Starting phenix.real_space_refine
on Thu Mar  6 04:09:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vti_43523/03_2025/8vti_43523.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vti_43523/03_2025/8vti_43523.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vti_43523/03_2025/8vti_43523.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vti_43523/03_2025/8vti_43523.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vti_43523/03_2025/8vti_43523.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vti_43523/03_2025/8vti_43523.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 66 atoms to isotropic.
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: 4
    Type Number    sf(0)   Gaussians
     S      23      5.16       5
     C    2917      2.51       5
     N     808      2.21       5
     O     919      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4667
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2781
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 358, 2781
          Classifications: {'peptide': 358}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 344}
    Chain: "B"
      Number of atoms: 85
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 85
          Classifications: {'peptide': 11}
          Link IDs: {'TRANS': 10}
    Chain: "C"
      Number of atoms: 792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 792
          Classifications: {'peptide': 105}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98}
    Chain: "D"
      Number of atoms: 956
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 956
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.91, per 1000 atoms: 1.27
  Number of scatterers: 4667
  At special positions: 0
  Unit cell: (79.9085, 98.039, 106.769, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      23     16.00
     O     919      8.00
     N     808      7.00
     C    2917      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 498 " - pdb=" SG  CYS A 533 " distance=2.00
    Simple disulfide: pdb=" SG  CYS A 521 " - pdb=" SG  CYS A 550 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 818 " - pdb=" SG  CYS A 849 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 837 " - pdb=" SG  CYS A 851 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  24 " - pdb=" SG  CYS C  89 " distance=2.01
    Simple disulfide: pdb=" SG  CYS D  25 " - pdb=" SG  CYS D  99 " distance=2.04

  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
  Links applied
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
    NAG-ASN
      " NAG A 901 " - " ASN A 843 "
      " NAG E   1 " - " ASN A 817 "
  Time building additional restraints: 1.14
  Conformation dependent library (CDL) restraints added in 628.1 milliseconds
  

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1114

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 10 sheets defined
      23.3% alpha, 29.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 553 through 565
      removed outlier: 4.042A  pdb=" N   HIS A 557 " --> pdb=" O   PRO A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 579
      removed outlier: 3.682A  pdb=" N   ILE A 571 " --> pdb=" O   THR A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 584 through 609
      removed outlier: 3.813A  pdb=" N   VAL A 599 " --> pdb=" O   MET A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 618 through 646
      removed outlier: 3.522A  pdb=" N   GLU A 640 " --> pdb=" O   GLN A 636 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 649
      No H-bonds generated for 'chain 'A' and resid 647 through 649'
    Processing helix  chain 'A' and resid 650 through 657
      removed outlier: 3.871A  pdb=" N   TRP A 654 " --> pdb=" O   ALA A 650 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 658 through 683
      removed outlier: 3.509A  pdb=" N   ARG A 664 " --> pdb=" O   SER A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 735
    Processing helix  chain 'A' and resid 751 through 755
    Processing helix  chain 'D' and resid 64 through 68
    Processing helix  chain 'D' and resid 77 through 79
      No H-bonds generated for 'chain 'D' and resid 77 through 79'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 501 through 502
      removed outlier: 3.903A  pdb=" N   ILE A 506 " --> pdb=" O   GLU A 502 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 520
    Processing sheet with id=AA3, first strand: chain 'A' and resid 689 through 690
    Processing sheet with id=AA4, first strand: chain 'A' and resid 689 through 690
      removed outlier: 4.360A  pdb=" N   ASN B 856 " --> pdb=" O   TRP A 821 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   THR A 829 " --> pdb=" O   SER A 824 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 714 through 715
      removed outlier: 3.565A  pdb=" N   VAL A 801 " --> pdb=" O   GLN A 726 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   VAL A 794 " --> pdb=" O   LEU A 854 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   ASN A 852 " --> pdb=" O   LEU A 796 " (cutoff:3.500A)
      removed outlier: 11.251A  pdb=" N   ASP A 798 " --> pdb=" O   SER A 850 " (cutoff:3.500A)
      removed outlier: 10.035A  pdb=" N   SER A 850 " --> pdb=" O   ASP A 798 " (cutoff:3.500A)
      removed outlier: 10.510A  pdb=" N   VAL A 800 " --> pdb=" O   THR A 848 " (cutoff:3.500A)
      removed outlier: 9.446A  pdb=" N   THR A 848 " --> pdb=" O   VAL A 800 " (cutoff:3.500A)
      removed outlier: 10.817A  pdb=" N   PHE A 802 " --> pdb=" O   HIS A 846 " (cutoff:3.500A)
      removed outlier: 9.157A  pdb=" N   HIS A 846 " --> pdb=" O   PHE A 802 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   HIS A 846 " --> pdb=" O   THR A 842 " (cutoff:3.500A)
      removed outlier: 5.406A  pdb=" N   THR A 842 " --> pdb=" O   HIS A 846 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   THR A 848 " --> pdb=" O   LEU A 840 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.640A  pdb=" N   THR C  86 " --> pdb=" O   GLN C  39 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   VAL C  34 " --> pdb=" O   TYR C  50 " (cutoff:3.500A)
      removed outlier: 5.271A  pdb=" N   TYR C  50 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   TRP C  36 " --> pdb=" O   LEU C  48 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   SER C  54 " --> pdb=" O   TYR C  50 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.640A  pdb=" N   THR C  86 " --> pdb=" O   GLN C  39 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 20 through 22
      removed outlier: 3.764A  pdb=" N   VAL C  20 " --> pdb=" O   ILE C  76 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 6 through 10
    Processing sheet with id=AB1, first strand: chain 'D' and resid 13 through 14
      removed outlier: 6.100A  pdb=" N   GLY D  13 " --> pdb=" O   THR D 124 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA D  95 " --> pdb=" O   VAL D 123 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   ILE D  37 " --> pdb=" O   SER D  53 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   SER D  53 " --> pdb=" O   ILE D  37 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   TRP D  39 " --> pdb=" O   VAL D  51 " (cutoff:3.500A)

    203 hydrogen bonds defined for protein.
    561 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: 1.30

  Time building geometry restraints manager: 1.32 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 901
        1.33 -     1.45: 1195
        1.45 -     1.57: 2633
        1.57 -     1.69: 0
        1.69 -     1.81: 33
  Bond restraints: 4762
  Sorted by residual:
  bond pdb=" N   LYS A 518 "
       pdb=" CA  LYS A 518 "
    ideal  model  delta    sigma   weight residual
    1.454  1.503 -0.049 1.29e-02 6.01e+03 1.42e+01
  bond pdb=" N   ILE A 516 "
       pdb=" CA  ILE A 516 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.19e-02 7.06e+03 1.13e+01
  bond pdb=" N   VAL A 775 "
       pdb=" CA  VAL A 775 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.15e-02 7.56e+03 1.09e+01
  bond pdb=" N   ILE A 776 "
       pdb=" CA  ILE A 776 "
    ideal  model  delta    sigma   weight residual
    1.461  1.500 -0.039 1.22e-02 6.72e+03 1.02e+01
  bond pdb=" N   GLU A 499 "
       pdb=" CA  GLU A 499 "
    ideal  model  delta    sigma   weight residual
    1.454  1.494 -0.040 1.27e-02 6.20e+03 9.95e+00
  ... (remaining 4757 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 5530
        2.26 -     4.53: 917
        4.53 -     6.79: 22
        6.79 -     9.06: 2
        9.06 -    11.32: 1
  Bond angle restraints: 6472
  Sorted by residual:
  angle pdb=" C   THR A 511 "
        pdb=" CA  THR A 511 "
        pdb=" CB  THR A 511 "
      ideal   model   delta    sigma   weight residual
     110.77  122.09  -11.32 1.67e+00 3.59e-01 4.60e+01
  angle pdb=" N   GLU A 812 "
        pdb=" CA  GLU A 812 "
        pdb=" C   GLU A 812 "
      ideal   model   delta    sigma   weight residual
     114.12  106.43    7.69 1.39e+00 5.18e-01 3.06e+01
  angle pdb=" C   LEU A 645 "
        pdb=" N   LEU A 646 "
        pdb=" CA  LEU A 646 "
      ideal   model   delta    sigma   weight residual
     122.73  115.00    7.73 1.61e+00 3.86e-01 2.31e+01
  angle pdb=" CA  GLN A 515 "
        pdb=" C   GLN A 515 "
        pdb=" O   GLN A 515 "
      ideal   model   delta    sigma   weight residual
     121.28  115.81    5.47 1.18e+00 7.18e-01 2.15e+01
  angle pdb=" N   LEU A 751 "
        pdb=" CA  LEU A 751 "
        pdb=" C   LEU A 751 "
      ideal   model   delta    sigma   weight residual
     113.18  107.60    5.58 1.33e+00 5.65e-01 1.76e+01
  ... (remaining 6467 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.25: 2709
       21.25 -    42.50: 153
       42.50 -    63.76: 33
       63.76 -    85.01: 7
       85.01 -   106.26: 5
  Dihedral angle restraints: 2907
    sinusoidal: 1176
      harmonic: 1731
  Sorted by residual:
  dihedral pdb=" CA  PHE A 715 "
           pdb=" C   PHE A 715 "
           pdb=" N   PRO A 716 "
           pdb=" CA  PRO A 716 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -38.08   38.08     0      5.00e+00 4.00e-02 5.80e+01
  dihedral pdb=" CA  TYR C  95 "
           pdb=" C   TYR C  95 "
           pdb=" N   PRO C  96 "
           pdb=" CA  PRO C  96 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   31.99  -31.99     0      5.00e+00 4.00e-02 4.09e+01
  dihedral pdb=" C   THR A 511 "
           pdb=" N   THR A 511 "
           pdb=" CA  THR A 511 "
           pdb=" CB  THR A 511 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -134.78   12.78     0      2.50e+00 1.60e-01 2.61e+01
  ... (remaining 2904 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 435
       0.084 -    0.167: 261
       0.167 -    0.250: 44
       0.250 -    0.334: 2
       0.334 -    0.417: 1
  Chirality restraints: 743
  Sorted by residual:
  chirality pdb=" C1  BMA E   3 "
            pdb=" O4  NAG E   2 "
            pdb=" C2  BMA E   3 "
            pdb=" O5  BMA E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.22   -0.18 2.00e-02 2.50e+03 8.11e+01
  chirality pdb=" C1  NAG E   2 "
            pdb=" O4  NAG E   1 "
            pdb=" C2  NAG E   2 "
            pdb=" O5  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.33   -0.07 2.00e-02 2.50e+03 1.16e+01
  chirality pdb=" C1  NAG A 901 "
            pdb=" ND2 ASN A 843 "
            pdb=" C2  NAG A 901 "
            pdb=" O5  NAG A 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.98   -0.42 2.00e-01 2.50e+01 4.34e+00
  ... (remaining 740 not shown)

  Planarity restraints: 827
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 901 "    0.116 2.00e-02 2.50e+03   9.66e-02 1.17e+02
        pdb=" C7  NAG A 901 "   -0.033 2.00e-02 2.50e+03
        pdb=" C8  NAG A 901 "    0.087 2.00e-02 2.50e+03
        pdb=" N2  NAG A 901 "   -0.155 2.00e-02 2.50e+03
        pdb=" O7  NAG A 901 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG E   2 "    0.044 2.00e-02 2.50e+03   3.61e-02 1.63e+01
        pdb=" C7  NAG E   2 "   -0.012 2.00e-02 2.50e+03
        pdb=" C8  NAG E   2 "    0.033 2.00e-02 2.50e+03
        pdb=" N2  NAG E   2 "   -0.057 2.00e-02 2.50e+03
        pdb=" O7  NAG E   2 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG E   1 "    0.042 2.00e-02 2.50e+03   3.47e-02 1.50e+01
        pdb=" C7  NAG E   1 "   -0.014 2.00e-02 2.50e+03
        pdb=" C8  NAG E   1 "    0.033 2.00e-02 2.50e+03
        pdb=" N2  NAG E   1 "   -0.055 2.00e-02 2.50e+03
        pdb=" O7  NAG E   1 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 824 not shown)

  Histogram of nonbonded interaction distances:
        2.50 -     2.98: 2411
        2.98 -     3.46: 4319
        3.46 -     3.94: 7753
        3.94 -     4.42: 8548
        4.42 -     4.90: 13639
  Nonbonded interactions: 36670
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 596 "
            pdb=" OD1 ASP A 596 "
     model   vdw
     2.503 3.040
  nonbonded pdb=" O   GLN C  80 "
            pdb=" N   GLU C  82 "
     model   vdw
     2.529 3.120
  nonbonded pdb=" OD1 ASP A 615 "
            pdb=" N   ARG A 619 "
     model   vdw
     2.547 3.120
  nonbonded pdb=" O   LEU A 601 "
            pdb=" OE1 GLN A 605 "
     model   vdw
     2.550 3.040
  nonbonded pdb=" N   PHE A 509 "
            pdb=" O   PHE A 509 "
     model   vdw
     2.571 2.496
  ... (remaining 36665 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             13.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     18.040
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6751
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      :  0.012   0.049   4762  Z= 0.792
  Angle     :  1.487  11.324   6472  Z= 1.100
  Chirality :  0.094   0.417    743
  Planarity :  0.006   0.097    825
  Dihedral  : 14.581 106.262   1775
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  9.35 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  :  7.87 %
    Favored  : 88.58 %
  Cbeta Deviations :  0.18 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    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: -3.01 (0.32), residues: 588
  helix:  0.12 (0.45), residues: 124
  sheet: -2.45 (0.34), residues: 195
  loop : -2.62 (0.33), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 554 
 HIS   0.004   0.001   HIS A 846 
 PHE   0.015   0.002   PHE A 745 
 TYR   0.017   0.002   TYR D  36 
 ARG   0.003   0.000   ARG C  62 

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 207
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  531 TYR cc_start: 0.4269 (t80) cc_final: 0.4017 (t80)
REVERT: A  554 TRP cc_start: 0.7629 (p90) cc_final: 0.7172 (p90)
REVERT: A  573 ARG cc_start: 0.7588 (mtm-85) cc_final: 0.7294 (mtm-85)
REVERT: A  634 TYR cc_start: 0.7787 (t80) cc_final: 0.7355 (t80)
REVERT: A  688 ASP cc_start: 0.8574 (t0) cc_final: 0.7996 (m-30)
REVERT: A  701 VAL cc_start: 0.9408 (t) cc_final: 0.8988 (p)
REVERT: A  763 LYS cc_start: 0.7409 (ttpt) cc_final: 0.7140 (ttmm)
REVERT: A  782 ILE cc_start: 0.8420 (tp) cc_final: 0.8198 (tt)
REVERT: A  790 PHE cc_start: 0.8482 (m-80) cc_final: 0.7743 (m-10)
REVERT: B  860 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8145 (mm)
REVERT: B  865 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6758 (mm-30)
REVERT: C   24 CYS cc_start: 0.5699 (t) cc_final: 0.5046 (t)
REVERT: C   34 VAL cc_start: 0.7955 (OUTLIER) cc_final: 0.7680 (m)
REVERT: C   36 TRP cc_start: 0.8500 (m100) cc_final: 0.8203 (m100)
REVERT: C   48 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8368 (mm)
REVERT: C   83 ASP cc_start: 0.7748 (t70) cc_final: 0.7469 (t70)
REVERT: C   94 GLN cc_start: 0.7723 (pp30) cc_final: 0.6748 (pp30)
REVERT: C  104 LYS cc_start: 0.7498 (mtpt) cc_final: 0.6934 (mtpp)
REVERT: D   39 TRP cc_start: 0.7896 (m100) cc_final: 0.7251 (m100)
REVERT: D   40 VAL cc_start: 0.7922 (t) cc_final: 0.7679 (m)
REVERT: D   42 GLN cc_start: 0.7972 (tt0) cc_final: 0.7288 (tt0)
REVERT: D   48 LEU cc_start: 0.6942 (mt) cc_final: 0.5852 (mt)
REVERT: D   81 THR cc_start: 0.6707 (p) cc_final: 0.6246 (p)
REVERT: D   83 TYR cc_start: 0.7883 (m-80) cc_final: 0.7276 (m-80)
REVERT: D   87 ASN cc_start: 0.8501 (m-40) cc_final: 0.8171 (m110)
REVERT: D   96 VAL cc_start: 0.7433 (t) cc_final: 0.7205 (p)
REVERT: D   98 TYR cc_start: 0.6608 (m-80) cc_final: 0.6064 (m-80)
REVERT: D  101 ARG cc_start: 0.7492 (tmm160) cc_final: 0.5878 (tmm-80)
REVERT: D  107 TRP cc_start: 0.6382 (t60) cc_final: 0.6074 (t60)
  outliers start: 18
  outliers final: 4
  residues processed: 217
  average time/residue: 0.1944
  time to fit residues: 51.2679
Evaluate side-chains
  144 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 137
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  540 TRP
Chi-restraints excluded: chain A residue  550 CYS
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  817 ASN
Chi-restraints excluded: chain B residue  860 LEU
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   48 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 15 optimal weight:    0.1980
   chunk 29 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 662 GLN
A 773 HIS
C  94 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.126184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.112454 restraints weight = 12209.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.117018 restraints weight = 10651.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.119733 restraints weight = 4588.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.3409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4762  Z= 0.233
  Angle     :  0.681   7.163   6472  Z= 0.354
  Chirality :  0.044   0.180    743
  Planarity :  0.005   0.046    825
  Dihedral  :  8.510  79.781    737
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 15.55 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.34), residues: 588
  helix:  1.83 (0.43), residues: 129
  sheet: -2.10 (0.34), residues: 189
  loop : -1.40 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 554 
 HIS   0.003   0.001   HIS A 773 
 PHE   0.019   0.002   PHE A 745 
 TYR   0.029   0.002   TYR C  56 
 ARG   0.008   0.001   ARG A 593 

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  688 ASP cc_start: 0.8259 (t0) cc_final: 0.7926 (m-30)
REVERT: A  743 VAL cc_start: 0.9618 (t) cc_final: 0.9363 (m)
REVERT: A  790 PHE cc_start: 0.7667 (m-80) cc_final: 0.7410 (m-80)
REVERT: B  865 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7172 (mm-30)
REVERT: C   36 TRP cc_start: 0.9295 (m100) cc_final: 0.8387 (m100)
REVERT: C   90 GLN cc_start: 0.9355 (tm-30) cc_final: 0.8605 (tm-30)
REVERT: C   94 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7598 (pp30)
REVERT: C  104 LYS cc_start: 0.7455 (mtpt) cc_final: 0.7224 (mtpp)
REVERT: D   39 TRP cc_start: 0.8141 (m100) cc_final: 0.7798 (m100)
REVERT: D   48 LEU cc_start: 0.8231 (mt) cc_final: 0.7837 (mt)
REVERT: D   87 ASN cc_start: 0.8083 (m-40) cc_final: 0.7583 (m-40)
REVERT: D   92 GLU cc_start: 0.8440 (mp0) cc_final: 0.8191 (mp0)
REVERT: D   93 ASP cc_start: 0.8042 (m-30) cc_final: 0.7795 (m-30)
REVERT: D  101 ARG cc_start: 0.7680 (tmm160) cc_final: 0.6850 (tmm-80)
  outliers start: 24
  outliers final: 16
  residues processed: 146
  average time/residue: 0.1819
  time to fit residues: 32.9644
Evaluate side-chains
  122 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  540 TRP
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  658 THR
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain A residue  762 MET
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   94 GLN
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   63 TYR
Chi-restraints excluded: chain D residue  110 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 20 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0980
   chunk 23 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 644 ASN
A 671 HIS
C  94 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.122373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.108116 restraints weight = 12172.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.112805 restraints weight = 10741.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.115267 restraints weight = 4559.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.4183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   4762  Z= 0.227
  Angle     :  0.637   7.868   6472  Z= 0.333
  Chirality :  0.042   0.149    743
  Planarity :  0.005   0.047    825
  Dihedral  :  6.370  77.344    728
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 18.11 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    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: -1.04 (0.35), residues: 588
  helix:  2.65 (0.46), residues: 123
  sheet: -1.91 (0.35), residues: 184
  loop : -1.31 (0.37), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 554 
 HIS   0.003   0.001   HIS D 102 
 PHE   0.016   0.001   PHE A 745 
 TYR   0.032   0.002   TYR A 634 
 ARG   0.012   0.001   ARG A 593 

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 109
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
REVERT: A  592 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8846 (t)
REVERT: A  634 TYR cc_start: 0.8350 (t80) cc_final: 0.7744 (t80)
REVERT: A  638 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8121 (tpp)
REVERT: A  651 LEU cc_start: 0.8148 (pp) cc_final: 0.7881 (pp)
REVERT: A  688 ASP cc_start: 0.8237 (t0) cc_final: 0.7909 (m-30)
REVERT: A  715 PHE cc_start: 0.8819 (t80) cc_final: 0.8332 (t80)
REVERT: A  743 VAL cc_start: 0.9625 (t) cc_final: 0.9293 (m)
REVERT: A  790 PHE cc_start: 0.7780 (m-80) cc_final: 0.6946 (m-10)
REVERT: C   36 TRP cc_start: 0.9448 (m100) cc_final: 0.8529 (m100)
REVERT: C   90 GLN cc_start: 0.9396 (tm-30) cc_final: 0.8753 (tm-30)
REVERT: D   22 ARG cc_start: 0.7701 (ttt-90) cc_final: 0.7067 (mmm-85)
REVERT: D   39 TRP cc_start: 0.8619 (m100) cc_final: 0.8197 (m100)
REVERT: D   87 ASN cc_start: 0.8048 (m-40) cc_final: 0.7562 (m-40)
REVERT: D   92 GLU cc_start: 0.8398 (mp0) cc_final: 0.8108 (mp0)
REVERT: D   98 TYR cc_start: 0.8763 (m-80) cc_final: 0.8291 (m-80)
REVERT: D  101 ARG cc_start: 0.7904 (tmm160) cc_final: 0.7035 (tmm-80)
  outliers start: 25
  outliers final: 18
  residues processed: 124
  average time/residue: 0.1599
  time to fit residues: 25.4487
Evaluate side-chains
  115 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  540 TRP
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  627 ARG
Chi-restraints excluded: chain A residue  638 MET
Chi-restraints excluded: chain A residue  644 ASN
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  762 MET
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue   63 TYR
Chi-restraints excluded: chain D residue  110 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0270
   chunk 45 optimal weight:    0.2980
   chunk 55 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    1.0642

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

Flipped N/Q/H residues before XYZ refinement:
A 644 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.119176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.104180 restraints weight = 12344.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.109237 restraints weight = 11686.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.111511 restraints weight = 4796.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.4867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4762  Z= 0.287
  Angle     :  0.655   8.419   6472  Z= 0.345
  Chirality :  0.042   0.154    743
  Planarity :  0.005   0.050    825
  Dihedral  :  6.062  74.937    728
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  5.91 %
    Allowed  : 18.70 %
    Favored  : 75.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    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: -1.01 (0.35), residues: 588
  helix:  2.71 (0.46), residues: 123
  sheet: -1.62 (0.35), residues: 188
  loop : -1.53 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 554 
 HIS   0.003   0.001   HIS D 102 
 PHE   0.016   0.002   PHE A 509 
 TYR   0.030   0.002   TYR A 754 
 ARG   0.012   0.001   ARG A 593 

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 103
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  634 TYR cc_start: 0.8419 (t80) cc_final: 0.8019 (t80)
REVERT: A  675 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7693 (mt-10)
REVERT: A  688 ASP cc_start: 0.8261 (t0) cc_final: 0.7916 (m-30)
REVERT: A  715 PHE cc_start: 0.8899 (t80) cc_final: 0.8443 (t80)
REVERT: A  790 PHE cc_start: 0.7871 (m-80) cc_final: 0.7434 (m-10)
REVERT: C   36 TRP cc_start: 0.9504 (m100) cc_final: 0.8541 (m100)
REVERT: C   90 GLN cc_start: 0.9394 (tm-30) cc_final: 0.8744 (tm-30)
REVERT: D   22 ARG cc_start: 0.7726 (ttt-90) cc_final: 0.7430 (mtp-110)
REVERT: D   54 ILE cc_start: 0.9202 (mt) cc_final: 0.8457 (tp)
REVERT: D   83 TYR cc_start: 0.8684 (m-80) cc_final: 0.8273 (m-80)
REVERT: D   92 GLU cc_start: 0.8233 (mp0) cc_final: 0.7940 (mp0)
REVERT: D  101 ARG cc_start: 0.8167 (tmm160) cc_final: 0.7243 (tmm-80)
  outliers start: 30
  outliers final: 22
  residues processed: 121
  average time/residue: 0.1559
  time to fit residues: 24.3273
Evaluate side-chains
  113 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  540 TRP
Chi-restraints excluded: chain A residue  627 ARG
Chi-restraints excluded: chain A residue  658 THR
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  762 MET
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue   63 TYR
Chi-restraints excluded: chain D residue   66 SER
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain D residue  102 HIS
Chi-restraints excluded: chain D residue  110 TYR
Chi-restraints excluded: chain D residue  121 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.9584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.118236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.103135 restraints weight = 12253.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.108263 restraints weight = 11581.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.109580 restraints weight = 4748.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.5225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4762  Z= 0.269
  Angle     :  0.641   8.693   6472  Z= 0.331
  Chirality :  0.042   0.142    743
  Planarity :  0.005   0.052    825
  Dihedral  :  5.861  72.938    728
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 20.47 %
    Favored  : 74.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    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: -0.97 (0.36), residues: 588
  helix:  2.91 (0.48), residues: 123
  sheet: -1.83 (0.35), residues: 189
  loop : -1.39 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 654 
 HIS   0.003   0.001   HIS D 102 
 PHE   0.014   0.001   PHE A 745 
 TYR   0.026   0.002   TYR C  56 
 ARG   0.003   0.000   ARG A 580 

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 99
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  634 TYR cc_start: 0.8617 (t80) cc_final: 0.8001 (t80)
REVERT: A  668 MET cc_start: 0.8692 (tpt) cc_final: 0.8417 (tpp)
REVERT: A  688 ASP cc_start: 0.8236 (t0) cc_final: 0.7921 (m-30)
REVERT: A  700 GLU cc_start: 0.8360 (tp30) cc_final: 0.7932 (tp30)
REVERT: A  715 PHE cc_start: 0.8911 (t80) cc_final: 0.8485 (t80)
REVERT: A  790 PHE cc_start: 0.7982 (m-80) cc_final: 0.7477 (m-10)
REVERT: C   36 TRP cc_start: 0.9524 (m100) cc_final: 0.8612 (m100)
REVERT: C   90 GLN cc_start: 0.9363 (tm-30) cc_final: 0.9046 (tm-30)
REVERT: D   22 ARG cc_start: 0.7705 (ttt-90) cc_final: 0.7480 (mtp-110)
REVERT: D   41 ARG cc_start: 0.8703 (ptt180) cc_final: 0.8198 (ptm160)
REVERT: D   54 ILE cc_start: 0.9288 (mt) cc_final: 0.8553 (tp)
REVERT: D   83 TYR cc_start: 0.8762 (m-80) cc_final: 0.8451 (m-80)
REVERT: D  101 ARG cc_start: 0.8294 (tmm160) cc_final: 0.7397 (tmm-80)
  outliers start: 28
  outliers final: 21
  residues processed: 118
  average time/residue: 0.1483
  time to fit residues: 22.7656
Evaluate side-chains
  114 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  540 TRP
Chi-restraints excluded: chain A residue  627 ARG
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  644 ASN
Chi-restraints excluded: chain A residue  658 THR
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  762 MET
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue   63 TYR
Chi-restraints excluded: chain D residue   66 SER
Chi-restraints excluded: chain D residue  110 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 22 optimal weight:    0.0470
   chunk 50 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 43 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.6678

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.119248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.104437 restraints weight = 12374.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.109521 restraints weight = 11406.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.111952 restraints weight = 4723.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.5478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4762  Z= 0.219
  Angle     :  0.636   9.145   6472  Z= 0.327
  Chirality :  0.042   0.148    743
  Planarity :  0.004   0.052    825
  Dihedral  :  5.664  69.921    728
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 22.64 %
    Favored  : 72.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    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 (0.36), residues: 588
  helix:  2.96 (0.47), residues: 123
  sheet: -1.56 (0.36), residues: 186
  loop : -1.51 (0.36), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 554 
 HIS   0.003   0.001   HIS D 102 
 PHE   0.012   0.001   PHE A 745 
 TYR   0.032   0.002   TYR A 754 
 ARG   0.002   0.000   ARG A 655 

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 99
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 TRP cc_start: 0.8662 (OUTLIER) cc_final: 0.8311 (p90)
REVERT: A  634 TYR cc_start: 0.8531 (t80) cc_final: 0.8105 (t80)
REVERT: A  675 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7601 (mt-10)
REVERT: A  688 ASP cc_start: 0.8099 (t0) cc_final: 0.7835 (m-30)
REVERT: A  700 GLU cc_start: 0.8305 (tp30) cc_final: 0.7876 (tp30)
REVERT: A  715 PHE cc_start: 0.8890 (t80) cc_final: 0.8433 (t80)
REVERT: A  790 PHE cc_start: 0.7889 (m-80) cc_final: 0.7491 (m-10)
REVERT: A  846 HIS cc_start: 0.8166 (m-70) cc_final: 0.7923 (m-70)
REVERT: C   36 TRP cc_start: 0.9512 (m100) cc_final: 0.8605 (m100)
REVERT: C   90 GLN cc_start: 0.9332 (tm-30) cc_final: 0.9015 (tm-30)
REVERT: D   22 ARG cc_start: 0.7693 (ttt-90) cc_final: 0.7490 (mtp-110)
REVERT: D   41 ARG cc_start: 0.8754 (ptt180) cc_final: 0.8379 (ptm160)
REVERT: D   54 ILE cc_start: 0.9285 (mt) cc_final: 0.8573 (tp)
REVERT: D   83 TYR cc_start: 0.8758 (m-80) cc_final: 0.8445 (m-80)
REVERT: D  101 ARG cc_start: 0.8349 (tmm160) cc_final: 0.7481 (tmm-80)
  outliers start: 26
  outliers final: 18
  residues processed: 112
  average time/residue: 0.1660
  time to fit residues: 23.7737
Evaluate side-chains
  114 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  526 ILE
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  540 TRP
Chi-restraints excluded: chain A residue  554 TRP
Chi-restraints excluded: chain A residue  627 ARG
Chi-restraints excluded: chain A residue  658 THR
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  762 MET
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   63 TYR
Chi-restraints excluded: chain D residue  110 TYR
Chi-restraints excluded: chain D residue  121 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 54 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 773 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.117945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.102610 restraints weight = 12260.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.107886 restraints weight = 11477.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.110041 restraints weight = 4701.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.5665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   4762  Z= 0.260
  Angle     :  0.648   7.778   6472  Z= 0.334
  Chirality :  0.042   0.146    743
  Planarity :  0.004   0.052    825
  Dihedral  :  5.675  67.858    728
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 21.65 %
    Favored  : 72.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    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: -0.92 (0.36), residues: 588
  helix:  2.90 (0.47), residues: 123
  sheet: -1.72 (0.35), residues: 197
  loop : -1.37 (0.38), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 654 
 HIS   0.003   0.001   HIS D 102 
 PHE   0.012   0.001   PHE A 509 
 TYR   0.029   0.002   TYR C  56 
 ARG   0.002   0.000   ARG D  41 

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 96
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  540 TRP cc_start: 0.4524 (OUTLIER) cc_final: 0.4178 (m100)
REVERT: A  554 TRP cc_start: 0.8651 (OUTLIER) cc_final: 0.8293 (p90)
REVERT: A  634 TYR cc_start: 0.8579 (t80) cc_final: 0.8004 (t80)
REVERT: A  638 MET cc_start: 0.8384 (tpp) cc_final: 0.7964 (ttm)
REVERT: A  675 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7640 (mt-10)
REVERT: A  688 ASP cc_start: 0.8088 (t0) cc_final: 0.7822 (m-30)
REVERT: A  700 GLU cc_start: 0.8289 (tp30) cc_final: 0.7857 (tp30)
REVERT: A  715 PHE cc_start: 0.8961 (t80) cc_final: 0.8537 (t80)
REVERT: A  790 PHE cc_start: 0.7990 (m-80) cc_final: 0.7577 (m-10)
REVERT: A  846 HIS cc_start: 0.8200 (m-70) cc_final: 0.7990 (m-70)
REVERT: B  861 MET cc_start: 0.6812 (OUTLIER) cc_final: 0.6292 (tmm)
REVERT: C   28 GLN cc_start: 0.9161 (tm-30) cc_final: 0.8930 (tm-30)
REVERT: C   90 GLN cc_start: 0.9307 (tm-30) cc_final: 0.8717 (tm-30)
REVERT: D   22 ARG cc_start: 0.7712 (ttt-90) cc_final: 0.7498 (mtp-110)
REVERT: D   41 ARG cc_start: 0.8834 (ptt180) cc_final: 0.8555 (ptm160)
REVERT: D   54 ILE cc_start: 0.9340 (mt) cc_final: 0.8638 (tp)
REVERT: D  101 ARG cc_start: 0.8446 (tmm160) cc_final: 0.7565 (tmm-80)
  outliers start: 31
  outliers final: 25
  residues processed: 115
  average time/residue: 0.1725
  time to fit residues: 26.2110
Evaluate side-chains
  120 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 92
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  526 ILE
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  540 TRP
Chi-restraints excluded: chain A residue  554 TRP
Chi-restraints excluded: chain A residue  627 ARG
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  644 ASN
Chi-restraints excluded: chain A residue  658 THR
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  697 ILE
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  762 MET
Chi-restraints excluded: chain A residue  810 SER
Chi-restraints excluded: chain A residue  817 ASN
Chi-restraints excluded: chain B residue  861 MET
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   63 TYR
Chi-restraints excluded: chain D residue  110 TYR
Chi-restraints excluded: chain D residue  121 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 48 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
C   4 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.117796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.102239 restraints weight = 12372.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.107622 restraints weight = 11843.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.109538 restraints weight = 4947.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.5855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   4762  Z= 0.251
  Angle     :  0.639   8.204   6472  Z= 0.332
  Chirality :  0.042   0.149    743
  Planarity :  0.004   0.052    825
  Dihedral  :  5.683  69.320    728
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 23.82 %
    Favored  : 70.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    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: -0.94 (0.36), residues: 588
  helix:  2.87 (0.47), residues: 123
  sheet: -1.73 (0.35), residues: 197
  loop : -1.37 (0.38), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 654 
 HIS   0.003   0.001   HIS D 102 
 PHE   0.011   0.001   PHE A 745 
 TYR   0.029   0.002   TYR C  56 
 ARG   0.002   0.000   ARG A 504 

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 92
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 TRP cc_start: 0.8642 (OUTLIER) cc_final: 0.8335 (p90)
REVERT: A  634 TYR cc_start: 0.8561 (t80) cc_final: 0.8021 (t80)
REVERT: A  675 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7646 (mt-10)
REVERT: A  688 ASP cc_start: 0.8085 (t0) cc_final: 0.7817 (m-30)
REVERT: A  700 GLU cc_start: 0.8295 (tp30) cc_final: 0.7874 (tp30)
REVERT: A  715 PHE cc_start: 0.8978 (t80) cc_final: 0.8538 (t80)
REVERT: A  790 PHE cc_start: 0.8036 (m-80) cc_final: 0.7605 (m-10)
REVERT: B  861 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.6594 (tmm)
REVERT: C   90 GLN cc_start: 0.9323 (tm-30) cc_final: 0.9080 (tm-30)
REVERT: D   54 ILE cc_start: 0.9360 (mt) cc_final: 0.8685 (tp)
REVERT: D  101 ARG cc_start: 0.8469 (tmm160) cc_final: 0.7605 (tmm-80)
  outliers start: 28
  outliers final: 23
  residues processed: 109
  average time/residue: 0.1574
  time to fit residues: 22.2460
Evaluate side-chains
  111 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 86
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  526 ILE
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  540 TRP
Chi-restraints excluded: chain A residue  554 TRP
Chi-restraints excluded: chain A residue  627 ARG
Chi-restraints excluded: chain A residue  644 ASN
Chi-restraints excluded: chain A residue  658 THR
Chi-restraints excluded: chain A residue  697 ILE
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  762 MET
Chi-restraints excluded: chain A residue  810 SER
Chi-restraints excluded: chain A residue  817 ASN
Chi-restraints excluded: chain B residue  861 MET
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   63 TYR
Chi-restraints excluded: chain D residue   66 SER
Chi-restraints excluded: chain D residue  110 TYR
Chi-restraints excluded: chain D residue  121 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 53 optimal weight:    0.0770
   chunk 33 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 35 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0770
   chunk 18 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
C   4 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.119462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.104401 restraints weight = 12235.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.109590 restraints weight = 11076.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.111715 restraints weight = 4560.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.5983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4762  Z= 0.195
  Angle     :  0.619   7.993   6472  Z= 0.319
  Chirality :  0.042   0.143    743
  Planarity :  0.004   0.053    825
  Dihedral  :  5.431  63.720    728
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 23.82 %
    Favored  : 71.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    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: -0.87 (0.36), residues: 588
  helix:  2.93 (0.47), residues: 123
  sheet: -1.61 (0.35), residues: 186
  loop : -1.43 (0.37), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 554 
 HIS   0.003   0.001   HIS D 102 
 PHE   0.011   0.001   PHE A 745 
 TYR   0.030   0.002   TYR C  56 
 ARG   0.002   0.000   ARG D  22 

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 90
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 TRP cc_start: 0.8627 (OUTLIER) cc_final: 0.8381 (p90)
REVERT: A  634 TYR cc_start: 0.8458 (t80) cc_final: 0.8038 (t80)
REVERT: A  668 MET cc_start: 0.8666 (tpt) cc_final: 0.8377 (tpp)
REVERT: A  675 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7641 (mt-10)
REVERT: A  688 ASP cc_start: 0.8071 (t0) cc_final: 0.7820 (m-30)
REVERT: A  700 GLU cc_start: 0.8244 (tp30) cc_final: 0.7809 (tp30)
REVERT: A  715 PHE cc_start: 0.8922 (t80) cc_final: 0.8514 (t80)
REVERT: A  790 PHE cc_start: 0.7983 (m-80) cc_final: 0.7565 (m-10)
REVERT: C   28 GLN cc_start: 0.9158 (tm-30) cc_final: 0.8875 (tm-30)
REVERT: C   90 GLN cc_start: 0.9269 (tm-30) cc_final: 0.9011 (tm-30)
REVERT: D   41 ARG cc_start: 0.9043 (ptt180) cc_final: 0.8552 (ptm-80)
REVERT: D   54 ILE cc_start: 0.9334 (mt) cc_final: 0.8681 (tp)
  outliers start: 26
  outliers final: 22
  residues processed: 106
  average time/residue: 0.1554
  time to fit residues: 21.3425
Evaluate side-chains
  108 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  526 ILE
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  540 TRP
Chi-restraints excluded: chain A residue  554 TRP
Chi-restraints excluded: chain A residue  627 ARG
Chi-restraints excluded: chain A residue  644 ASN
Chi-restraints excluded: chain A residue  697 ILE
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  762 MET
Chi-restraints excluded: chain A residue  794 VAL
Chi-restraints excluded: chain A residue  810 SER
Chi-restraints excluded: chain A residue  817 ASN
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   63 TYR
Chi-restraints excluded: chain D residue  110 TYR
Chi-restraints excluded: chain D residue  121 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 0 optimal weight:    7.9990
   chunk 40 optimal weight:    0.0030
   chunk 15 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.5790

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

Flipped N/Q/H residues before XYZ refinement:
C   4 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.119460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.104489 restraints weight = 12164.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.109594 restraints weight = 11122.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.111616 restraints weight = 4614.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.6124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4762  Z= 0.208
  Angle     :  0.641   8.094   6472  Z= 0.327
  Chirality :  0.042   0.148    743
  Planarity :  0.004   0.052    825
  Dihedral  :  5.504  64.708    728
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 24.80 %
    Favored  : 70.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    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: -0.80 (0.36), residues: 588
  helix:  3.01 (0.47), residues: 123
  sheet: -1.56 (0.35), residues: 184
  loop : -1.41 (0.37), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 554 
 HIS   0.002   0.001   HIS D 102 
 PHE   0.011   0.001   PHE A 745 
 TYR   0.027   0.002   TYR C  56 
 ARG   0.002   0.000   ARG D  41 

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 TRP cc_start: 0.8603 (OUTLIER) cc_final: 0.8359 (p90)
REVERT: A  634 TYR cc_start: 0.8440 (t80) cc_final: 0.8014 (t80)
REVERT: A  675 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7621 (mt-10)
REVERT: A  688 ASP cc_start: 0.8003 (t0) cc_final: 0.7801 (m-30)
REVERT: A  700 GLU cc_start: 0.8215 (tp30) cc_final: 0.7810 (tp30)
REVERT: A  715 PHE cc_start: 0.8942 (t80) cc_final: 0.8521 (t80)
REVERT: A  790 PHE cc_start: 0.7994 (m-80) cc_final: 0.7643 (m-80)
REVERT: C   28 GLN cc_start: 0.9140 (tm-30) cc_final: 0.8849 (tm-30)
REVERT: C   90 GLN cc_start: 0.9227 (tm-30) cc_final: 0.9000 (tm-30)
REVERT: D   41 ARG cc_start: 0.9047 (ptt180) cc_final: 0.8659 (ptm160)
REVERT: D   54 ILE cc_start: 0.9335 (mt) cc_final: 0.8704 (tp)
  outliers start: 23
  outliers final: 21
  residues processed: 100
  average time/residue: 0.1931
  time to fit residues: 25.1277
Evaluate side-chains
  106 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  526 ILE
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  540 TRP
Chi-restraints excluded: chain A residue  554 TRP
Chi-restraints excluded: chain A residue  627 ARG
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  644 ASN
Chi-restraints excluded: chain A residue  697 ILE
Chi-restraints excluded: chain A residue  762 MET
Chi-restraints excluded: chain A residue  794 VAL
Chi-restraints excluded: chain A residue  810 SER
Chi-restraints excluded: chain A residue  817 ASN
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   63 TYR
Chi-restraints excluded: chain D residue  110 TYR
Chi-restraints excluded: chain D residue  121 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 41 optimal weight:    0.2980
   chunk 5 optimal weight:    0.0980
   chunk 6 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   chunk 0 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
C   4 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.119655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.104674 restraints weight = 12225.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.109852 restraints weight = 11080.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.112031 restraints weight = 4550.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.6221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4762  Z= 0.206
  Angle     :  0.629   7.876   6472  Z= 0.322
  Chirality :  0.042   0.149    743
  Planarity :  0.004   0.053    825
  Dihedral  :  5.468  64.635    728
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 24.61 %
    Favored  : 71.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    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: -0.78 (0.36), residues: 588
  helix:  3.04 (0.47), residues: 123
  sheet: -1.60 (0.35), residues: 186
  loop : -1.36 (0.38), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 554 
 HIS   0.003   0.001   HIS D 102 
 PHE   0.010   0.001   PHE A 745 
 TYR   0.026   0.002   TYR C  56 
 ARG   0.003   0.000   ARG D  41 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2857.87 seconds
wall clock time: 51 minutes 25.73 seconds (3085.73 seconds total)