Starting phenix.real_space_refine
on Tue Jun 10 08:23:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7way_32389/06_2025/7way_32389.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7way_32389/06_2025/7way_32389.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7way_32389/06_2025/7way_32389.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7way_32389/06_2025/7way_32389.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7way_32389/06_2025/7way_32389.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7way_32389/06_2025/7way_32389.cif"
  }
  resolution = 2.9
  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=   0.003
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     175      5.49       5
     S      28      5.16       5
     C    6630      2.51       5
     N    2041      2.21       5
     O    2579      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 11453
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 674
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 674
          Classifications: {'DNA': 33}
          Link IDs: {'rna3p': 32}
    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: 2446
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 2446
          Classifications: {'RNA': 115}
          Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 55, 'rna3p_pyr': 48}
          Link IDs: {'rna2p': 12, 'rna3p': 102}
          Chain breaks: 1
    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: 7.59, per 1000 atoms: 0.66
  Number of scatterers: 11453
  At special positions: 0
  Unit cell: (100.58, 141.94, 125.02, 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     175     15.00
     O    2579      8.00
     N    2041      7.00
     C    6630      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: 3.61
  Conformation dependent library (CDL) restraints added in 1.3 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:
      34 helices and 10 sheets defined
      49.6% alpha, 22.4% beta
      61 base pairs and 103 stacking pairs defined.
    Time for finding SS restraints: 5.96
  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
    Processing helix  chain 'A' and resid 92 through 101
    Processing helix  chain 'A' and resid 196 through 201
    Processing helix  chain 'A' and resid 210 through 215
    Processing helix  chain 'A' and resid 221 through 272
      removed outlier: 3.644A  pdb=" N   VAL A 225 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ASP A 231 " --> pdb=" O   LYS A 227 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   ALA A 236 " --> pdb=" O   ALA A 232 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   LEU A 249 " --> pdb=" O   GLN A 245 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   GLU A 250 " --> pdb=" O   ASP A 246 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLN A 252 " --> pdb=" O   ILE A 248 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LYS A 260 " --> pdb=" O   LYS A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 309
    Processing helix  chain 'A' and resid 343 through 358
      removed outlier: 3.689A  pdb=" N   LYS A 358 " --> pdb=" O   LEU A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 368
    Processing helix  chain 'A' and resid 371 through 378
      removed outlier: 4.135A  pdb=" N   GLN A 375 " --> pdb=" O   GLY A 371 " (cutoff:3.500A)
      removed outlier: 3.729A  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
    Processing helix  chain 'A' and resid 394 through 411
    Processing helix  chain 'A' and resid 413 through 443
      removed outlier: 3.532A  pdb=" N   VAL A 417 " --> pdb=" O   ASP A 413 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ASP A 419 " --> pdb=" O   GLY A 415 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ARG A 442 " --> pdb=" O   LEU A 438 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ARG A 443 " --> pdb=" O   GLU A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 466
    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 510 through 513
    Processing helix  chain 'A' and resid 589 through 596
    Processing helix  chain 'A' and resid 697 through 717
    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 775 through 790
      removed outlier: 3.550A  pdb=" N   MET A 779 " --> pdb=" O   GLN A 775 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   GLU A 790 " --> pdb=" O   LYS A 786 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 793 through 796
    Processing helix  chain 'A' and resid 818 through 829
    Processing helix  chain 'A' and resid 866 through 876
      removed outlier: 3.981A  pdb=" N   GLU A 876 " --> pdb=" O   ARG A 872 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 881 through 885
    Processing helix  chain 'A' and resid 886 through 901
    Processing helix  chain 'A' and resid 921 through 936
      removed outlier: 3.594A  pdb=" N   ALA A 930 " --> pdb=" O   ALA A 926 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 939 through 949
      removed outlier: 3.518A  pdb=" N   THR A 949 " --> pdb=" O   GLN A 945 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 973
      removed outlier: 3.887A  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: 3.643A  pdb=" N   GLY A 614 " --> pdb=" O   ILE A 506 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   THR A 638 " --> pdb=" O   ALA A 612 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   GLY A 614 " --> pdb=" O   ALA A 636 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ALA A 636 " --> pdb=" O   GLY A 614 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   VAL A 616 " --> pdb=" O   PHE A 634 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   PHE A 634 " --> pdb=" O   VAL A 616 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   GLU A 618 " --> pdb=" O   ALA A 632 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   ALA A 632 " --> pdb=" O   GLU A 618 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   THR A 620 " --> pdb=" O   GLU A 630 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   GLU A 630 " --> pdb=" O   THR A 620 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   TYR A 622 " --> pdb=" O   GLN A 628 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   GLN A 628 " --> pdb=" O   TYR A 622 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   LEU A 633 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 502 through 506
      removed outlier: 3.643A  pdb=" N   GLY A 614 " --> pdb=" O   ILE A 506 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   THR A 638 " --> pdb=" O   ALA A 612 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   GLY A 614 " --> pdb=" O   ALA A 636 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ALA A 636 " --> pdb=" O   GLY A 614 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   VAL A 616 " --> pdb=" O   PHE A 634 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   PHE A 634 " --> pdb=" O   VAL A 616 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   GLU A 618 " --> pdb=" O   ALA A 632 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   ALA A 632 " --> pdb=" O   GLU A 618 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   THR A 620 " --> pdb=" O   GLU A 630 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   GLU A 630 " --> pdb=" O   THR A 620 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   TYR A 622 " --> pdb=" O   GLN A 628 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   GLN A 628 " --> pdb=" O   TYR A 622 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   LEU A 633 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
      removed outlier: 13.056A  pdb=" N   CYS A 515 " --> pdb=" O   ASN A 561 " (cutoff:3.500A)
      removed outlier: 10.231A  pdb=" N   ASN A 561 " --> pdb=" O   CYS A 515 " (cutoff:3.500A)
      removed outlier: 7.142A  pdb=" N   PHE A 517 " --> pdb=" O   VAL A 559 " (cutoff:3.500A)
      removed outlier: 5.554A  pdb=" N   VAL A 559 " --> pdb=" O   PHE A 517 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   PHE A 556 " --> pdb=" O   VAL A 572 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 117
      removed outlier: 4.365A  pdb=" N   ILE A 114 " --> pdb=" O   LYS A 141 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   VAL A 139 " --> pdb=" O   VAL A 116 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   PHE A 128 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   VAL A 139 " --> pdb=" O   SER A 126 " (cutoff:3.500A)
      removed outlier: 7.702A  pdb=" N   SER A 126 " --> pdb=" O   VAL A 139 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 114 through 117
      removed outlier: 4.365A  pdb=" N   ILE A 114 " --> pdb=" O   LYS A 141 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   VAL A 139 " --> pdb=" O   VAL A 116 " (cutoff:3.500A)
      removed outlier: 10.689A  pdb=" N   THR A 153 " --> pdb=" O   PRO A 172 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   TYR A 155 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 691 through 694
      removed outlier: 4.520A  pdb=" N   ALA A 756 " --> pdb=" O   ILE A 658 " (cutoff:3.500A)
      removed outlier: 8.147A  pdb=" N   ARG A 660 " --> pdb=" O   ALA A 756 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682
    Processing sheet with id=AA8, first strand: chain 'A' and resid 830 through 832
      removed outlier: 3.747A  pdb=" N   THR A 838 " --> pdb=" O   LEU A 845 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 850 through 855
    Processing sheet with id=AB1, first strand: chain 'A' and resid 909 through 911

    447 hydrogen bonds defined for protein.
    1266 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      151 hydrogen bonds
      290 hydrogen bond angles
      0 basepair planarities
      61 basepair parallelities
      103 stacking parallelities
  Total time for adding SS restraints: 7.48

  Time building geometry restraints manager: 3.46 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: 2340
        1.33 -     1.45: 3480
        1.45 -     1.57: 5834
        1.57 -     1.69: 346
        1.69 -     1.81: 41
  Bond restraints: 12041
  Sorted by residual:
  bond pdb=" CG  LEU A 894 "
       pdb=" CD2 LEU A 894 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.30e+00
  bond pdb=" N   ASN A 528 "
       pdb=" CA  ASN A 528 "
    ideal  model  delta    sigma   weight residual
    1.453  1.466 -0.012 1.22e-02 6.72e+03 1.02e+00
  bond pdb=" CA  ILE A 108 "
       pdb=" CB  ILE A 108 "
    ideal  model  delta    sigma   weight residual
    1.540  1.527  0.013 1.36e-02 5.41e+03 9.61e-01
  bond pdb=" N   TYR A 530 "
       pdb=" CA  TYR A 530 "
    ideal  model  delta    sigma   weight residual
    1.455  1.467 -0.012 1.29e-02 6.01e+03 9.27e-01
  bond pdb=" O4'  DA B  24 "
       pdb=" C1'  DA B  24 "
    ideal  model  delta    sigma   weight residual
    1.414  1.397  0.017 2.00e-02 2.50e+03 7.00e-01
  ... (remaining 12036 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 16845
        2.10 -     4.20: 176
        4.20 -     6.30: 12
        6.30 -     8.40: 4
        8.40 -    10.50: 1
  Bond angle restraints: 17038
  Sorted by residual:
  angle pdb=" N   VAL A 524 "
        pdb=" CA  VAL A 524 "
        pdb=" C   VAL A 524 "
      ideal   model   delta    sigma   weight residual
     112.96  109.33    3.63 1.00e+00 1.00e+00 1.32e+01
  angle pdb=" N   ASN A 107 "
        pdb=" CA  ASN A 107 "
        pdb=" C   ASN A 107 "
      ideal   model   delta    sigma   weight residual
     114.75  110.90    3.85 1.26e+00 6.30e-01 9.34e+00
  angle pdb=" CA  LEU A 894 "
        pdb=" CB  LEU A 894 "
        pdb=" CG  LEU A 894 "
      ideal   model   delta    sigma   weight residual
     116.30  126.80  -10.50 3.50e+00 8.16e-02 8.99e+00
  angle pdb=" N   LEU A 529 "
        pdb=" CA  LEU A 529 "
        pdb=" C   LEU A 529 "
      ideal   model   delta    sigma   weight residual
     108.13  113.01   -4.88 1.72e+00 3.38e-01 8.03e+00
  angle pdb=" CA  TYR A 530 "
        pdb=" CB  TYR A 530 "
        pdb=" CG  TYR A 530 "
      ideal   model   delta    sigma   weight residual
     113.90  118.58   -4.68 1.80e+00 3.09e-01 6.76e+00
  ... (remaining 17033 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.00: 6651
       32.00 -    64.00: 557
       64.00 -    96.01: 57
       96.01 -   128.01: 0
      128.01 -   160.01: 2
  Dihedral angle restraints: 7267
    sinusoidal: 4465
      harmonic: 2802
  Sorted by residual:
  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
     232.00   90.82  141.18     1      1.70e+01 3.46e-03 5.91e+01
  dihedral pdb=" CA  ARG A 443 "
           pdb=" C   ARG A 443 "
           pdb=" N   SER A 444 "
           pdb=" CA  SER A 444 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.38  -25.62     0      5.00e+00 4.00e-02 2.62e+01
  dihedral pdb=" CA  LEU A 527 "
           pdb=" C   LEU A 527 "
           pdb=" N   ASN A 528 "
           pdb=" CA  ASN A 528 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.00   21.00     0      5.00e+00 4.00e-02 1.76e+01
  ... (remaining 7264 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1760
       0.057 -    0.115: 179
       0.115 -    0.172: 21
       0.172 -    0.229: 0
       0.229 -    0.286: 1
  Chirality restraints: 1961
  Sorted by residual:
  chirality pdb=" CG  LEU A 529 "
            pdb=" CB  LEU A 529 "
            pdb=" CD1 LEU A 529 "
            pdb=" CD2 LEU A 529 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.30   -0.29 2.00e-01 2.50e+01 2.05e+00
  chirality pdb=" C3'   C D  40 "
            pdb=" C4'   C D  40 "
            pdb=" O3'   C D  40 "
            pdb=" C2'   C D  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.33   -0.15 2.00e-01 2.50e+01 5.74e-01
  chirality pdb=" C1'   C D  19 "
            pdb=" O4'   C D  19 "
            pdb=" C2'   C D  19 "
            pdb=" N1    C D  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.33    0.14 2.00e-01 2.50e+01 4.64e-01
  ... (remaining 1958 not shown)

  Planarity restraints: 1543
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  56 "   -0.024 2.00e-02 2.50e+03   1.08e-02 3.18e+00
        pdb=" N9    A D  56 "    0.024 2.00e-02 2.50e+03
        pdb=" C8    A D  56 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    A D  56 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    A D  56 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    A D  56 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6    A D  56 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    A D  56 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A D  56 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    A D  56 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    A D  56 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  38 "    0.028 5.00e-02 4.00e+02   4.27e-02 2.92e+00
        pdb=" N   PRO A  39 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A  39 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A  39 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 529 "   -0.008 2.00e-02 2.50e+03   1.54e-02 2.36e+00
        pdb=" C   LEU A 529 "    0.027 2.00e-02 2.50e+03
        pdb=" O   LEU A 529 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   TYR A 530 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1540 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 592
        2.72 -     3.26: 10071
        3.26 -     3.81: 19637
        3.81 -     4.35: 24195
        4.35 -     4.90: 37246
  Nonbonded interactions: 91741
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 816 "
            pdb=" NE2 GLN A 963 "
     model   vdw
     2.172 3.120
  nonbonded pdb=" OG1 THR A  38 "
            pdb=" OD1 ASP A  40 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" O2'   C D  40 "
            pdb=" OP1   U D  41 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   HIS A 173 "
            pdb=" OG1 THR A 183 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OD1 ASP A 865 "
            pdb=" OG  SER A 867 "
     model   vdw
     2.233 3.040
  ... (remaining 91736 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:             0.840
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     37.390
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.050
  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:32.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   72.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
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   0.038  12041  Z= 0.164
  Angle     :  0.542  10.496  17038  Z= 0.297
  Chirality :  0.036   0.286   1961
  Planarity :  0.004   0.043   1543
  Dihedral  : 19.589 160.010   5457
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  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:  1.31 (0.28), residues: 954
  helix:  2.23 (0.25), residues: 430
  sheet: -0.08 (0.43), residues: 139
  loop : -0.28 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 519 
 HIS   0.005   0.001   HIS A 251 
 PHE   0.008   0.001   PHE A 543 
 TYR   0.019   0.001   TYR A 776 
 ARG   0.006   0.000   ARG A 956 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11559 (  571)
  hydrogen bonds       : angle       4.76739 ( 1556)
  covalent geometry    : bond        0.00353 (12041)
  covalent geometry    : angle       0.54240 (17038)

*********************** 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
  54 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 1.039 
Fit side-chains
  outliers start: 0
  outliers final: 1
  residues processed: 54
  average time/residue: 1.5078
  time to fit residues: 87.8214
Evaluate side-chains
  35 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 34
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  267 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 84 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0170
   chunk 28 optimal weight:    0.4980
   chunk 57 optimal weight:    7.9990
   chunk 45 optimal weight:    7.9990
   chunk 87 optimal weight:    0.8980
   chunk 33 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   chunk 65 optimal weight:    2.9990
   chunk 101 optimal weight:    3.9990
   overall best weight:    1.6822

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

Flipped N/Q/H residues before XYZ refinement:
** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 340 ASN
A 368 ASN
A 907 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.112663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.077553 restraints weight = 22239.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 2.52
r_work: 0.2814 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.0699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  12041  Z= 0.154
  Angle     :  0.526   6.697  17038  Z= 0.285
  Chirality :  0.035   0.197   1961
  Planarity :  0.004   0.045   1543
  Dihedral  : 21.712 162.134   3449
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  4.53 %
    Favored  : 94.76 %
  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:  1.44 (0.28), residues: 954
  helix:  2.28 (0.25), residues: 441
  sheet: -0.03 (0.43), residues: 138
  loop : -0.23 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 598 
 HIS   0.008   0.001   HIS A 251 
 PHE   0.010   0.001   PHE A 517 
 TYR   0.023   0.001   TYR A 372 
 ARG   0.004   0.000   ARG A 627 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05442 (  571)
  hydrogen bonds       : angle       3.89787 ( 1556)
  covalent geometry    : bond        0.00331 (12041)
  covalent geometry    : angle       0.52570 (17038)

*********************** 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
  43 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 1.044 
Fit side-chains
  outliers start: 6
  outliers final: 1
  residues processed: 40
  average time/residue: 1.5081
  time to fit residues: 65.8556
Evaluate side-chains
  36 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 35
  time to evaluate  : 1.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  267 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 109 optimal weight:    0.5980
   chunk 43 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 29 optimal weight:    9.9990
   chunk 67 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 245 GLN
A 340 ASN
A 737 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.113583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.078774 restraints weight = 22644.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 2.49
r_work: 0.2842 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.0994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12041  Z= 0.125
  Angle     :  0.482   6.305  17038  Z= 0.264
  Chirality :  0.034   0.187   1961
  Planarity :  0.003   0.041   1543
  Dihedral  : 21.605 154.916   3449
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  5.72 %
    Favored  : 93.56 %
  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:  1.63 (0.28), residues: 954
  helix:  2.48 (0.25), residues: 443
  sheet: -0.05 (0.41), residues: 157
  loop : -0.15 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 598 
 HIS   0.007   0.001   HIS A 251 
 PHE   0.009   0.001   PHE A 196 
 TYR   0.016   0.001   TYR A  85 
 ARG   0.005   0.000   ARG A 956 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04744 (  571)
  hydrogen bonds       : angle       3.70218 ( 1556)
  covalent geometry    : bond        0.00263 (12041)
  covalent geometry    : angle       0.48184 (17038)

*********************** 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
  50 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 1.156 
Fit side-chains
  outliers start: 6
  outliers final: 2
  residues processed: 48
  average time/residue: 1.3754
  time to fit residues: 72.1073
Evaluate side-chains
  39 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  780 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 108 optimal weight:    0.7980
   chunk 100 optimal weight:   30.0000
   chunk 96 optimal weight:    5.9990
   chunk 85 optimal weight:    0.9980
   chunk 76 optimal weight:    0.0570
   chunk 26 optimal weight:    0.7980
   chunk 88 optimal weight:    4.9990
   chunk 64 optimal weight:    5.9990
   overall best weight:    0.7300

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.115182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.080703 restraints weight = 22694.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 2.48
r_work: 0.2886 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.1308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  12041  Z= 0.104
  Angle     :  0.474   9.435  17038  Z= 0.255
  Chirality :  0.033   0.213   1961
  Planarity :  0.003   0.039   1543
  Dihedral  : 21.541 159.796   3449
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  8.34 %
    Favored  : 91.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.82 (0.28), residues: 954
  helix:  2.72 (0.25), residues: 437
  sheet:  0.10 (0.41), residues: 155
  loop : -0.16 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 598 
 HIS   0.003   0.001   HIS A 251 
 PHE   0.010   0.001   PHE A 196 
 TYR   0.024   0.001   TYR A 372 
 ARG   0.005   0.000   ARG A 824 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04132 (  571)
  hydrogen bonds       : angle       3.54205 ( 1556)
  covalent geometry    : bond        0.00214 (12041)
  covalent geometry    : angle       0.47389 (17038)

*********************** 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
  47 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.971 
Fit side-chains
REVERT: A  109 ASP cc_start: 0.7748 (t70) cc_final: 0.7375 (OUTLIER)
REVERT: A  426 ASP cc_start: 0.8415 (m-30) cc_final: 0.8158 (m-30)
  outliers start: 5
  outliers final: 3
  residues processed: 45
  average time/residue: 1.4100
  time to fit residues: 69.1019
Evaluate side-chains
  40 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  780 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 81 optimal weight:    2.9990
   chunk 58 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   chunk 87 optimal weight:    0.5980
   chunk 8 optimal weight:    8.9990
   chunk 36 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 97 optimal weight:    6.9990
   overall best weight:    1.3188

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.113474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.078728 restraints weight = 22227.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 2.45
r_work: 0.2843 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.1294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12041  Z= 0.128
  Angle     :  0.487  10.427  17038  Z= 0.263
  Chirality :  0.034   0.198   1961
  Planarity :  0.003   0.039   1543
  Dihedral  : 21.496 157.868   3447
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  9.18 %
    Favored  : 90.11 %
  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:  1.80 (0.28), residues: 954
  helix:  2.73 (0.25), residues: 437
  sheet:  0.02 (0.41), residues: 157
  loop : -0.16 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  86 
 HIS   0.005   0.001   HIS A 251 
 PHE   0.011   0.001   PHE A 196 
 TYR   0.014   0.001   TYR A 853 
 ARG   0.005   0.000   ARG A 956 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04672 (  571)
  hydrogen bonds       : angle       3.58543 ( 1556)
  covalent geometry    : bond        0.00274 (12041)
  covalent geometry    : angle       0.48663 (17038)

*********************** 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
  47 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.943 
Fit side-chains
REVERT: A  109 ASP cc_start: 0.7658 (t70) cc_final: 0.7319 (OUTLIER)
  outliers start: 6
  outliers final: 3
  residues processed: 44
  average time/residue: 1.4316
  time to fit residues: 68.5327
Evaluate side-chains
  40 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  780 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 79 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9990
   chunk 95 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0870
   chunk 22 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 86 optimal weight:    2.9990
   chunk 108 optimal weight:    0.3980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.8962

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.114043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.079499 restraints weight = 22465.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 2.42
r_work: 0.2858 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.1344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12041  Z= 0.112
  Angle     :  0.483  10.150  17038  Z= 0.260
  Chirality :  0.033   0.185   1961
  Planarity :  0.003   0.039   1543
  Dihedral  : 21.514 158.367   3447
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  9.54 %
    Favored  : 89.75 %
  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:  1.83 (0.28), residues: 954
  helix:  2.67 (0.25), residues: 443
  sheet:  0.03 (0.41), residues: 157
  loop : -0.06 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 598 
 HIS   0.004   0.001   HIS A 251 
 PHE   0.009   0.001   PHE A 196 
 TYR   0.026   0.001   TYR A 372 
 ARG   0.005   0.000   ARG A 956 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04458 (  571)
  hydrogen bonds       : angle       3.53588 ( 1556)
  covalent geometry    : bond        0.00231 (12041)
  covalent geometry    : angle       0.48307 (17038)

*********************** 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
  44 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.914 
Fit side-chains
REVERT: A  109 ASP cc_start: 0.7647 (t70) cc_final: 0.7298 (p0)
  outliers start: 6
  outliers final: 3
  residues processed: 42
  average time/residue: 1.4380
  time to fit residues: 65.9351
Evaluate side-chains
  41 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  780 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 110 optimal weight:    8.9990
   chunk 69 optimal weight:    0.7980
   chunk 100 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 2 optimal weight:    5.9990
   chunk 27 optimal weight:   10.0000
   chunk 62 optimal weight:    7.9990
   chunk 99 optimal weight:    0.5980
   chunk 88 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    3.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.110134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.074623 restraints weight = 22362.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 2.54
r_work: 0.2754 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8634
moved from start:          0.1298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  12041  Z= 0.240
  Angle     :  0.582   9.209  17038  Z= 0.313
  Chirality :  0.039   0.210   1961
  Planarity :  0.004   0.040   1543
  Dihedral  : 21.528 155.611   3447
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 10.25 %
    Favored  : 89.27 %
  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:  1.58 (0.28), residues: 954
  helix:  2.51 (0.25), residues: 434
  sheet: -0.27 (0.42), residues: 151
  loop : -0.10 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  86 
 HIS   0.011   0.001   HIS A 251 
 PHE   0.011   0.002   PHE A 196 
 TYR   0.017   0.002   TYR A  85 
 ARG   0.005   0.001   ARG A 824 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06523 (  571)
  hydrogen bonds       : angle       3.91195 ( 1556)
  covalent geometry    : bond        0.00537 (12041)
  covalent geometry    : angle       0.58192 (17038)

*********************** 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
  46 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.962 
Fit side-chains
REVERT: A  109 ASP cc_start: 0.7776 (t70) cc_final: 0.7289 (p0)
REVERT: A  486 TRP cc_start: 0.8127 (m-10) cc_final: 0.7857 (m-10)
  outliers start: 4
  outliers final: 4
  residues processed: 44
  average time/residue: 1.4553
  time to fit residues: 69.6440
Evaluate side-chains
  43 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 39
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 ARG
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  780 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 90 optimal weight:    6.9990
   chunk 2 optimal weight:    4.9990
   chunk 6 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 103 optimal weight:    7.9990
   chunk 95 optimal weight:    1.9990
   chunk 111 optimal weight:    0.9990
   chunk 97 optimal weight:    7.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.111128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.076302 restraints weight = 22424.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 2.43
r_work: 0.2787 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8654
moved from start:          0.1304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  12041  Z= 0.167
  Angle     :  0.535   9.203  17038  Z= 0.288
  Chirality :  0.036   0.187   1961
  Planarity :  0.004   0.040   1543
  Dihedral  : 21.520 155.695   3447
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 10.61 %
    Favored  : 88.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.62 (0.28), residues: 954
  helix:  2.53 (0.25), residues: 436
  sheet: -0.15 (0.42), residues: 153
  loop : -0.13 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 598 
 HIS   0.006   0.001   HIS A 251 
 PHE   0.010   0.001   PHE A 196 
 TYR   0.022   0.001   TYR A 372 
 ARG   0.008   0.000   ARG A 956 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05520 (  571)
  hydrogen bonds       : angle       3.77711 ( 1556)
  covalent geometry    : bond        0.00365 (12041)
  covalent geometry    : angle       0.53453 (17038)

*********************** 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
  47 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 1.020 
Fit side-chains
REVERT: A  109 ASP cc_start: 0.7577 (t70) cc_final: 0.7141 (p0)
  outliers start: 6
  outliers final: 4
  residues processed: 44
  average time/residue: 1.4292
  time to fit residues: 68.5442
Evaluate side-chains
  43 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 39
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  780 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 13 optimal weight:   10.0000
   chunk 23 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 107 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 102 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   chunk 3 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 104 optimal weight:    5.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.112022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.077043 restraints weight = 22436.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 2.41
r_work: 0.2809 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8678
moved from start:          0.1342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12041  Z= 0.143
  Angle     :  0.546  17.921  17038  Z= 0.288
  Chirality :  0.035   0.187   1961
  Planarity :  0.004   0.042   1543
  Dihedral  : 21.527 155.487   3447
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 10.97 %
    Favored  : 88.44 %
  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:  1.65 (0.28), residues: 954
  helix:  2.57 (0.25), residues: 436
  sheet: -0.13 (0.42), residues: 153
  loop : -0.13 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 598 
 HIS   0.005   0.001   HIS A 251 
 PHE   0.010   0.001   PHE A 196 
 TYR   0.015   0.001   TYR A  85 
 ARG   0.008   0.000   ARG A 956 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05258 (  571)
  hydrogen bonds       : angle       3.75083 ( 1556)
  covalent geometry    : bond        0.00308 (12041)
  covalent geometry    : angle       0.54624 (17038)

*********************** 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
  44 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.986 
Fit side-chains
REVERT: A  109 ASP cc_start: 0.7464 (t70) cc_final: 0.7091 (p0)
  outliers start: 5
  outliers final: 4
  residues processed: 43
  average time/residue: 1.3953
  time to fit residues: 65.6150
Evaluate side-chains
  44 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  780 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 25 optimal weight:    0.4980
   chunk 74 optimal weight:    3.9990
   chunk 31 optimal weight:    0.1980
   chunk 87 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9980
   chunk 76 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 66 optimal weight:    4.9990
   chunk 41 optimal weight:    6.9990
   chunk 83 optimal weight:    6.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.112957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.078349 restraints weight = 22364.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 2.39
r_work: 0.2836 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.1404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12041  Z= 0.125
  Angle     :  0.532  16.623  17038  Z= 0.281
  Chirality :  0.034   0.185   1961
  Planarity :  0.004   0.048   1543
  Dihedral  : 21.520 155.402   3447
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 11.08 %
    Favored  : 88.32 %
  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:  1.72 (0.28), residues: 954
  helix:  2.62 (0.25), residues: 436
  sheet: -0.07 (0.42), residues: 153
  loop : -0.11 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 598 
 HIS   0.005   0.001   HIS A 251 
 PHE   0.008   0.001   PHE A 196 
 TYR   0.027   0.001   TYR A 372 
 ARG   0.012   0.000   ARG A 824 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04823 (  571)
  hydrogen bonds       : angle       3.68428 ( 1556)
  covalent geometry    : bond        0.00266 (12041)
  covalent geometry    : angle       0.53187 (17038)

********************** 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
  48 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 4
  residues processed: 46
  average time/residue: 1.3872
  time to fit residues: 69.6686
Evaluate side-chains
  45 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  780 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 47 optimal weight:    0.5980
   chunk 43 optimal weight:    4.9990
   chunk 100 optimal weight:   30.0000
   chunk 74 optimal weight:    0.5980
   chunk 69 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 3 optimal weight:    6.9990
   chunk 107 optimal weight:    2.9990
   chunk 78 optimal weight:    5.9990
   chunk 86 optimal weight:    4.9990
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.111970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.077150 restraints weight = 22348.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 2.41
r_work: 0.2806 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8684
moved from start:          0.1403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12041  Z= 0.159
  Angle     :  0.557  15.683  17038  Z= 0.294
  Chirality :  0.035   0.188   1961
  Planarity :  0.004   0.041   1543
  Dihedral  : 21.497 155.391   3447
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 11.20 %
    Favored  : 88.20 %
  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:  1.70 (0.28), residues: 954
  helix:  2.59 (0.25), residues: 436
  sheet: -0.07 (0.42), residues: 153
  loop : -0.11 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  86 
 HIS   0.006   0.001   HIS A 251 
 PHE   0.011   0.001   PHE A 196 
 TYR   0.015   0.001   TYR A  85 
 ARG   0.019   0.001   ARG A 824 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05302 (  571)
  hydrogen bonds       : angle       3.74260 ( 1556)
  covalent geometry    : bond        0.00349 (12041)
  covalent geometry    : angle       0.55737 (17038)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6802.27 seconds
wall clock time: 117 minutes 38.40 seconds (7058.40 seconds total)