR   0.014   0.002   TYR A 138 
 ARG   0.003   0.000   ARG A 642 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06652 (  531)
  hydrogen bonds       : angle       4.35558 ( 1371)
  covalent geometry    : bond        0.00424 (12124)
  covalent geometry    : angle       0.63388 (17171)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 57
  time to evaluate  : 1.009 
Fit side-chains
REVERT: A  486 TRP cc_start: 0.7005 (m-10) cc_final: 0.6742 (m-10)
REVERT: A  570 MET cc_start: 0.7833 (tpt) cc_final: 0.7582 (mmm)
  outliers start: 21
  outliers final: 15
  residues processed: 70
  average time/residue: 0.1783
  time to fit residues: 20.3722
Evaluate side-chains
  69 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 54
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 CYS
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  233 CYS
Chi-restraints excluded: chain A residue  251 HIS
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  630 GLU
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  732 ASP
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  934 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 14 optimal weight:   10.0000
   chunk 101 optimal weight:    8.9990
   chunk 0 optimal weight:    6.9990
   chunk 82 optimal weight:   10.0000
   chunk 48 optimal weight:    3.9990
   chunk 103 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 83 optimal weight:    0.2980
   chunk 16 optimal weight:   10.0000
   chunk 31 optimal weight:    9.9990
   overall best weight:    3.4588

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

Flipped N/Q/H residues before XYZ refinement:
** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 804 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.091435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.065708 restraints weight = 44416.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.067740 restraints weight = 24158.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.068975 restraints weight = 17209.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.2557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12124  Z= 0.218
  Angle     :  0.672   9.857  17171  Z= 0.355
  Chirality :  0.040   0.221   1979
  Planarity :  0.005   0.051   1546
  Dihedral  : 24.757 179.838   3482
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 14.78 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.27), residues: 954
  helix:  1.25 (0.25), residues: 420
  sheet: -1.15 (0.44), residues: 143
  loop : -1.15 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 344 
 HIS   0.007   0.002   HIS A 251 
 PHE   0.015   0.002   PHE A 463 
 TYR   0.022   0.002   TYR A 138 
 ARG   0.004   0.001   ARG A 642 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07014 (  531)
  hydrogen bonds       : angle       4.44789 ( 1371)
  covalent geometry    : bond        0.00460 (12124)
  covalent geometry    : angle       0.67238 (17171)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 58
  time to evaluate  : 0.999 
Fit side-chains
REVERT: A  134 CYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7879 (t)
REVERT: A  439 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6694 (pt0)
REVERT: A  486 TRP cc_start: 0.7037 (m-10) cc_final: 0.6762 (m-10)
REVERT: A  837 MET cc_start: 0.6592 (OUTLIER) cc_final: 0.5623 (ppp)
  outliers start: 23
  outliers final: 15
  residues processed: 73
  average time/residue: 0.1936
  time to fit residues: 22.7089
Evaluate side-chains
  68 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 51
  time to evaluate  : 1.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 CYS
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  233 CYS
Chi-restraints excluded: chain A residue  251 HIS
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain A residue  630 GLU
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  732 ASP
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  837 MET
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  857 TYR
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue  970 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 109 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 13 optimal weight:   20.0000
   chunk 48 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   chunk 73 optimal weight:    6.9990
   chunk 96 optimal weight:    7.9990
   chunk 100 optimal weight:    8.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 286 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.091519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.065696 restraints weight = 44797.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.067745 restraints weight = 24093.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.069021 restraints weight = 17001.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.2742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12124  Z= 0.203
  Angle     :  0.660   9.538  17171  Z= 0.346
  Chirality :  0.040   0.221   1979
  Planarity :  0.005   0.050   1546
  Dihedral  : 24.732 179.635   3482
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.38 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.27), residues: 954
  helix:  1.24 (0.25), residues: 417
  sheet: -1.45 (0.41), residues: 160
  loop : -1.17 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 344 
 HIS   0.006   0.002   HIS A 251 
 PHE   0.016   0.002   PHE A 463 
 TYR   0.019   0.002   TYR A 138 
 ARG   0.003   0.000   ARG A 642 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06694 (  531)
  hydrogen bonds       : angle       4.41396 ( 1371)
  covalent geometry    : bond        0.00428 (12124)
  covalent geometry    : angle       0.66009 (17171)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 57
  time to evaluate  : 1.048 
Fit side-chains
REVERT: A  134 CYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7860 (t)
REVERT: A  357 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7696 (mm-30)
REVERT: A  486 TRP cc_start: 0.7071 (m-10) cc_final: 0.6637 (m-10)
  outliers start: 21
  outliers final: 10
  residues processed: 70
  average time/residue: 0.1807
  time to fit residues: 20.6153
Evaluate side-chains
  66 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 CYS
Chi-restraints excluded: chain A residue  233 CYS
Chi-restraints excluded: chain A residue  251 HIS
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  357 GLU
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  732 ASP
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  857 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 96 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   chunk 18 optimal weight:    0.4980
   chunk 48 optimal weight:    2.9990
   chunk 73 optimal weight:    0.4980
   chunk 19 optimal weight:    2.9990
   chunk 4 optimal weight:   10.0000
   overall best weight:    1.3986

-------------------------------------------------------------------------------
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 = 0.3904 r_free = 0.3904 target = 0.093306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.067682 restraints weight = 43844.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.069761 restraints weight = 23515.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.071069 restraints weight = 16437.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12124  Z= 0.135
  Angle     :  0.582   9.255  17171  Z= 0.307
  Chirality :  0.037   0.219   1979
  Planarity :  0.004   0.052   1546
  Dihedral  : 24.586 179.284   3482
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 16.92 %
    Favored  : 81.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.28), residues: 954
  helix:  1.68 (0.26), residues: 419
  sheet: -1.15 (0.41), residues: 160
  loop : -1.07 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 366 
 HIS   0.004   0.001   HIS A 251 
 PHE   0.014   0.001   PHE A 463 
 TYR   0.011   0.001   TYR A 138 
 ARG   0.003   0.000   ARG A 443 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05829 (  531)
  hydrogen bonds       : angle       4.14238 ( 1371)
  covalent geometry    : bond        0.00281 (12124)
  covalent geometry    : angle       0.58223 (17171)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 1.112 
Fit side-chains
   revert: symmetry clash
REVERT: A  134 CYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7706 (t)
REVERT: A  357 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7612 (mm-30)
REVERT: A  489 ASP cc_start: 0.7741 (m-30) cc_final: 0.7366 (m-30)
REVERT: A  500 GLU cc_start: 0.6245 (tp30) cc_final: 0.5657 (tm-30)
REVERT: A  837 MET cc_start: 0.6732 (mtp) cc_final: 0.6341 (mmp)
  outliers start: 15
  outliers final: 10
  residues processed: 71
  average time/residue: 0.2059
  time to fit residues: 23.0647
Evaluate side-chains
  68 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 CYS
Chi-restraints excluded: chain A residue  251 HIS
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  357 GLU
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  732 ASP
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  857 TYR
Chi-restraints excluded: chain A residue  934 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 13 optimal weight:   20.0000
   chunk 84 optimal weight:   10.0000
   chunk 67 optimal weight:    3.9990
   chunk 3 optimal weight:    7.9990
   chunk 75 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 110 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 65 optimal weight:    0.8980
   chunk 82 optimal weight:    3.9990
   overall best weight:    1.7384

-------------------------------------------------------------------------------
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 = 0.3899 r_free = 0.3899 target = 0.093005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.067422 restraints weight = 43608.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.069473 restraints weight = 23294.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.070752 restraints weight = 16329.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.2816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12124  Z= 0.144
  Angle     :  0.600  11.338  17171  Z= 0.315
  Chirality :  0.037   0.218   1979
  Planarity :  0.004   0.052   1546
  Dihedral  : 24.612 179.241   3482
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 17.16 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.28), residues: 954
  helix:  1.58 (0.26), residues: 426
  sheet: -1.11 (0.41), residues: 160
  loop : -0.98 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 782 
 HIS   0.004   0.001   HIS A 251 
 PHE   0.039   0.002   PHE A 399 
 TYR   0.012   0.001   TYR A 138 
 ARG   0.004   0.000   ARG A 478 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05867 (  531)
  hydrogen bonds       : angle       4.18853 ( 1371)
  covalent geometry    : bond        0.00303 (12124)
  covalent geometry    : angle       0.59997 (17171)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 1.187 
Fit side-chains
REVERT: A  134 CYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7711 (t)
REVERT: A  204 GLU cc_start: 0.7491 (mp0) cc_final: 0.7197 (mp0)
REVERT: A  357 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7611 (mm-30)
REVERT: A  489 ASP cc_start: 0.7743 (m-30) cc_final: 0.7374 (m-30)
REVERT: A  500 GLU cc_start: 0.6225 (tp30) cc_final: 0.5642 (tm-30)
REVERT: A  837 MET cc_start: 0.6728 (mtp) cc_final: 0.6334 (mmp)
  outliers start: 15
  outliers final: 11
  residues processed: 67
  average time/residue: 0.1747
  time to fit residues: 19.2978
Evaluate side-chains
  69 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 CYS
Chi-restraints excluded: chain A residue  251 HIS
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  357 GLU
Chi-restraints excluded: chain A residue  436 ILE
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  732 ASP
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  857 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 42 optimal weight:    0.0770
   chunk 26 optimal weight:    0.9980
   chunk 18 optimal weight:    0.1980
   chunk 63 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9980
   chunk 8 optimal weight:   10.0000
   chunk 93 optimal weight:    0.9980
   chunk 83 optimal weight:    5.9990
   chunk 91 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
A 663 ASN
A 804 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.095660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.070096 restraints weight = 43874.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.072202 restraints weight = 23568.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.073553 restraints weight = 16479.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.2985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  12124  Z= 0.115
  Angle     :  0.562   9.257  17171  Z= 0.293
  Chirality :  0.036   0.215   1979
  Planarity :  0.004   0.059   1546
  Dihedral  : 24.502 178.478   3482
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 16.81 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.29), residues: 954
  helix:  1.90 (0.26), residues: 429
  sheet: -0.73 (0.43), residues: 152
  loop : -0.77 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 366 
 HIS   0.004   0.001   HIS A 405 
 PHE   0.039   0.001   PHE A 399 
 TYR   0.008   0.001   TYR A 822 
 ARG   0.005   0.000   ARG A 442 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05381 (  531)
  hydrogen bonds       : angle       3.97350 ( 1371)
  covalent geometry    : bond        0.00236 (12124)
  covalent geometry    : angle       0.56232 (17171)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.6464 (ppp) cc_final: 0.5843 (ppp)
REVERT: A  152 HIS cc_start: 0.6757 (m90) cc_final: 0.6424 (m90)
REVERT: A  489 ASP cc_start: 0.7842 (m-30) cc_final: 0.7474 (m-30)
REVERT: A  837 MET cc_start: 0.6722 (mtp) cc_final: 0.6329 (mmp)
  outliers start: 12
  outliers final: 8
  residues processed: 73
  average time/residue: 0.1836
  time to fit residues: 22.0071
Evaluate side-chains
  66 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 HIS
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  732 ASP
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  840 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0770
   chunk 82 optimal weight:    5.9990
   chunk 108 optimal weight:    8.9990
   chunk 25 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9980
   chunk 39 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.7940

-------------------------------------------------------------------------------
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 = 0.3945 r_free = 0.3945 target = 0.095599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.069950 restraints weight = 44145.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.072066 restraints weight = 23593.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 69)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.073409 restraints weight = 16527.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.3040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.065  12124  Z= 0.116
  Angle     :  0.565   8.887  17171  Z= 0.295
  Chirality :  0.036   0.216   1979
  Planarity :  0.004   0.058   1546
  Dihedral  : 24.501 179.536   3482
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 16.92 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.29), residues: 954
  helix:  1.92 (0.26), residues: 429
  sheet: -0.71 (0.43), residues: 152
  loop : -0.72 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 366 
 HIS   0.004   0.001   HIS A 405 
 PHE   0.053   0.001   PHE A 399 
 TYR   0.008   0.001   TYR A 698 
 ARG   0.002   0.000   ARG A 740 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05384 (  531)
  hydrogen bonds       : angle       4.01482 ( 1371)
  covalent geometry    : bond        0.00244 (12124)
  covalent geometry    : angle       0.56507 (17171)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4167.52 seconds
wall clock time: 72 minutes 53.98 seconds (4373.98 seconds total)