Starting phenix.real_space_refine
on Wed Feb 12 00:58:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cd0_16565/02_2025/8cd0_16565.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cd0_16565/02_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_16565/02_2025/8cd0_16565.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cd0_16565/02_2025/8cd0_16565.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cd0_16565/02_2025/8cd0_16565.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cd0_16565/02_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-5592/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: 2.78, per 1000 atoms: 0.41
  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: 1.45
  Conformation dependent library (CDL) restraints added in 957.0 milliseconds
  

  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: 0.85
  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: 2.18

  Time building geometry restraints manager: 1.71 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:             16.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     15.320
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.100
-------------------------------------------------------------------------------
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  : 0.707 
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: 1.0269
  time to fit residues: 144.3643
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  : 0.715 
-------------------------------------------------------------------------------
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 = 0.155370 restraints weight = 26082.410|
|-----------------------------------------------------------------------------|
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 = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4020
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6999
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  : 0.683 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 GLU cc_start: 0.7708 (tp30) cc_final: 0.7432 (mm-30)
REVERT: A  143 LYS cc_start: 0.6364 (mttp) cc_final: 0.6069 (mtpm)
REVERT: A  203 LYS cc_start: 0.7174 (mptt) cc_final: 0.6890 (mttp)
REVERT: A  308 LEU cc_start: 0.8226 (mt) cc_final: 0.7959 (tp)
REVERT: A  413 LYS cc_start: 0.4886 (ttmt) cc_final: 0.4564 (ttmm)
REVERT: A  452 SER cc_start: 0.8121 (OUTLIER) cc_final: 0.7839 (m)
REVERT: A  688 ARG cc_start: 0.7271 (ttp-110) cc_final: 0.6932 (ptt-90)
REVERT: A  708 ASP cc_start: 0.6472 (t70) cc_final: 0.6137 (t70)
REVERT: A  743 LYS cc_start: 0.7875 (mttt) cc_final: 0.7250 (mptt)
REVERT: A  784 GLU cc_start: 0.6334 (pp20) cc_final: 0.5836 (pp20)
REVERT: A  853 ARG cc_start: 0.5518 (OUTLIER) cc_final: 0.5115 (ttm170)
REVERT: A  864 TYR cc_start: 0.5948 (OUTLIER) cc_final: 0.5615 (m-80)
  outliers start: 31
  outliers final: 12
  residues processed: 122
  average time/residue: 1.0442
  time to fit residues: 135.5961
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  : 0.699 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 49 optimal weight:    7.9990
   chunk 0 optimal weight:    7.9990
   chunk 53 optimal weight:    4.9990
   chunk 71 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 45 optimal weight:    0.1980
   chunk 3 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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
A 769 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.173517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.147889 restraints weight = 20326.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.4053 rms_B_bonded: 2.95
r_work: 0.3945 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3952
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3952 r_free = 0.3952    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3952 r_free = 0.3952    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3952
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7121
moved from start:          0.2576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7051  Z= 0.251
  Angle     :  0.641   9.123   9565  Z= 0.331
  Chirality :  0.044   0.167   1016
  Planarity :  0.005   0.042   1212
  Dihedral  :  7.113  63.361    952
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 21.95 %
    Favored  : 73.31 %
  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: -0.88 (0.29), residues: 820
  helix: -0.38 (0.27), residues: 316
  sheet: -0.99 (0.50), residues: 118
  loop : -0.45 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 391 
 HIS   0.013   0.002   HIS A 400 
 PHE   0.020   0.002   PHE A 543 
 TYR   0.016   0.002   TYR C  32 
 ARG   0.004   0.001   ARG A 709 

*********************** 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
  135 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 100
  time to evaluate  : 0.725 
Fit side-chains
REVERT: A   98 GLN cc_start: 0.7335 (mm-40) cc_final: 0.6906 (mm-40)
REVERT: A  114 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7393 (mm-30)
REVERT: A  143 LYS cc_start: 0.6431 (mttp) cc_final: 0.6073 (mttm)
REVERT: A  203 LYS cc_start: 0.7121 (mptt) cc_final: 0.6887 (mttp)
REVERT: A  208 TYR cc_start: 0.8195 (t80) cc_final: 0.7957 (t80)
REVERT: A  413 LYS cc_start: 0.4807 (ttmt) cc_final: 0.4502 (ttmm)
REVERT: A  447 TRP cc_start: 0.8019 (OUTLIER) cc_final: 0.7524 (m-10)
REVERT: A  452 SER cc_start: 0.8202 (OUTLIER) cc_final: 0.7967 (m)
REVERT: A  634 TYR cc_start: 0.7294 (m-80) cc_final: 0.7084 (m-80)
REVERT: A  688 ARG cc_start: 0.7319 (ttp-110) cc_final: 0.6995 (ptt-90)
REVERT: A  743 LYS cc_start: 0.7876 (mttt) cc_final: 0.7277 (mptt)
REVERT: A  782 ARG cc_start: 0.5210 (OUTLIER) cc_final: 0.4544 (mtp85)
REVERT: A  784 GLU cc_start: 0.6437 (pp20) cc_final: 0.5908 (pp20)
REVERT: A  853 ARG cc_start: 0.5625 (OUTLIER) cc_final: 0.5106 (ttm170)
REVERT: A  864 TYR cc_start: 0.6179 (OUTLIER) cc_final: 0.5827 (m-80)
  outliers start: 35
  outliers final: 17
  residues processed: 123
  average time/residue: 0.9849
  time to fit residues: 129.5484
Evaluate side-chains
  112 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0980
   chunk 67 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 19 optimal weight:    0.3980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.4345 r_free = 0.4345 target = 0.174354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.149023 restraints weight = 25169.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.4067 rms_B_bonded: 3.29
r_work: 0.3949 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3955
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3955 r_free = 0.3955    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3955 r_free = 0.3955    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3955
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7051  Z= 0.196
  Angle     :  0.576   8.346   9565  Z= 0.297
  Chirality :  0.042   0.161   1016
  Planarity :  0.004   0.038   1212
  Dihedral  :  6.659  58.222    952
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 22.63 %
    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: -0.51 (0.29), residues: 820
  helix:  0.10 (0.28), residues: 316
  sheet: -1.05 (0.52), residues: 108
  loop : -0.33 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 391 
 HIS   0.014   0.001   HIS A 400 
 PHE   0.016   0.001   PHE C 108 
 TYR   0.016   0.001   TYR C  32 
 ARG   0.004   0.000   ARG A 709 

*********************** 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
  133 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 100
  time to evaluate  : 1.089 
Fit side-chains
REVERT: A   89 VAL cc_start: 0.6393 (m) cc_final: 0.6122 (t)
REVERT: A   98 GLN cc_start: 0.7339 (mm-40) cc_final: 0.6844 (mm110)
REVERT: A  114 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7426 (mm-30)
REVERT: A  143 LYS cc_start: 0.6408 (mttp) cc_final: 0.6055 (mttm)
REVERT: A  203 LYS cc_start: 0.7103 (mptt) cc_final: 0.6900 (mttp)
REVERT: A  413 LYS cc_start: 0.4725 (ttmt) cc_final: 0.4444 (ttmm)
REVERT: A  447 TRP cc_start: 0.8010 (OUTLIER) cc_final: 0.7251 (m-10)
REVERT: A  452 SER cc_start: 0.8153 (OUTLIER) cc_final: 0.7910 (m)
REVERT: A  634 TYR cc_start: 0.7315 (m-80) cc_final: 0.7099 (m-80)
REVERT: A  688 ARG cc_start: 0.7287 (ttp-110) cc_final: 0.6965 (ptt-90)
REVERT: A  743 LYS cc_start: 0.7837 (mttt) cc_final: 0.7235 (mptt)
REVERT: A  782 ARG cc_start: 0.5265 (OUTLIER) cc_final: 0.4552 (mtp85)
REVERT: A  784 GLU cc_start: 0.6448 (pp20) cc_final: 0.5865 (pp20)
REVERT: A  853 ARG cc_start: 0.5568 (OUTLIER) cc_final: 0.5081 (ttm170)
REVERT: A  864 TYR cc_start: 0.6095 (OUTLIER) cc_final: 0.5718 (m-80)
  outliers start: 33
  outliers final: 18
  residues processed: 123
  average time/residue: 1.1290
  time to fit residues: 148.0878
Evaluate side-chains
  117 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
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  267 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  392 SER
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  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   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:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0870
   chunk 17 optimal weight:    8.9990
   chunk 21 optimal weight:    3.9990
   chunk 52 optimal weight:    7.9990
   chunk 76 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 67 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.3962

-------------------------------------------------------------------------------
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 = 0.4317 r_free = 0.4317 target = 0.171806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.147981 restraints weight = 19341.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.4056 rms_B_bonded: 3.10
r_work: 0.3927 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3933
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3933 r_free = 0.3933    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3933 r_free = 0.3933    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3933
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7144
moved from start:          0.2973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7051  Z= 0.252
  Angle     :  0.610   7.620   9565  Z= 0.317
  Chirality :  0.044   0.165   1016
  Planarity :  0.004   0.036   1212
  Dihedral  :  6.754  57.459    952
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 21.41 %
    Favored  : 73.04 %
  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 (0.29), residues: 820
  helix:  0.20 (0.29), residues: 316
  sheet: -1.09 (0.52), residues: 108
  loop : -0.27 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 391 
 HIS   0.014   0.002   HIS A 400 
 PHE   0.017   0.002   PHE A 543 
 TYR   0.019   0.002   TYR C  32 
 ARG   0.002   0.000   ARG A 782 

*********************** 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: 41
    poor density    : 97
  time to evaluate  : 0.817 
Fit side-chains
REVERT: A   87 VAL cc_start: 0.7114 (m) cc_final: 0.6744 (t)
REVERT: A   98 GLN cc_start: 0.7338 (mm-40) cc_final: 0.6835 (mm110)
REVERT: A  114 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7429 (mm-30)
REVERT: A  139 GLU cc_start: 0.7848 (mp0) cc_final: 0.7449 (mp0)
REVERT: A  143 LYS cc_start: 0.6371 (mttp) cc_final: 0.5988 (mttm)
REVERT: A  375 ASP cc_start: 0.6978 (m-30) cc_final: 0.6674 (m-30)
REVERT: A  413 LYS cc_start: 0.4893 (ttmt) cc_final: 0.4620 (ttmm)
REVERT: A  447 TRP cc_start: 0.8041 (OUTLIER) cc_final: 0.7390 (m-10)
REVERT: A  452 SER cc_start: 0.8249 (OUTLIER) cc_final: 0.8007 (m)
REVERT: A  688 ARG cc_start: 0.7299 (ttp-110) cc_final: 0.6976 (ptt-90)
REVERT: A  743 LYS cc_start: 0.7869 (mttt) cc_final: 0.7285 (mptt)
REVERT: A  782 ARG cc_start: 0.5288 (OUTLIER) cc_final: 0.4640 (mtp85)
REVERT: A  784 GLU cc_start: 0.6455 (pp20) cc_final: 0.5878 (pp20)
REVERT: A  853 ARG cc_start: 0.5633 (OUTLIER) cc_final: 0.5119 (ttm170)
REVERT: A  864 TYR cc_start: 0.6224 (OUTLIER) cc_final: 0.5863 (m-80)
REVERT: C   85 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6473 (mp)
  outliers start: 41
  outliers final: 19
  residues processed: 124
  average time/residue: 1.0143
  time to fit residues: 134.2784
Evaluate side-chains
  116 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 90
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
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  206 LEU
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 12 optimal weight:    0.1980
   chunk 39 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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 = 0.4340 r_free = 0.4340 target = 0.174097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.148033 restraints weight = 24867.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.4046 rms_B_bonded: 3.58
r_work: 0.3926 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3933
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3933 r_free = 0.3933    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3933 r_free = 0.3933    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3933
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7118
moved from start:          0.3024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7051  Z= 0.186
  Angle     :  0.568   7.303   9565  Z= 0.295
  Chirality :  0.042   0.155   1016
  Planarity :  0.004   0.034   1212
  Dihedral  :  6.501  55.606    952
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 21.41 %
    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: -0.25 (0.30), residues: 820
  helix:  0.39 (0.29), residues: 316
  sheet: -1.10 (0.53), residues: 108
  loop : -0.19 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 447 
 HIS   0.016   0.001   HIS A 400 
 PHE   0.014   0.001   PHE C 108 
 TYR   0.020   0.001   TYR C  32 
 ARG   0.003   0.000   ARG C  38 

*********************** 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
  131 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 93
  time to evaluate  : 0.765 
Fit side-chains
REVERT: A   87 VAL cc_start: 0.7101 (m) cc_final: 0.6676 (t)
REVERT: A   88 PHE cc_start: 0.6529 (m-10) cc_final: 0.6280 (m-80)
REVERT: A   98 GLN cc_start: 0.7313 (mm-40) cc_final: 0.6905 (mm-40)
REVERT: A  114 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7391 (mm-30)
REVERT: A  139 GLU cc_start: 0.7787 (mp0) cc_final: 0.7580 (mp0)
REVERT: A  143 LYS cc_start: 0.6338 (mttp) cc_final: 0.5972 (mttm)
REVERT: A  208 TYR cc_start: 0.8221 (t80) cc_final: 0.8012 (t80)
REVERT: A  413 LYS cc_start: 0.4801 (ttmt) cc_final: 0.4527 (ttmm)
REVERT: A  447 TRP cc_start: 0.8015 (OUTLIER) cc_final: 0.7382 (m-10)
REVERT: A  452 SER cc_start: 0.8198 (OUTLIER) cc_final: 0.7950 (m)
REVERT: A  504 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7340 (mm-30)
REVERT: A  688 ARG cc_start: 0.7229 (ttp-110) cc_final: 0.6900 (ptt-90)
REVERT: A  743 LYS cc_start: 0.7833 (mttt) cc_final: 0.7207 (mptt)
REVERT: A  784 GLU cc_start: 0.6531 (pp20) cc_final: 0.5878 (pp20)
REVERT: A  853 ARG cc_start: 0.5555 (OUTLIER) cc_final: 0.5186 (ttm170)
REVERT: A  864 TYR cc_start: 0.6199 (OUTLIER) cc_final: 0.5826 (m-80)
  outliers start: 38
  outliers final: 18
  residues processed: 120
  average time/residue: 0.9896
  time to fit residues: 127.0142
Evaluate side-chains
  115 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 91
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
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  267 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  367 THR
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  675 GLU
Chi-restraints excluded: chain A residue  701 THR
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  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
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:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   chunk 46 optimal weight:    0.8980
   chunk 72 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   overall best weight:    1.3386

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.172296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.145330 restraints weight = 35268.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.4012 rms_B_bonded: 4.22
r_work: 0.3878 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3884
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3884 r_free = 0.3884    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3884 r_free = 0.3884    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3884
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.3233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7051  Z= 0.248
  Angle     :  0.621   7.484   9565  Z= 0.325
  Chirality :  0.044   0.166   1016
  Planarity :  0.004   0.034   1212
  Dihedral  :  6.671  56.757    952
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 21.68 %
    Favored  : 72.76 %
  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: -0.31 (0.30), residues: 820
  helix:  0.33 (0.29), residues: 317
  sheet: -1.14 (0.52), residues: 108
  loop : -0.22 (0.33), residues: 395

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   0.017   0.002   PHE A 543 
 TYR   0.020   0.002   TYR C  32 
 ARG   0.003   0.000   ARG C  38 

*********************** 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
  135 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 94
  time to evaluate  : 0.779 
Fit side-chains
REVERT: A   87 VAL cc_start: 0.7133 (m) cc_final: 0.6740 (t)
REVERT: A   98 GLN cc_start: 0.7334 (mm-40) cc_final: 0.6851 (mm110)
REVERT: A  114 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7430 (mm-30)
REVERT: A  139 GLU cc_start: 0.7905 (mp0) cc_final: 0.7477 (mp0)
REVERT: A  143 LYS cc_start: 0.6348 (mttp) cc_final: 0.5962 (mttm)
REVERT: A  375 ASP cc_start: 0.7121 (m-30) cc_final: 0.6792 (m-30)
REVERT: A  413 LYS cc_start: 0.4947 (ttmt) cc_final: 0.4663 (ttmm)
REVERT: A  447 TRP cc_start: 0.8079 (OUTLIER) cc_final: 0.7436 (m-10)
REVERT: A  452 SER cc_start: 0.8249 (OUTLIER) cc_final: 0.8014 (m)
REVERT: A  504 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7512 (mm-30)
REVERT: A  688 ARG cc_start: 0.7283 (ttp-110) cc_final: 0.7015 (ptt-90)
REVERT: A  743 LYS cc_start: 0.7862 (mttt) cc_final: 0.7272 (mptt)
REVERT: A  782 ARG cc_start: 0.5230 (OUTLIER) cc_final: 0.4481 (mtp85)
REVERT: A  784 GLU cc_start: 0.6672 (pp20) cc_final: 0.5985 (pp20)
REVERT: A  853 ARG cc_start: 0.5606 (OUTLIER) cc_final: 0.5171 (ttm170)
REVERT: A  864 TYR cc_start: 0.6401 (OUTLIER) cc_final: 0.5772 (m-80)
  outliers start: 41
  outliers final: 19
  residues processed: 122
  average time/residue: 1.0260
  time to fit residues: 133.3089
Evaluate side-chains
  114 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 88
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
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  267 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  367 THR
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  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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 53 optimal weight:    0.5980
   chunk 65 optimal weight:    0.0070
   chunk 34 optimal weight:    0.0470
   chunk 57 optimal weight:    0.0370
   chunk 73 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 60 optimal weight:    0.5980
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.2574

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
A 408 GLN
A 475 HIS
** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.177074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.151281 restraints weight = 29013.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.4088 rms_B_bonded: 3.66
r_work: 0.3965 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3972
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3972 r_free = 0.3972    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3972 r_free = 0.3972    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3972
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7057
moved from start:          0.3112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7051  Z= 0.146
  Angle     :  0.555   8.059   9565  Z= 0.289
  Chirality :  0.042   0.154   1016
  Planarity :  0.004   0.041   1212
  Dihedral  :  6.206  53.331    952
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 23.71 %
    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: -0.07 (0.30), residues: 820
  helix:  0.62 (0.29), residues: 318
  sheet: -1.15 (0.52), residues: 108
  loop : -0.12 (0.33), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 447 
 HIS   0.005   0.001   HIS A 389 
 PHE   0.014   0.001   PHE A 847 
 TYR   0.016   0.001   TYR C  32 
 ARG   0.006   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
  129 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 98
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 GLN cc_start: 0.7276 (mm-40) cc_final: 0.6842 (mm110)
REVERT: A  114 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7257 (mm-30)
REVERT: A  143 LYS cc_start: 0.6304 (mttp) cc_final: 0.5950 (mttm)
REVERT: A  308 LEU cc_start: 0.8172 (mt) cc_final: 0.7955 (tp)
REVERT: A  413 LYS cc_start: 0.4768 (ttmt) cc_final: 0.4505 (ttmm)
REVERT: A  447 TRP cc_start: 0.7888 (OUTLIER) cc_final: 0.7351 (m-10)
REVERT: A  504 GLU cc_start: 0.7511 (tp30) cc_final: 0.7277 (mm-30)
REVERT: A  688 ARG cc_start: 0.7141 (ttp-110) cc_final: 0.6940 (ptt-90)
REVERT: A  708 ASP cc_start: 0.6024 (t70) cc_final: 0.5705 (t70)
REVERT: A  743 LYS cc_start: 0.7825 (mttt) cc_final: 0.7233 (mptt)
REVERT: A  784 GLU cc_start: 0.6589 (pp20) cc_final: 0.5835 (pp20)
REVERT: A  853 ARG cc_start: 0.5544 (OUTLIER) cc_final: 0.5239 (ttm170)
REVERT: A  858 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6151 (mp0)
REVERT: A  864 TYR cc_start: 0.6100 (OUTLIER) cc_final: 0.5768 (m-80)
  outliers start: 31
  outliers final: 13
  residues processed: 121
  average time/residue: 1.0274
  time to fit residues: 132.7772
Evaluate side-chains
  105 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
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  447 TRP
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  853 ARG
Chi-restraints excluded: chain A residue  858 GLU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 42 optimal weight:    0.4980
   chunk 49 optimal weight:    4.9990
   chunk 45 optimal weight:    9.9990
   chunk 68 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 408 GLN
A 475 HIS
** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.175379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.149730 restraints weight = 28111.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.4071 rms_B_bonded: 3.48
r_work: 0.3952 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3957
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3957 r_free = 0.3957    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3957 r_free = 0.3957    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3957
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7087
moved from start:          0.3219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7051  Z= 0.188
  Angle     :  0.587   6.943   9565  Z= 0.305
  Chirality :  0.043   0.200   1016
  Planarity :  0.004   0.047   1212
  Dihedral  :  6.280  53.811    952
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 25.07 %
    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: -0.07 (0.30), residues: 820
  helix:  0.58 (0.29), residues: 317
  sheet: -1.09 (0.52), residues: 108
  loop : -0.10 (0.33), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 447 
 HIS   0.005   0.001   HIS A 389 
 PHE   0.023   0.001   PHE A 543 
 TYR   0.017   0.001   TYR C  32 
 ARG   0.005   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
  117 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.693 
Fit side-chains
REVERT: A   89 VAL cc_start: 0.6420 (m) cc_final: 0.6158 (t)
REVERT: A   98 GLN cc_start: 0.7260 (mm-40) cc_final: 0.6815 (mm110)
REVERT: A  114 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7250 (mm-30)
REVERT: A  143 LYS cc_start: 0.6403 (mttp) cc_final: 0.6045 (mttm)
REVERT: A  413 LYS cc_start: 0.4783 (ttmt) cc_final: 0.4512 (ttmm)
REVERT: A  447 TRP cc_start: 0.7964 (OUTLIER) cc_final: 0.7549 (m-10)
REVERT: A  504 GLU cc_start: 0.7498 (tp30) cc_final: 0.7262 (mm-30)
REVERT: A  688 ARG cc_start: 0.7169 (ttp-110) cc_final: 0.6951 (ptt-90)
REVERT: A  708 ASP cc_start: 0.6031 (t70) cc_final: 0.5736 (t70)
REVERT: A  743 LYS cc_start: 0.7826 (mttt) cc_final: 0.7248 (mptt)
REVERT: A  784 GLU cc_start: 0.6505 (pp20) cc_final: 0.6084 (pp20)
REVERT: A  853 ARG cc_start: 0.5602 (OUTLIER) cc_final: 0.5287 (ttm170)
REVERT: A  858 GLU cc_start: 0.6541 (mp0) cc_final: 0.6118 (mp0)
  outliers start: 24
  outliers final: 14
  residues processed: 113
  average time/residue: 0.9530
  time to fit residues: 115.4145
Evaluate side-chains
  107 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
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  408 GLN
Chi-restraints excluded: chain A residue  447 TRP
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  853 ARG
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 70 optimal weight:    0.0870
   chunk 24 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 34 optimal weight:    0.0980
   chunk 67 optimal weight:    0.0010
   chunk 14 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.2964

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
A 408 GLN
A 475 HIS
** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.177516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.154781 restraints weight = 16794.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.4130 rms_B_bonded: 2.51
r_work: 0.4022 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.4022
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4028
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4028 r_free = 0.4028    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4028 r_free = 0.4028    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4028
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6993
moved from start:          0.3271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7051  Z= 0.158
  Angle     :  0.564   7.358   9565  Z= 0.295
  Chirality :  0.043   0.177   1016
  Planarity :  0.004   0.040   1212
  Dihedral  :  5.768  50.870    950
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 25.34 %
    Favored  : 71.95 %
  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:  0.01 (0.30), residues: 820
  helix:  0.64 (0.29), residues: 318
  sheet: -1.06 (0.52), residues: 108
  loop : -0.06 (0.33), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 391 
 HIS   0.005   0.001   HIS A 720 
 PHE   0.047   0.001   PHE A 339 
 TYR   0.019   0.001   TYR A 208 
 ARG   0.005   0.000   ARG A 709 

********************** 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
  113 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.725 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 GLN cc_start: 0.7256 (mm-40) cc_final: 0.6802 (mm110)
REVERT: A  114 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7244 (mm-30)
REVERT: A  143 LYS cc_start: 0.6311 (mttp) cc_final: 0.5982 (mttm)
REVERT: A  413 LYS cc_start: 0.4744 (ttmt) cc_final: 0.4502 (ttmm)
REVERT: A  504 GLU cc_start: 0.7388 (tp30) cc_final: 0.7171 (mm-30)
REVERT: A  688 ARG cc_start: 0.7071 (ttp-110) cc_final: 0.6830 (ptt-90)
REVERT: A  708 ASP cc_start: 0.5824 (t70) cc_final: 0.5610 (t70)
REVERT: A  743 LYS cc_start: 0.7803 (mttt) cc_final: 0.7230 (mptt)
REVERT: A  784 GLU cc_start: 0.6444 (pp20) cc_final: 0.6061 (pp20)
REVERT: A  853 ARG cc_start: 0.5542 (OUTLIER) cc_final: 0.5256 (ttm170)
REVERT: A  858 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.6082 (mp0)
  outliers start: 20
  outliers final: 12
  residues processed: 109
  average time/residue: 1.0054
  time to fit residues: 117.1626
Evaluate side-chains
  105 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
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  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  853 ARG
Chi-restraints excluded: chain A residue  858 GLU
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue  112 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 64 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 475 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 = 0.4347 r_free = 0.4347 target = 0.175108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.148637 restraints weight = 25140.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.4053 rms_B_bonded: 3.65
r_work: 0.3931 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3937
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3937 r_free = 0.3937    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3937 r_free = 0.3937    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3937
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7096
moved from start:          0.3340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7051  Z= 0.217
  Angle     :  0.604   8.874   9565  Z= 0.316
  Chirality :  0.044   0.171   1016
  Planarity :  0.004   0.045   1212
  Dihedral  :  5.969  51.894    950
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 24.93 %
    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: -0.04 (0.30), residues: 820
  helix:  0.59 (0.29), residues: 317
  sheet: -1.03 (0.53), residues: 108
  loop : -0.09 (0.33), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 447 
 HIS   0.006   0.001   HIS A 389 
 PHE   0.024   0.001   PHE A 543 
 TYR   0.022   0.002   TYR A 680 
 ARG   0.005   0.000   ARG A 709 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6398.80 seconds
wall clock time: 113 minutes 39.76 seconds (6819.76 seconds total)