Starting phenix.real_space_refine
on Wed Mar 12 00:36:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cd0_16565/03_2025/8cd0_16565.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cd0_16565/03_2025/8cd0_16565.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.42
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cd0_16565/03_2025/8cd0_16565.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cd0_16565/03_2025/8cd0_16565.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cd0_16565/03_2025/8cd0_16565.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cd0_16565/03_2025/8cd0_16565.cif"
  }
  resolution = 2.42
  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=   0.015 sd=   0.025
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: 6
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     P       2      5.49       5
     S      26      5.16       5
     C    4426      2.51       5
     N    1162      2.21       5
     O    1243      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6860
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 5883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 716, 5883
          Classifications: {'peptide': 716}
          Link IDs: {'PCIS': 4, 'PTRANS': 32, 'TRANS': 679}
          Chain breaks: 6
    Chain: "C"
      Number of atoms: 945
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 121, 937
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 2, 'TRANS': 118}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 121, 937
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 2, 'TRANS': 118}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 946
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'A3P': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1, 'water': 3}
          Link IDs: {None: 3}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 6.39, per 1000 atoms: 0.93
  Number of scatterers: 6860
  At special positions: 0
  Unit cell: (78.11, 97.82, 102.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      1     19.99
     S      26     16.00
     P       2     15.00
     O    1243      8.00
     N    1162      7.00
     C    4426      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 586 " - pdb=" SG  CYS A 601 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 818 " - pdb=" SG  CYS A 828 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  50 " - pdb=" SG  CYS C 103 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.48
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1566

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 8 sheets defined
      42.7% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.77
  Creating SS restraints...
    Processing helix  chain 'A' and resid 94 through 107
    Processing helix  chain 'A' and resid 141 through 146
    Processing helix  chain 'A' and resid 148 through 163
    Processing helix  chain 'A' and resid 287 through 302
      removed outlier: 3.849A  pdb=" N   THR A 302 " --> pdb=" O   VAL A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 349
    Processing helix  chain 'A' and resid 367 through 374
    Processing helix  chain 'A' and resid 375 through 379
    Processing helix  chain 'A' and resid 401 through 420
      removed outlier: 3.732A  pdb=" N   LEU A 405 " --> pdb=" O   ASN A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 451
      removed outlier: 3.544A  pdb=" N   TYR A 444 " --> pdb=" O   HIS A 440 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS A 448 " --> pdb=" O   TYR A 444 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   VAL A 450 " --> pdb=" O   ALA A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 470
    Processing helix  chain 'A' and resid 501 through 510
      removed outlier: 4.025A  pdb=" N   LEU A 505 " --> pdb=" O   GLY A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 521
    Processing helix  chain 'A' and resid 529 through 533
    Processing helix  chain 'A' and resid 537 through 554
      removed outlier: 3.886A  pdb=" N   ARG A 548 " --> pdb=" O   LYS A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 562 through 574
    Processing helix  chain 'A' and resid 575 through 579
      removed outlier: 3.649A  pdb=" N   LYS A 578 " --> pdb=" O   SER A 575 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   ASP A 579 " --> pdb=" O   GLU A 576 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 575 through 579'
    Processing helix  chain 'A' and resid 588 through 595
    Processing helix  chain 'A' and resid 616 through 626
    Processing helix  chain 'A' and resid 636 through 640
      removed outlier: 3.517A  pdb=" N   PHE A 640 " --> pdb=" O   SER A 637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 653
      removed outlier: 3.905A  pdb=" N   TYR A 651 " --> pdb=" O   GLY A 648 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   HIS A 652 " --> pdb=" O   HIS A 649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 659
    Processing helix  chain 'A' and resid 678 through 681
      removed outlier: 3.758A  pdb=" N   PHE A 681 " --> pdb=" O   ALA A 678 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 678 through 681'
    Processing helix  chain 'A' and resid 685 through 694
      removed outlier: 3.572A  pdb=" N   ARG A 689 " --> pdb=" O   VAL A 685 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 720
    Processing helix  chain 'A' and resid 722 through 728
    Processing helix  chain 'A' and resid 729 through 734
    Processing helix  chain 'A' and resid 742 through 753
    Processing helix  chain 'A' and resid 756 through 768
      removed outlier: 3.842A  pdb=" N   HIS A 760 " --> pdb=" O   TRP A 756 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ARG A 763 " --> pdb=" O   THR A 759 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 779 through 784
    Processing helix  chain 'A' and resid 784 through 796
      removed outlier: 4.291A  pdb=" N   VAL A 788 " --> pdb=" O   GLU A 784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 803 through 808
      removed outlier: 3.928A  pdb=" N   THR A 807 " --> pdb=" O   ASP A 803 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   LEU A 808 " --> pdb=" O   TYR A 804 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 803 through 808'
    Processing helix  chain 'A' and resid 841 through 852
    Processing helix  chain 'A' and resid 853 through 866
    Processing helix  chain 'A' and resid 871 through 880
    Processing helix  chain 'C' and resid 86 through 90
      removed outlier: 3.906A  pdb=" N   THR C  90 " --> pdb=" O   PRO C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 110 through 114
    Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 114
      removed outlier: 6.602A  pdb=" N   ILE A 166 " --> pdb=" O   VAL A 279 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ARG A 278 " --> pdb=" O   ASP A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 200
    Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 388
      removed outlier: 5.415A  pdb=" N   LEU A 356 " --> pdb=" O   PHE A 387 " (cutoff:3.500A)
      removed outlier: 8.693A  pdb=" N   ASN A 355 " --> pdb=" O   ILE A 314 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   VAL A 316 " --> pdb=" O   ASN A 355 " (cutoff:3.500A)
      removed outlier: 7.540A  pdb=" N   GLY A 357 " --> pdb=" O   VAL A 316 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   ILE A 318 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
      removed outlier: 10.967A  pdb=" N   ILE A 523 " --> pdb=" O   VAL A 480 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   ILE A 525 " --> pdb=" O   PRO A 482 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 455 through 458
      removed outlier: 6.666A  pdb=" N   THR A 456 " --> pdb=" O   LEU A 481 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   ARG A 483 " --> pdb=" O   THR A 456 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   THR A 458 " --> pdb=" O   ARG A 483 " (cutoff:3.500A)
      removed outlier: 10.967A  pdb=" N   ILE A 523 " --> pdb=" O   VAL A 480 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   ILE A 525 " --> pdb=" O   PRO A 482 " (cutoff:3.500A)
      removed outlier: 6.013A  pdb=" N   ARG A 312 " --> pdb=" O   GLN A 559 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 630 through 632
      removed outlier: 6.893A  pdb=" N   LEU A 607 " --> pdb=" O   GLU A 675 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   SER A 677 " --> pdb=" O   LEU A 607 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   ILE A 609 " --> pdb=" O   SER A 677 " (cutoff:3.500A)
      removed outlier: 4.684A  pdb=" N   ILE A 702 " --> pdb=" O   ILE A 610 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 809 through 811
      removed outlier: 3.565A  pdb=" N   ALA A 809 " --> pdb=" O   CYS A 818 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ASP A 811 " --> pdb=" O   PHE A 816 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   PHE A 816 " --> pdb=" O   ASP A 811 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 6
      removed outlier: 3.584A  pdb=" N   LEU C  18 " --> pdb=" O   MET C  82 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 57 through 59
      removed outlier: 6.885A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA C  91 " --> pdb=" O   VAL C 123 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR C 121 " --> pdb=" O   TYR C  93 " (cutoff:3.500A)

    273 hydrogen bonds defined for protein.
    759 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.39

  Time building geometry restraints manager: 1.79 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2039
        1.34 -     1.46: 1607
        1.46 -     1.58: 3357
        1.58 -     1.70: 8
        1.70 -     1.82: 40
  Bond restraints: 7051
  Sorted by residual:
  bond pdb=" C   ALA A 430 "
       pdb=" N   PRO A 431 "
    ideal  model  delta    sigma   weight residual
    1.335  1.385 -0.050 1.30e-02 5.92e+03 1.48e+01
  bond pdb=" CB  PHE A 362 "
       pdb=" CG  PHE A 362 "
    ideal  model  delta    sigma   weight residual
    1.502  1.573 -0.071 2.30e-02 1.89e+03 9.64e+00
  bond pdb=" C   VAL A 429 "
       pdb=" N   ALA A 430 "
    ideal  model  delta    sigma   weight residual
    1.330  1.370 -0.040 1.37e-02 5.33e+03 8.51e+00
  bond pdb=" CB  PHE A 847 "
       pdb=" CG  PHE A 847 "
    ideal  model  delta    sigma   weight residual
    1.502  1.561 -0.059 2.30e-02 1.89e+03 6.53e+00
  bond pdb=" C   ALA A 686 "
       pdb=" N   PRO A 687 "
    ideal  model  delta    sigma   weight residual
    1.336  1.366 -0.031 1.23e-02 6.61e+03 6.16e+00
  ... (remaining 7046 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.42: 9322
        3.42 -     6.84: 189
        6.84 -    10.26: 43
       10.26 -    13.68: 9
       13.68 -    17.11: 2
  Bond angle restraints: 9565
  Sorted by residual:
  angle pdb=" C   THR A 485 "
        pdb=" N   CYS A 486 "
        pdb=" CA  CYS A 486 "
      ideal   model   delta    sigma   weight residual
     121.54  132.61  -11.07 1.91e+00 2.74e-01 3.36e+01
  angle pdb=" C   PHE A 399 "
        pdb=" N   HIS A 400 "
        pdb=" CA  HIS A 400 "
      ideal   model   delta    sigma   weight residual
     121.54  132.56  -11.02 1.91e+00 2.74e-01 3.33e+01
  angle pdb=" CB  GLU A 858 "
        pdb=" CG  GLU A 858 "
        pdb=" CD  GLU A 858 "
      ideal   model   delta    sigma   weight residual
     112.60  121.92   -9.32 1.70e+00 3.46e-01 3.01e+01
  angle pdb=" C   SER A 213 "
        pdb=" N   GLU A 214 "
        pdb=" CA  GLU A 214 "
      ideal   model   delta    sigma   weight residual
     121.70  131.18   -9.48 1.80e+00 3.09e-01 2.77e+01
  angle pdb=" CG  ARG C  74 "
        pdb=" CD  ARG C  74 "
        pdb=" NE  ARG C  74 "
      ideal   model   delta    sigma   weight residual
     112.00  123.50  -11.50 2.20e+00 2.07e-01 2.73e+01
  ... (remaining 9560 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.31: 3539
       17.31 -    34.62: 433
       34.62 -    51.93: 119
       51.93 -    69.24: 41
       69.24 -    86.55: 10
  Dihedral angle restraints: 4142
    sinusoidal: 1701
      harmonic: 2441
  Sorted by residual:
  dihedral pdb=" CB  CYS A 586 "
           pdb=" SG  CYS A 586 "
           pdb=" SG  CYS A 601 "
           pdb=" CB  CYS A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  165.46  -72.46     1      1.00e+01 1.00e-02 6.71e+01
  dihedral pdb=" CA  ASN C  84 "
           pdb=" C   ASN C  84 "
           pdb=" N   LEU C  85 "
           pdb=" CA  LEU C  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.96  -26.04     0      5.00e+00 4.00e-02 2.71e+01
  dihedral pdb=" CA  SER C  11 "
           pdb=" C   SER C  11 "
           pdb=" N   VAL C  12 "
           pdb=" CA  VAL C  12 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.00   21.00     0      5.00e+00 4.00e-02 1.76e+01
  ... (remaining 4139 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 858
       0.080 -    0.161: 126
       0.161 -    0.241: 24
       0.241 -    0.322: 6
       0.322 -    0.402: 2
  Chirality restraints: 1016
  Sorted by residual:
  chirality pdb=" CB  ILE C  51 "
            pdb=" CA  ILE C  51 "
            pdb=" CG1 ILE C  51 "
            pdb=" CG2 ILE C  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.24    0.40 2.00e-01 2.50e+01 4.04e+00
  chirality pdb=" CB  THR C  90 "
            pdb=" CA  THR C  90 "
            pdb=" OG1 THR C  90 "
            pdb=" CG2 THR C  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.20    0.35 2.00e-01 2.50e+01 3.06e+00
  chirality pdb=" CB  ILE A 421 "
            pdb=" CA  ILE A 421 "
            pdb=" CG1 ILE A 421 "
            pdb=" CG2 ILE A 421 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.76e+00
  ... (remaining 1013 not shown)

  Planarity restraints: 1212
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 643 "   -0.017 2.00e-02 2.50e+03   3.39e-02 1.15e+01
        pdb=" C   ILE A 643 "    0.059 2.00e-02 2.50e+03
        pdb=" O   ILE A 643 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   GLN A 644 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 339 "    0.024 2.00e-02 2.50e+03   2.52e-02 1.11e+01
        pdb=" CG  PHE A 339 "   -0.058 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 339 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 339 "    0.016 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 339 "    0.010 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 339 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 339 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 627 "   -0.053 5.00e-02 4.00e+02   8.02e-02 1.03e+01
        pdb=" N   PRO A 628 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO A 628 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 628 "   -0.044 5.00e-02 4.00e+02
  ... (remaining 1209 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 133
        2.68 -     3.23: 5773
        3.23 -     3.79: 11421
        3.79 -     4.34: 15664
        4.34 -     4.90: 25121
  Nonbonded interactions: 58112
  Sorted by model distance:
  nonbonded pdb="CA    CA A 902 "
            pdb=" O   HOH A1003 "
     model   vdw
     2.122 2.510
  nonbonded pdb=" OD1 ASP A 320 "
            pdb="CA    CA A 902 "
     model   vdw
     2.162 2.510
  nonbonded pdb=" NE2 HIS A 393 "
            pdb="CA    CA A 902 "
     model   vdw
     2.198 2.590
  nonbonded pdb=" O   GLU A 513 "
            pdb=" OG1 THR A 517 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" OG  SER C  17 "
            pdb=" OD1 ASN C  83 "
     model   vdw
     2.335 3.040
  ... (remaining 58107 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.25 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.200
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.490
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  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:13.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6805
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      :  0.007   0.071   7051  Z= 0.423
  Angle     :  1.253  17.105   9565  Z= 0.680
  Chirality :  0.065   0.402   1016
  Planarity :  0.010   0.080   1212
  Dihedral  : 17.387  86.546   2564
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 22.09 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -3.15 (0.25), residues: 820
  helix: -3.33 (0.17), residues: 300
  sheet: -1.35 (0.45), residues: 133
  loop : -1.10 (0.29), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP A 595 
 HIS   0.027   0.003   HIS A 400 
 PHE   0.058   0.004   PHE A 339 
 TYR   0.038   0.003   TYR A 680 
 ARG   0.010   0.001   ARG A 557 

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 GLU cc_start: 0.7859 (tp30) cc_final: 0.7576 (mm-30)
REVERT: A  137 ILE cc_start: 0.6041 (OUTLIER) cc_final: 0.5649 (mt)
REVERT: A  143 LYS cc_start: 0.6523 (mttp) cc_final: 0.6191 (mttm)
REVERT: A  203 LYS cc_start: 0.7110 (mptt) cc_final: 0.6848 (mttm)
REVERT: A  206 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6795 (mp)
REVERT: A  208 TYR cc_start: 0.7867 (t80) cc_final: 0.7408 (t80)
REVERT: A  308 LEU cc_start: 0.7927 (mt) cc_final: 0.7636 (tp)
REVERT: A  400 HIS cc_start: 0.5718 (p-80) cc_final: 0.5414 (p90)
REVERT: A  413 LYS cc_start: 0.4280 (ttmt) cc_final: 0.3836 (ttmm)
REVERT: A  452 SER cc_start: 0.8106 (m) cc_final: 0.7894 (m)
REVERT: A  536 ASP cc_start: 0.6909 (m-30) cc_final: 0.6348 (t0)
REVERT: A  676 LYS cc_start: 0.7685 (tttt) cc_final: 0.7482 (tmtp)
REVERT: A  688 ARG cc_start: 0.6999 (ttp-110) cc_final: 0.6556 (ptm160)
REVERT: A  708 ASP cc_start: 0.6210 (t70) cc_final: 0.5944 (t70)
REVERT: A  743 LYS cc_start: 0.7804 (mttt) cc_final: 0.7075 (mptt)
REVERT: A  864 TYR cc_start: 0.5837 (OUTLIER) cc_final: 0.5160 (t80)
REVERT: C  106 LYS cc_start: 0.7626 (pttt) cc_final: 0.7251 (tttm)
  outliers start: 15
  outliers final: 7
  residues processed: 132
  average time/residue: 1.0963
  time to fit residues: 154.7879
Evaluate side-chains
  103 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  339 PHE
Chi-restraints excluded: chain A residue  447 TRP
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  864 TYR
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   98 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0870
   chunk 34 optimal weight:    0.1980
   chunk 21 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 48 optimal weight:   10.0000
   chunk 75 optimal weight:    3.9990
   overall best weight:    0.6160

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
A 343 ASN
A 400 HIS
A 408 GLN
** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 731 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.180372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.155373 restraints weight = 26082.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.4140 rms_B_bonded: 3.52
r_work: 0.4013 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.4013
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4020
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4020 r_free = 0.4020    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4020 r_free = 0.4020    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4020
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6998
moved from start:          0.1732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7051  Z= 0.182
  Angle     :  0.590   9.577   9565  Z= 0.309
  Chirality :  0.043   0.162   1016
  Planarity :  0.005   0.050   1212
  Dihedral  :  7.404  66.992    963
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 21.27 %
    Favored  : 74.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -1.53 (0.28), residues: 820
  helix: -1.24 (0.25), residues: 315
  sheet: -0.99 (0.48), residues: 124
  loop : -0.62 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 391 
 HIS   0.014   0.001   HIS A 400 
 PHE   0.014   0.001   PHE A 494 
 TYR   0.011   0.001   TYR C  59 
 ARG   0.006   0.001   ARG A 557 

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 105
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 GLU cc_start: 0.7709 (tp30) cc_final: 0.7433 (mm-30)
REVERT: A  143 LYS cc_start: 0.6359 (mttp) cc_final: 0.6065 (mtpm)
REVERT: A  203 LYS cc_start: 0.7170 (mptt) cc_final: 0.6889 (mttp)
REVERT: A  308 LEU cc_start: 0.8225 (mt) cc_final: 0.7956 (tp)
REVERT: A  413 LYS cc_start: 0.4886 (ttmt) cc_final: 0.4563 (ttmm)
REVERT: A  452 SER cc_start: 0.8122 (OUTLIER) cc_final: 0.7840 (m)
REVERT: A  688 ARG cc_start: 0.7271 (ttp-110) cc_final: 0.6927 (ptt-90)
REVERT: A  708 ASP cc_start: 0.6468 (t70) cc_final: 0.6131 (t70)
REVERT: A  743 LYS cc_start: 0.7880 (mttt) cc_final: 0.7251 (mptt)
REVERT: A  784 GLU cc_start: 0.6335 (pp20) cc_final: 0.5837 (pp20)
REVERT: A  853 ARG cc_start: 0.5520 (OUTLIER) cc_final: 0.5118 (ttm170)
REVERT: A  864 TYR cc_start: 0.5949 (OUTLIER) cc_final: 0.5616 (m-80)
  outliers start: 31
  outliers final: 12
  residues processed: 122
  average time/residue: 0.9816
  time to fit residues: 127.5871
Evaluate side-chains
  108 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  452 SER
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  716 HIS
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  853 ARG
Chi-restraints excluded: chain A residue  864 TYR
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  121 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 49 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 53 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0050
   chunk 15 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   overall best weight:    1.1396

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 400 HIS
** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.174775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.149296 restraints weight = 20348.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.4068 rms_B_bonded: 2.95
r_work: 0.3961 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3968
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3968 r_free = 0.3968    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3968 r_free = 0.3968    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3968
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7093
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7051  Z= 0.227
  Angle     :  0.617   8.983   9565  Z= 0.319
  Chirality :  0.043   0.162   1016
  Planarity :  0.005   0.041   1212
  Dihedral  :  6.996  62.677    952
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 21.82 %
    Favored  : 73.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -0.81 (0.29), residues: 820
  helix: -0.31 (0.27), residues: 316
  sheet: -0.88 (0.49), residues: 130
  loop : -0.43 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 391 
 HIS   0.014   0.001   HIS A 400 
 PHE   0.020   0.002   PHE C 108 
 TYR   0.016   0.002   TYR C  32 
 ARG   0.004   0.001   ARG A 557 

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 100
  time to evaluate  : 0.778 
Fit side-chains
REVERT: A   98 GLN cc_start: 0.7322 (mm-40) cc_final: 0.6894 (mm-40)
REVERT: A  114 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7394 (mm-30)
REVERT: A  143 LYS cc_start: 0.6402 (mttp) cc_final: 0.6059 (mttm)
REVERT: A  203 LYS cc_start: 0.7104 (mptt) cc_final: 0.6867 (mttp)
REVERT: A  330 MET cc_start: 0.4647 (mtp) cc_final: 0.4407 (mtt)
REVERT: A  413 LYS cc_start: 0.4778 (ttmt) cc_final: 0.4452 (tptm)
REVERT: A  447 TRP cc_start: 0.8003 (OUTLIER) cc_final: 0.7481 (m-10)
REVERT: A  452 SER cc_start: 0.8194 (OUTLIER) cc_final: 0.7961 (m)
REVERT: A  634 TYR cc_start: 0.7246 (m-80) cc_final: 0.7044 (m-80)
REVERT: A  688 ARG cc_start: 0.7310 (ttp-110) cc_final: 0.7022 (ptt-90)
REVERT: A  743 LYS cc_start: 0.7882 (mttt) cc_final: 0.7271 (mptt)
REVERT: A  784 GLU cc_start: 0.6398 (pp20) cc_final: 0.5877 (pp20)
REVERT: A  853 ARG cc_start: 0.5544 (OUTLIER) cc_final: 0.5057 (ttm170)
REVERT: A  864 TYR cc_start: 0.6160 (OUTLIER) cc_final: 0.5788 (m-80)
  outliers start: 34
  outliers final: 16
  residues processed: 122
  average time/residue: 0.9242
  time to fit residues: 120.8941
Evaluate side-chains
  112 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  447 TRP
Chi-restraints excluded: chain A residue  452 SER
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  617 THR
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  716 HIS
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  853 ARG
Chi-restraints excluded: chain A residue  864 TYR
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  123 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 67 optimal weight:    9.9990
   chunk 77 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 400 HIS
A 408 GLN
A 442 GLN
** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.170015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.144236 restraints weight = 25091.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.4009 rms_B_bonded: 3.37
r_work: 0.3890 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3897
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3897 r_free = 0.3897    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3897 r_free = 0.3897    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3897
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
moved from start:          0.3125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7051  Z= 0.321
  Angle     :  0.673   8.505   9565  Z= 0.349
  Chirality :  0.046   0.178   1016
  Planarity :  0.005   0.038   1212
  Dihedral  :  7.051  58.885    952
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 20.87 %
    Favored  : 73.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -0.73 (0.29), residues: 820
  helix: -0.23 (0.28), residues: 315
  sheet: -1.10 (0.52), residues: 106
  loop : -0.36 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 391 
 HIS   0.013   0.002   HIS A 400 
 PHE   0.027   0.002   PHE A 339 
 TYR   0.019   0.002   TYR C  32 
 ARG   0.003   0.001   ARG A 454 

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 96
  time to evaluate  : 0.701 
Fit side-chains
REVERT: A   98 GLN cc_start: 0.7337 (mm-40) cc_final: 0.6826 (mm110)
REVERT: A  114 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7469 (mm-30)
REVERT: A  208 TYR cc_start: 0.8240 (t80) cc_final: 0.7990 (t80)
REVERT: A  375 ASP cc_start: 0.7149 (m-30) cc_final: 0.6756 (m-30)
REVERT: A  413 LYS cc_start: 0.4987 (ttmt) cc_final: 0.4666 (ttmm)
REVERT: A  447 TRP cc_start: 0.8080 (OUTLIER) cc_final: 0.7259 (m-10)
REVERT: A  452 SER cc_start: 0.8271 (OUTLIER) cc_final: 0.8012 (m)
REVERT: A  688 ARG cc_start: 0.7290 (ttp-110) cc_final: 0.7015 (ptt-90)
REVERT: A  743 LYS cc_start: 0.7848 (mttt) cc_final: 0.7244 (mptt)
REVERT: A  782 ARG cc_start: 0.5351 (OUTLIER) cc_final: 0.4778 (mtp85)
REVERT: A  784 GLU cc_start: 0.6569 (pp20) cc_final: 0.5965 (pp20)
REVERT: A  853 ARG cc_start: 0.5654 (OUTLIER) cc_final: 0.5134 (ttm170)
REVERT: A  864 TYR cc_start: 0.6438 (OUTLIER) cc_final: 0.5804 (m-80)
  outliers start: 42
  outliers final: 21
  residues processed: 127
  average time/residue: 0.9657
  time to fit residues: 130.9668
Evaluate side-chains
  119 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  128 LYS
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  148 ASP
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  447 TRP
Chi-restraints excluded: chain A residue  452 SER
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  583 GLN
Chi-restraints excluded: chain A residue  675 GLU
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  716 HIS
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  782 ARG
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  853 ARG
Chi-restraints excluded: chain A residue  864 TYR
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  123 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0670
   chunk 21 optimal weight:    3.9990
   chunk 52 optimal weight:    6.9990
   chunk 76 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9980
   chunk 67 optimal weight:    9.9990
   chunk 35 optimal weight:    0.1980
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
A 400 HIS
** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.174487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.150698 restraints weight = 19337.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.4084 rms_B_bonded: 2.83
r_work: 0.3975 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3975
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3982
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3982 r_free = 0.3982    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3982 r_free = 0.3982    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3982
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7068
moved from start:          0.3044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7051  Z= 0.165
  Angle     :  0.565   7.830   9565  Z= 0.290
  Chirality :  0.042   0.150   1016
  Planarity :  0.004   0.034   1212
  Dihedral  :  6.519  55.636    952
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 21.95 %
    Favored  : 72.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -0.41 (0.30), residues: 820
  helix:  0.18 (0.29), residues: 316
  sheet: -1.15 (0.52), residues: 108
  loop : -0.23 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 447 
 HIS   0.014   0.001   HIS A 400 
 PHE   0.015   0.001   PHE C 108 
 TYR   0.018   0.001   TYR C  32 
 ARG   0.003   0.000   ARG A 557 

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 100
  time to evaluate  : 0.672 
Fit side-chains
REVERT: A   87 VAL cc_start: 0.7111 (m) cc_final: 0.6703 (t)
REVERT: A   98 GLN cc_start: 0.7325 (mm-40) cc_final: 0.6885 (mm110)
REVERT: A  114 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7352 (mm-30)
REVERT: A  143 LYS cc_start: 0.6588 (mttp) cc_final: 0.6367 (mttm)
REVERT: A  375 ASP cc_start: 0.6778 (m-30) cc_final: 0.6493 (m-30)
REVERT: A  413 LYS cc_start: 0.4767 (ttmt) cc_final: 0.4502 (ttmm)
REVERT: A  447 TRP cc_start: 0.7865 (OUTLIER) cc_final: 0.7114 (m-10)
REVERT: A  452 SER cc_start: 0.8160 (OUTLIER) cc_final: 0.7913 (m)
REVERT: A  504 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7117 (mm-30)
REVERT: A  688 ARG cc_start: 0.7146 (ttp-110) cc_final: 0.6852 (ptt-90)
REVERT: A  743 LYS cc_start: 0.7834 (mttt) cc_final: 0.7234 (mptt)
REVERT: A  784 GLU cc_start: 0.6409 (pp20) cc_final: 0.5843 (pp20)
REVERT: A  853 ARG cc_start: 0.5567 (OUTLIER) cc_final: 0.5158 (ttm170)
REVERT: A  864 TYR cc_start: 0.6217 (OUTLIER) cc_final: 0.5851 (m-80)
  outliers start: 38
  outliers final: 16
  residues processed: 125
  average time/residue: 0.9013
  time to fit residues: 120.8281
Evaluate side-chains
  111 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  128 LYS
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  447 TRP
Chi-restraints excluded: chain A residue  452 SER
Chi-restraints excluded: chain A residue  504 GLU
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  583 GLN
Chi-restraints excluded: chain A residue  617 THR
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  853 ARG
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  864 TYR
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  121 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 49 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.171842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.146292 restraints weight = 24876.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.4030 rms_B_bonded: 3.30
r_work: 0.3911 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3918
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3918 r_free = 0.3918    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3918 r_free = 0.3918    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3918
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7160
moved from start:          0.3221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7051  Z= 0.254
  Angle     :  0.627   7.283   9565  Z= 0.326
  Chirality :  0.044   0.165   1016
  Planarity :  0.004   0.050   1212
  Dihedral  :  6.695  57.322    952
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 22.22 %
    Favored  : 72.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -0.34 (0.30), residues: 820
  helix:  0.22 (0.29), residues: 315
  sheet: -0.99 (0.53), residues: 104
  loop : -0.23 (0.32), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 391 
 HIS   0.007   0.001   HIS A 389 
 PHE   0.016   0.002   PHE A 543 
 TYR   0.021   0.002   TYR C  32 
 ARG   0.003   0.000   ARG A 709 

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 91
  time to evaluate  : 0.704 
Fit side-chains
REVERT: A   89 VAL cc_start: 0.6415 (m) cc_final: 0.6150 (t)
REVERT: A   98 GLN cc_start: 0.7319 (mm-40) cc_final: 0.6827 (mm110)
REVERT: A  114 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7316 (mm-30)
REVERT: A  143 LYS cc_start: 0.6555 (mttp) cc_final: 0.6337 (mttm)
REVERT: A  208 TYR cc_start: 0.8253 (t80) cc_final: 0.8025 (t80)
REVERT: A  375 ASP cc_start: 0.7075 (m-30) cc_final: 0.6754 (m-30)
REVERT: A  413 LYS cc_start: 0.4894 (ttmt) cc_final: 0.4599 (ttmm)
REVERT: A  447 TRP cc_start: 0.8068 (OUTLIER) cc_final: 0.7437 (m-10)
REVERT: A  452 SER cc_start: 0.8229 (OUTLIER) cc_final: 0.7979 (m)
REVERT: A  504 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7351 (mm-30)
REVERT: A  688 ARG cc_start: 0.7215 (ttp-110) cc_final: 0.6902 (ptt-90)
REVERT: A  743 LYS cc_start: 0.7848 (mttt) cc_final: 0.7257 (mptt)
REVERT: A  782 ARG cc_start: 0.5331 (OUTLIER) cc_final: 0.4551 (mtp85)
REVERT: A  784 GLU cc_start: 0.6624 (pp20) cc_final: 0.5961 (pp20)
REVERT: A  853 ARG cc_start: 0.5616 (OUTLIER) cc_final: 0.5124 (ttm170)
REVERT: A  864 TYR cc_start: 0.6418 (OUTLIER) cc_final: 0.5795 (m-80)
  outliers start: 39
  outliers final: 18
  residues processed: 116
  average time/residue: 1.0302
  time to fit residues: 127.3797
Evaluate side-chains
  110 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 85
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  128 LYS
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  447 TRP
Chi-restraints excluded: chain A residue  452 SER
Chi-restraints excluded: chain A residue  504 GLU
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  583 GLN
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  716 HIS
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  782 ARG
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  853 ARG
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  864 TYR
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  123 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 10 optimal weight:    9.9990
   chunk 31 optimal weight:    0.6980
   chunk 74 optimal weight:    4.9990
   chunk 46 optimal weight:    0.6980
   chunk 72 optimal weight:    0.8980
   chunk 58 optimal weight:    0.3980
   chunk 29 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.174543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.149009 restraints weight = 35333.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.4057 rms_B_bonded: 4.38
r_work: 0.3914 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3920
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3920 r_free = 0.3920    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3920 r_free = 0.3920    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3920
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.3194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7051  Z= 0.176
  Angle     :  0.572   7.799   9565  Z= 0.297
  Chirality :  0.042   0.153   1016
  Planarity :  0.004   0.036   1212
  Dihedral  :  6.407  54.987    952
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 23.98 %
    Favored  : 71.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -0.27 (0.30), residues: 820
  helix:  0.38 (0.29), residues: 318
  sheet: -1.16 (0.52), residues: 108
  loop : -0.20 (0.33), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 447 
 HIS   0.005   0.001   HIS A 389 
 PHE   0.013   0.001   PHE C 108 
 TYR   0.018   0.001   TYR C  32 
 ARG   0.004   0.000   ARG A 709 

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 95
  time to evaluate  : 0.760 
Fit side-chains
REVERT: A   98 GLN cc_start: 0.7296 (mm-40) cc_final: 0.6880 (mm-40)
REVERT: A  114 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7380 (mm-30)
REVERT: A  208 TYR cc_start: 0.8249 (t80) cc_final: 0.8023 (t80)
REVERT: A  375 ASP cc_start: 0.6999 (m-30) cc_final: 0.6734 (m-30)
REVERT: A  413 LYS cc_start: 0.4817 (ttmt) cc_final: 0.4549 (ttmm)
REVERT: A  447 TRP cc_start: 0.7986 (OUTLIER) cc_final: 0.7384 (m-10)
REVERT: A  452 SER cc_start: 0.8188 (OUTLIER) cc_final: 0.7960 (m)
REVERT: A  504 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7345 (mm-30)
REVERT: A  688 ARG cc_start: 0.7230 (ttp-110) cc_final: 0.6956 (ptt-90)
REVERT: A  743 LYS cc_start: 0.7842 (mttt) cc_final: 0.7234 (mptt)
REVERT: A  782 ARG cc_start: 0.5214 (OUTLIER) cc_final: 0.4376 (mtp85)
REVERT: A  784 GLU cc_start: 0.6587 (pp20) cc_final: 0.5959 (pp20)
REVERT: A  853 ARG cc_start: 0.5586 (OUTLIER) cc_final: 0.5246 (ttm170)
REVERT: A  864 TYR cc_start: 0.6222 (OUTLIER) cc_final: 0.5556 (m-80)
  outliers start: 32
  outliers final: 16
  residues processed: 117
  average time/residue: 0.9853
  time to fit residues: 123.1082
Evaluate side-chains
  114 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  128 LYS
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  447 TRP
Chi-restraints excluded: chain A residue  452 SER
Chi-restraints excluded: chain A residue  504 GLU
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  583 GLN
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  716 HIS
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  782 ARG
Chi-restraints excluded: chain A residue  853 ARG
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  864 TYR
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  121 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 53 optimal weight:    8.9990
   chunk 65 optimal weight:    0.0050
   chunk 34 optimal weight:    0.6980
   chunk 57 optimal weight:    6.9990
   chunk 73 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 58 optimal weight:    5.9990
   overall best weight:    1.1400

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.173038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.146684 restraints weight = 28755.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.4029 rms_B_bonded: 3.67
r_work: 0.3905 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3905
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3911
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3911 r_free = 0.3911    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3911 r_free = 0.3911    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3911
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7162
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7051  Z= 0.228
  Angle     :  0.610   7.314   9565  Z= 0.317
  Chirality :  0.043   0.160   1016
  Planarity :  0.004   0.036   1212
  Dihedral  :  6.516  55.517    952
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 23.58 %
    Favored  : 71.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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 (0.30), residues: 820
  helix:  0.32 (0.29), residues: 316
  sheet: -1.14 (0.52), residues: 105
  loop : -0.18 (0.33), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 391 
 HIS   0.006   0.001   HIS A 389 
 PHE   0.014   0.002   PHE A 543 
 TYR   0.020   0.002   TYR C  32 
 ARG   0.004   0.000   ARG A 709 

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 92
  time to evaluate  : 0.681 
Fit side-chains
REVERT: A   98 GLN cc_start: 0.7263 (mm-40) cc_final: 0.6867 (mm-40)
REVERT: A  114 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7441 (mm-30)
REVERT: A  208 TYR cc_start: 0.8234 (t80) cc_final: 0.8017 (t80)
REVERT: A  375 ASP cc_start: 0.7059 (m-30) cc_final: 0.6770 (m-30)
REVERT: A  413 LYS cc_start: 0.4888 (ttmt) cc_final: 0.4608 (ttmm)
REVERT: A  447 TRP cc_start: 0.8046 (OUTLIER) cc_final: 0.7446 (m-10)
REVERT: A  452 SER cc_start: 0.8226 (OUTLIER) cc_final: 0.7989 (m)
REVERT: A  504 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7236 (mm-30)
REVERT: A  688 ARG cc_start: 0.7238 (ttp-110) cc_final: 0.6947 (ptt-90)
REVERT: A  743 LYS cc_start: 0.7840 (mttt) cc_final: 0.7243 (mptt)
REVERT: A  782 ARG cc_start: 0.5209 (OUTLIER) cc_final: 0.4433 (mtp85)
REVERT: A  784 GLU cc_start: 0.6645 (pp20) cc_final: 0.5860 (pp20)
REVERT: A  853 ARG cc_start: 0.5569 (OUTLIER) cc_final: 0.5226 (ttm170)
REVERT: A  858 GLU cc_start: 0.6622 (mp0) cc_final: 0.6210 (mp0)
REVERT: A  864 TYR cc_start: 0.6363 (OUTLIER) cc_final: 0.5773 (m-80)
  outliers start: 36
  outliers final: 20
  residues processed: 120
  average time/residue: 0.9519
  time to fit residues: 122.0190
Evaluate side-chains
  115 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 88
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  128 LYS
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  203 LYS
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  447 TRP
Chi-restraints excluded: chain A residue  452 SER
Chi-restraints excluded: chain A residue  504 GLU
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  583 GLN
Chi-restraints excluded: chain A residue  617 THR
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  716 HIS
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  782 ARG
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  853 ARG
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  864 TYR
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  121 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 45 optimal weight:    8.9990
   chunk 68 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.171587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.145346 restraints weight = 27964.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.4018 rms_B_bonded: 3.59
r_work: 0.3896 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3902
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3902 r_free = 0.3902    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3902 r_free = 0.3902    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3902
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7171
moved from start:          0.3450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7051  Z= 0.253
  Angle     :  0.623   7.380   9565  Z= 0.326
  Chirality :  0.044   0.182   1016
  Planarity :  0.004   0.035   1212
  Dihedral  :  6.560  54.592    952
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 23.44 %
    Favored  : 71.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -0.38 (0.30), residues: 820
  helix:  0.19 (0.28), residues: 323
  sheet: -1.31 (0.51), residues: 107
  loop : -0.14 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 391 
 HIS   0.007   0.001   HIS A 389 
 PHE   0.016   0.002   PHE A 543 
 TYR   0.019   0.002   TYR A 680 
 ARG   0.003   0.000   ARG A 709 

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 91
  time to evaluate  : 0.747 
Fit side-chains
REVERT: A   98 GLN cc_start: 0.7279 (mm-40) cc_final: 0.6860 (mm110)
REVERT: A  114 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7452 (mm-30)
REVERT: A  208 TYR cc_start: 0.8247 (t80) cc_final: 0.8015 (t80)
REVERT: A  375 ASP cc_start: 0.7079 (m-30) cc_final: 0.6774 (m-30)
REVERT: A  413 LYS cc_start: 0.4919 (ttmt) cc_final: 0.4634 (ttmm)
REVERT: A  447 TRP cc_start: 0.8076 (OUTLIER) cc_final: 0.7508 (m-10)
REVERT: A  452 SER cc_start: 0.8215 (OUTLIER) cc_final: 0.7982 (m)
REVERT: A  504 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7313 (mm-30)
REVERT: A  688 ARG cc_start: 0.7218 (ttp-110) cc_final: 0.6924 (ptt-90)
REVERT: A  743 LYS cc_start: 0.7821 (mttt) cc_final: 0.7235 (mptt)
REVERT: A  782 ARG cc_start: 0.5278 (OUTLIER) cc_final: 0.4345 (mtp85)
REVERT: A  784 GLU cc_start: 0.6602 (pp20) cc_final: 0.6113 (pp20)
REVERT: A  853 ARG cc_start: 0.5568 (OUTLIER) cc_final: 0.5219 (ttm170)
REVERT: A  864 TYR cc_start: 0.6409 (OUTLIER) cc_final: 0.5834 (m-80)
  outliers start: 35
  outliers final: 20
  residues processed: 116
  average time/residue: 0.9765
  time to fit residues: 121.0450
Evaluate side-chains
  116 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 89
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  128 LYS
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  447 TRP
Chi-restraints excluded: chain A residue  452 SER
Chi-restraints excluded: chain A residue  504 GLU
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  583 GLN
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  716 HIS
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  782 ARG
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  847 PHE
Chi-restraints excluded: chain A residue  853 ARG
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  864 TYR
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  123 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 70 optimal weight:    0.0870
   chunk 24 optimal weight:    0.0070
   chunk 0 optimal weight:    6.9990
   chunk 34 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 72 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0970
   chunk 18 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.2974

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.174910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.151437 restraints weight = 16616.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.4089 rms_B_bonded: 2.60
r_work: 0.3981 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3981
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3987
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3987 r_free = 0.3987    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3987 r_free = 0.3987    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3987
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7053
moved from start:          0.3327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7051  Z= 0.164
  Angle     :  0.581   7.519   9565  Z= 0.303
  Chirality :  0.042   0.149   1016
  Planarity :  0.004   0.033   1212
  Dihedral  :  6.305  52.490    952
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 24.80 %
    Favored  : 72.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -0.20 (0.30), residues: 820
  helix:  0.40 (0.29), residues: 317
  sheet: -1.19 (0.51), residues: 107
  loop : -0.11 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 447 
 HIS   0.006   0.001   HIS A 720 
 PHE   0.044   0.002   PHE A 339 
 TYR   0.023   0.001   TYR A 680 
 ARG   0.004   0.000   ARG A 845 

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.745 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6815 (mm110)
REVERT: A  114 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7404 (mm-30)
REVERT: A  413 LYS cc_start: 0.4776 (ttmt) cc_final: 0.4512 (ttmm)
REVERT: A  452 SER cc_start: 0.8210 (OUTLIER) cc_final: 0.7999 (m)
REVERT: A  504 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7114 (mm-30)
REVERT: A  688 ARG cc_start: 0.7112 (ttp-110) cc_final: 0.6902 (ptt-90)
REVERT: A  743 LYS cc_start: 0.7794 (mttt) cc_final: 0.7228 (mptt)
REVERT: A  784 GLU cc_start: 0.6477 (pp20) cc_final: 0.5995 (pp20)
REVERT: A  853 ARG cc_start: 0.5469 (OUTLIER) cc_final: 0.5158 (ttm170)
REVERT: A  864 TYR cc_start: 0.6196 (OUTLIER) cc_final: 0.5629 (m-80)
  outliers start: 23
  outliers final: 12
  residues processed: 109
  average time/residue: 0.9805
  time to fit residues: 114.4225
Evaluate side-chains
  108 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  452 SER
Chi-restraints excluded: chain A residue  504 GLU
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  583 GLN
Chi-restraints excluded: chain A residue  716 HIS
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  853 ARG
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  864 TYR
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  121 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 57 optimal weight:    0.3980
   chunk 36 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 67 optimal weight:   10.0000
   chunk 22 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.174460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.148250 restraints weight = 25045.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.4051 rms_B_bonded: 3.35
r_work: 0.3941 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3946
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3946 r_free = 0.3946    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3946 r_free = 0.3946    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3946
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7119
moved from start:          0.3418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7051  Z= 0.200
  Angle     :  0.595   7.293   9565  Z= 0.312
  Chirality :  0.043   0.157   1016
  Planarity :  0.004   0.033   1212
  Dihedral  :  6.258  52.544    951
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 25.47 %
    Favored  : 71.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -0.21 (0.30), residues: 820
  helix:  0.37 (0.29), residues: 323
  sheet: -1.31 (0.50), residues: 109
  loop : -0.04 (0.33), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP A 447 
 HIS   0.005   0.001   HIS A 389 
 PHE   0.013   0.001   PHE A 362 
 TYR   0.027   0.002   TYR A 680 
 ARG   0.004   0.000   ARG C  38 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6631.54 seconds
wall clock time: 113 minutes 28.74 seconds (6808.74 seconds total)