Starting phenix.real_space_refine
on Thu Jun  5 13:27:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7to0_26025/06_2025/7to0_26025.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7to0_26025/06_2025/7to0_26025.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7to0_26025/06_2025/7to0_26025.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7to0_26025/06_2025/7to0_26025.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7to0_26025/06_2025/7to0_26025.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7to0_26025/06_2025/7to0_26025.cif"
  }
  resolution = 3.5
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      23      5.49       5
     S      33      5.16       5
     C    3727      2.51       5
     N    1027      2.21       5
     O    1178      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5989
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5479
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 682, 5479
          Classifications: {'peptide': 682}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 28, 'TRANS': 653}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "B"
      Number of atoms: 256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 256
          Classifications: {'RNA': 12}
          Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 5}
          Link IDs: {'rna3p': 11}
    Chain: "C"
      Number of atoms: 253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 253
          Classifications: {'RNA': 12}
          Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 7}
          Link IDs: {'rna3p': 11}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   4555  SG  CYS A 810      22.813  42.767  28.664  1.00 39.79           S
  ATOM   4994  SG  CYS A 864      21.545  40.805  25.017  1.00 55.33           S
  ATOM   5033  SG  CYS A 869      23.244  44.391  24.842  1.00 53.89           S

  Time building chain proxies: 4.08, per 1000 atoms: 0.68
  Number of scatterers: 5989
  At special positions: 0
  Unit cell: (97.188, 85.44, 77.964, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      33     16.00
     P      23     15.00
     O    1178      8.00
     N    1027      7.00
     C    3727      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.42
  Conformation dependent library (CDL) restraints added in 696.9 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1001 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 869 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 864 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 810 "


  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1300

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 6 sheets defined
      47.5% alpha, 6.9% beta
      9 base pairs and 19 stacking pairs defined.
    Time for finding SS restraints: 1.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 244 through 252
      removed outlier: 3.693A  pdb=" N   LEU A 248 " --> pdb=" O   ARG A 244 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLU A 249 " --> pdb=" O   ASN A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 282
      removed outlier: 4.041A  pdb=" N   LYS A 270 " --> pdb=" O   THR A 266 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   THR A 271 " --> pdb=" O   GLY A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 315
    Processing helix  chain 'A' and resid 333 through 340
    Processing helix  chain 'A' and resid 347 through 358
      removed outlier: 3.603A  pdb=" N   GLY A 358 " --> pdb=" O   ASN A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 377
    Processing helix  chain 'A' and resid 381 through 396
    Processing helix  chain 'A' and resid 419 through 434
      removed outlier: 3.697A  pdb=" N   ASP A 425 " --> pdb=" O   ASP A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 450
    Processing helix  chain 'A' and resid 469 through 488
      removed outlier: 3.909A  pdb=" N   TYR A 473 " --> pdb=" O   ASP A 469 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   ILE A 474 " --> pdb=" O   LYS A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 497
      removed outlier: 4.150A  pdb=" N   SER A 497 " --> pdb=" O   GLU A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 521
      removed outlier: 3.626A  pdb=" N   VAL A 514 " --> pdb=" O   GLU A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 558
      removed outlier: 3.591A  pdb=" N   HIS A 557 " --> pdb=" O   ILE A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 576
    Processing helix  chain 'A' and resid 580 through 603
      removed outlier: 3.689A  pdb=" N   ASP A 585 " --> pdb=" O   GLU A 581 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LEU A 586 " --> pdb=" O   ILE A 582 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   LYS A 593 " --> pdb=" O   ARG A 589 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   GLN A 595 " --> pdb=" O   GLU A 591 " (cutoff:3.500A)
      removed outlier: 5.419A  pdb=" N   GLU A 596 " --> pdb=" O   GLU A 592 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ASP A 603 " --> pdb=" O   SER A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 625
    Processing helix  chain 'A' and resid 636 through 649
      removed outlier: 3.783A  pdb=" N   ASP A 641 " --> pdb=" O   ARG A 637 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ALA A 642 " --> pdb=" O   ALA A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 674 through 684
      removed outlier: 3.631A  pdb=" N   ILE A 681 " --> pdb=" O   ALA A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 701
    Processing helix  chain 'A' and resid 720 through 729
    Processing helix  chain 'A' and resid 744 through 769
      removed outlier: 3.760A  pdb=" N   ILE A 748 " --> pdb=" O   ASN A 744 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 794
    Processing sheet with id=AA1, first strand: chain 'A' and resid 294 through 296
    Processing sheet with id=AA2, first strand: chain 'A' and resid 321 through 322
    Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 460
      removed outlier: 6.842A  pdb=" N   GLN A 457 " --> pdb=" O   CYS A 738 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   LEU A 740 " --> pdb=" O   GLN A 457 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   PHE A 459 " --> pdb=" O   LEU A 740 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 819
      removed outlier: 7.293A  pdb=" N   LEU A 816 " --> pdb=" O   CYS A 810 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   CYS A 810 " --> pdb=" O   LEU A 816 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   CYS A 818 " --> pdb=" O   LEU A 808 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 831 through 832
    Processing sheet with id=AA6, first strand: chain 'A' and resid 842 through 846
      removed outlier: 6.652A  pdb=" N   LYS A 858 " --> pdb=" O   LYS A 878 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   LYS A 878 " --> pdb=" O   LYS A 858 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ILE A 862 " --> pdb=" O   GLY A 874 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   GLY A 874 " --> pdb=" O   ILE A 862 " (cutoff:3.500A)

    243 hydrogen bonds defined for protein.
    708 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      23 hydrogen bonds
      46 hydrogen bond angles
      0 basepair planarities
      9 basepair parallelities
      19 stacking parallelities
  Total time for adding SS restraints: 1.82

  Time building geometry restraints manager: 1.70 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1640
        1.33 -     1.45: 1039
        1.45 -     1.58: 3388
        1.58 -     1.70: 45
        1.70 -     1.82: 46
  Bond restraints: 6158
  Sorted by residual:
  bond pdb=" N   VAL A 452 "
       pdb=" CA  VAL A 452 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 9.10e-03 1.21e+04 1.51e+01
  bond pdb=" CA  SER A 891 "
       pdb=" CB  SER A 891 "
    ideal  model  delta    sigma   weight residual
    1.524  1.486  0.037 1.31e-02 5.83e+03 8.09e+00
  bond pdb=" N   ILE A 489 "
       pdb=" CA  ILE A 489 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.22e-02 6.72e+03 8.02e+00
  bond pdb=" N   ILE A 262 "
       pdb=" CA  ILE A 262 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.95e+00
  bond pdb=" N   VAL A 414 "
       pdb=" CA  VAL A 414 "
    ideal  model  delta    sigma   weight residual
    1.452  1.485 -0.033 1.18e-02 7.18e+03 7.89e+00
  ... (remaining 6153 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 7073
        1.69 -     3.38: 1308
        3.38 -     5.07: 36
        5.07 -     6.77: 3
        6.77 -     8.46: 1
  Bond angle restraints: 8421
  Sorted by residual:
  angle pdb=" C   THR A 347 "
        pdb=" N   PRO A 348 "
        pdb=" CA  PRO A 348 "
      ideal   model   delta    sigma   weight residual
     119.47  127.93   -8.46 1.16e+00 7.43e-01 5.32e+01
  angle pdb=" N   VAL A 414 "
        pdb=" CA  VAL A 414 "
        pdb=" C   VAL A 414 "
      ideal   model   delta    sigma   weight residual
     112.96  107.77    5.19 1.00e+00 1.00e+00 2.69e+01
  angle pdb=" N   ARG A 316 "
        pdb=" CA  ARG A 316 "
        pdb=" C   ARG A 316 "
      ideal   model   delta    sigma   weight residual
     114.75  109.47    5.28 1.26e+00 6.30e-01 1.75e+01
  angle pdb=" C   THR A 347 "
        pdb=" CA  THR A 347 "
        pdb=" CB  THR A 347 "
      ideal   model   delta    sigma   weight residual
     109.31  113.67   -4.36 1.23e+00 6.61e-01 1.26e+01
  angle pdb=" N   THR A 347 "
        pdb=" CA  THR A 347 "
        pdb=" C   THR A 347 "
      ideal   model   delta    sigma   weight residual
     109.62  104.76    4.86 1.45e+00 4.76e-01 1.13e+01
  ... (remaining 8416 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.65: 3347
       17.65 -    35.30: 309
       35.30 -    52.95: 94
       52.95 -    70.60: 35
       70.60 -    88.25: 14
  Dihedral angle restraints: 3799
    sinusoidal: 1797
      harmonic: 2002
  Sorted by residual:
  dihedral pdb=" O4'   G B  12 "
           pdb=" C1'   G B  12 "
           pdb=" N9    G B  12 "
           pdb=" C4    G B  12 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -155.28   49.28     1      1.70e+01 3.46e-03 1.15e+01
  dihedral pdb=" CA  GLY A 659 "
           pdb=" C   GLY A 659 "
           pdb=" N   ILE A 660 "
           pdb=" CA  ILE A 660 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.49  -16.51     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CA  ASP A 822 "
           pdb=" CB  ASP A 822 "
           pdb=" CG  ASP A 822 "
           pdb=" OD1 ASP A 822 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.56   55.56     1      2.00e+01 2.50e-03 1.04e+01
  ... (remaining 3796 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 543
       0.058 -    0.116: 327
       0.116 -    0.174: 84
       0.174 -    0.232: 1
       0.232 -    0.290: 1
  Chirality restraints: 956
  Sorted by residual:
  chirality pdb=" CB  VAL A 442 "
            pdb=" CA  VAL A 442 "
            pdb=" CG1 VAL A 442 "
            pdb=" CG2 VAL A 442 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.10e+00
  chirality pdb=" CB  VAL A 453 "
            pdb=" CA  VAL A 453 "
            pdb=" CG1 VAL A 453 "
            pdb=" CG2 VAL A 453 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CB  ILE A 780 "
            pdb=" CA  ILE A 780 "
            pdb=" CG1 ILE A 780 "
            pdb=" CG2 ILE A 780 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 6.87e-01
  ... (remaining 953 not shown)

  Planarity restraints: 994
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B   9 "   -0.025 2.00e-02 2.50e+03   1.30e-02 5.09e+00
        pdb=" N9    G B   9 "    0.025 2.00e-02 2.50e+03
        pdb=" C8    G B   9 "   -0.005 2.00e-02 2.50e+03
        pdb=" N7    G B   9 "   -0.011 2.00e-02 2.50e+03
        pdb=" C5    G B   9 "    0.009 2.00e-02 2.50e+03
        pdb=" C6    G B   9 "   -0.001 2.00e-02 2.50e+03
        pdb=" O6    G B   9 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1    G B   9 "   -0.004 2.00e-02 2.50e+03
        pdb=" C2    G B   9 "    0.003 2.00e-02 2.50e+03
        pdb=" N2    G B   9 "   -0.012 2.00e-02 2.50e+03
        pdb=" N3    G B   9 "    0.011 2.00e-02 2.50e+03
        pdb=" C4    G B   9 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 566 "    0.026 2.00e-02 2.50e+03   1.45e-02 4.18e+00
        pdb=" CG  TYR A 566 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 566 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 566 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 566 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 566 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 566 "    0.014 2.00e-02 2.50e+03
        pdb=" OH  TYR A 566 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B   7 "   -0.024 2.00e-02 2.50e+03   1.03e-02 2.92e+00
        pdb=" N9    A B   7 "    0.018 2.00e-02 2.50e+03
        pdb=" C8    A B   7 "    0.003 2.00e-02 2.50e+03
        pdb=" N7    A B   7 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    A B   7 "    0.005 2.00e-02 2.50e+03
        pdb=" C6    A B   7 "    0.004 2.00e-02 2.50e+03
        pdb=" N6    A B   7 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1    A B   7 "   -0.008 2.00e-02 2.50e+03
        pdb=" C2    A B   7 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    A B   7 "    0.006 2.00e-02 2.50e+03
        pdb=" C4    A B   7 "    0.006 2.00e-02 2.50e+03
  ... (remaining 991 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1243
        2.81 -     3.33: 5567
        3.33 -     3.86: 9870
        3.86 -     4.38: 11248
        4.38 -     4.90: 19078
  Nonbonded interactions: 47006
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 723 "
            pdb=" OG1 THR A 727 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" O   GLU A 503 "
            pdb=" OG1 THR A 506 "
     model   vdw
     2.346 3.040
  nonbonded pdb=" O   HIS A 557 "
            pdb=" OH  TYR A 715 "
     model   vdw
     2.364 3.040
  nonbonded pdb=" O   PHE A 789 "
            pdb=" OG  SER A 793 "
     model   vdw
     2.365 3.040
  nonbonded pdb=" OD1 ASP A 392 "
            pdb=" NH2 ARG A 791 "
     model   vdw
     2.414 3.120
  ... (remaining 47001 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     19.840
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
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      :  0.014   0.418   6161  Z= 0.865
  Angle     :  1.168   8.457   8421  Z= 0.849
  Chirality :  0.069   0.290    956
  Planarity :  0.004   0.024    994
  Dihedral  : 16.440  88.252   2499
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 12.66 %
    Favored  : 86.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.27), residues: 680
  helix: -0.59 (0.25), residues: 300
  sheet: -3.23 (0.48), residues: 90
  loop : -3.09 (0.27), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.004   TRP A 873 
 HIS   0.010   0.003   HIS A 876 
 PHE   0.016   0.004   PHE A 388 
 TYR   0.026   0.004   TYR A 566 
 ARG   0.008   0.001   ARG A 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12240 (  266)
  hydrogen bonds       : angle       5.04160 (  754)
  metal coordination   : bond        0.40450 (    3)
  covalent geometry    : bond        0.01096 ( 6158)
  covalent geometry    : angle       1.16819 ( 8421)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 138
  time to evaluate  : 0.660 
Fit side-chains
REVERT: A  272 PHE cc_start: 0.8675 (t80) cc_final: 0.8435 (t80)
REVERT: A  279 GLU cc_start: 0.8652 (tp30) cc_final: 0.8441 (tp30)
REVERT: A  283 LYS cc_start: 0.8818 (mtpm) cc_final: 0.8608 (mtpp)
REVERT: A  435 ASP cc_start: 0.8367 (t70) cc_final: 0.7873 (t70)
REVERT: A  613 ASP cc_start: 0.7795 (t70) cc_final: 0.7566 (t0)
REVERT: A  679 LYS cc_start: 0.7585 (tppt) cc_final: 0.7367 (tttt)
REVERT: A  732 ARG cc_start: 0.6464 (ptt90) cc_final: 0.5340 (ptm160)
REVERT: A  758 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8201 (tm-30)
REVERT: A  889 ILE cc_start: 0.8863 (tp) cc_final: 0.8458 (tp)
REVERT: A  895 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7778 (tm-30)
  outliers start: 5
  outliers final: 2
  residues processed: 142
  average time/residue: 0.2360
  time to fit residues: 42.4829
Evaluate side-chains
  81 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  324 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 289 GLN
A 299 GLN
A 305 GLN
A 336 GLN
A 354 ASN
A 381 HIS
A 384 ASN
A 501 ASN
A 517 GLN
A 608 ASN
A 619 GLN
A 623 HIS
A 769 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.126088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.104440 restraints weight = 8191.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.107644 restraints weight = 4791.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.109837 restraints weight = 3406.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.2200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6161  Z= 0.136
  Angle     :  0.526   7.947   8421  Z= 0.261
  Chirality :  0.038   0.144    956
  Planarity :  0.003   0.031    994
  Dihedral  : 14.415  73.562   1108
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 13.82 %
    Favored  : 83.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.31), residues: 680
  helix:  1.05 (0.29), residues: 307
  sheet: -3.01 (0.48), residues: 99
  loop : -2.70 (0.31), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 646 
 HIS   0.007   0.001   HIS A 623 
 PHE   0.026   0.002   PHE A 685 
 TYR   0.011   0.001   TYR A 383 
 ARG   0.004   0.001   ARG A 811 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03391 (  266)
  hydrogen bonds       : angle       3.57787 (  754)
  metal coordination   : bond        0.01377 (    3)
  covalent geometry    : bond        0.00315 ( 6158)
  covalent geometry    : angle       0.52558 ( 8421)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.748 
Fit side-chains
REVERT: A  283 LYS cc_start: 0.8730 (mtpm) cc_final: 0.8264 (mttp)
REVERT: A  435 ASP cc_start: 0.8443 (t70) cc_final: 0.7870 (t70)
REVERT: A  454 TYR cc_start: 0.7054 (OUTLIER) cc_final: 0.6702 (m-10)
REVERT: A  613 ASP cc_start: 0.7719 (t70) cc_final: 0.7510 (t70)
REVERT: A  732 ARG cc_start: 0.6607 (ptt90) cc_final: 0.5812 (ptm160)
REVERT: A  754 ASN cc_start: 0.7844 (m-40) cc_final: 0.7608 (m-40)
REVERT: A  758 GLU cc_start: 0.8476 (tm-30) cc_final: 0.7992 (tm-30)
REVERT: A  805 ASN cc_start: 0.7499 (t0) cc_final: 0.7200 (t0)
REVERT: A  889 ILE cc_start: 0.9230 (tp) cc_final: 0.8943 (tp)
REVERT: A  895 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7329 (tm-30)
REVERT: A  907 LYS cc_start: 0.8943 (mttt) cc_final: 0.8728 (mttm)
  outliers start: 19
  outliers final: 13
  residues processed: 94
  average time/residue: 0.2418
  time to fit residues: 31.6948
Evaluate side-chains
  81 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  454 TYR
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  673 MET
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  742 THR
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  853 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 46 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 557 HIS
A 623 HIS
A 678 GLN
A 708 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.120309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.098126 restraints weight = 8467.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.101268 restraints weight = 4942.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.103393 restraints weight = 3560.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.3111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   6161  Z= 0.190
  Angle     :  0.559   6.917   8421  Z= 0.279
  Chirality :  0.040   0.141    956
  Planarity :  0.003   0.033    994
  Dihedral  : 14.204  73.377   1105
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 13.49 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.32), residues: 680
  helix:  1.45 (0.30), residues: 307
  sheet: -3.17 (0.48), residues: 93
  loop : -2.59 (0.32), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 771 
 HIS   0.006   0.001   HIS A 623 
 PHE   0.023   0.002   PHE A 685 
 TYR   0.012   0.002   TYR A 383 
 ARG   0.008   0.001   ARG A 811 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03801 (  266)
  hydrogen bonds       : angle       3.74253 (  754)
  metal coordination   : bond        0.00313 (    3)
  covalent geometry    : bond        0.00452 ( 6158)
  covalent geometry    : angle       0.55887 ( 8421)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 69
  time to evaluate  : 0.644 
Fit side-chains
REVERT: A  425 ASP cc_start: 0.7673 (t0) cc_final: 0.7466 (t0)
REVERT: A  454 TYR cc_start: 0.7209 (OUTLIER) cc_final: 0.6782 (m-80)
REVERT: A  584 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7198 (mt0)
REVERT: A  613 ASP cc_start: 0.7847 (t70) cc_final: 0.7510 (t70)
REVERT: A  620 GLU cc_start: 0.8117 (tp30) cc_final: 0.7619 (tp30)
REVERT: A  758 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8051 (tm-30)
REVERT: A  760 MET cc_start: 0.8556 (ttp) cc_final: 0.8071 (ttm)
REVERT: A  889 ILE cc_start: 0.9263 (tp) cc_final: 0.9002 (tp)
REVERT: A  895 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7475 (tm-30)
  outliers start: 24
  outliers final: 14
  residues processed: 85
  average time/residue: 0.1491
  time to fit residues: 17.8751
Evaluate side-chains
  73 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  372 ASP
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  454 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  584 GLN
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  673 MET
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  742 THR
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  775 VAL
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  853 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 22 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 57 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 623 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.121723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.099689 restraints weight = 8480.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.102958 restraints weight = 4902.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.105139 restraints weight = 3467.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.3218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6161  Z= 0.129
  Angle     :  0.505   6.422   8421  Z= 0.253
  Chirality :  0.039   0.214    956
  Planarity :  0.003   0.033    994
  Dihedral  : 14.270  73.595   1105
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 15.46 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.33), residues: 680
  helix:  1.84 (0.30), residues: 306
  sheet: -3.14 (0.49), residues: 88
  loop : -2.40 (0.32), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 512 
 HIS   0.007   0.001   HIS A 623 
 PHE   0.017   0.001   PHE A 685 
 TYR   0.011   0.001   TYR A 383 
 ARG   0.006   0.000   ARG A 811 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03376 (  266)
  hydrogen bonds       : angle       3.59947 (  754)
  metal coordination   : bond        0.00168 (    3)
  covalent geometry    : bond        0.00303 ( 6158)
  covalent geometry    : angle       0.50515 ( 8421)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 66
  time to evaluate  : 1.406 
Fit side-chains
REVERT: A  425 ASP cc_start: 0.7643 (t0) cc_final: 0.7437 (t0)
REVERT: A  454 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.6756 (m-80)
REVERT: A  613 ASP cc_start: 0.7839 (t70) cc_final: 0.7516 (t70)
REVERT: A  754 ASN cc_start: 0.7808 (m-40) cc_final: 0.7528 (m-40)
REVERT: A  758 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8005 (tm-30)
REVERT: A  889 ILE cc_start: 0.9275 (tp) cc_final: 0.9003 (tp)
REVERT: A  895 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7495 (tm-30)
  outliers start: 21
  outliers final: 15
  residues processed: 78
  average time/residue: 0.1820
  time to fit residues: 19.9269
Evaluate side-chains
  70 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 54
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  454 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  673 MET
Chi-restraints excluded: chain A residue  709 CYS
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  742 THR
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  853 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 63 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0040
   chunk 35 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0980
   chunk 36 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
A 623 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.123585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.101616 restraints weight = 8331.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.104874 restraints weight = 4791.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.107105 restraints weight = 3398.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.3250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6161  Z= 0.104
  Angle     :  0.487   7.036   8421  Z= 0.241
  Chirality :  0.039   0.233    956
  Planarity :  0.003   0.032    994
  Dihedral  : 14.216  73.606   1105
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 17.27 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.33), residues: 680
  helix:  2.10 (0.31), residues: 305
  sheet: -3.08 (0.49), residues: 88
  loop : -2.32 (0.33), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 512 
 HIS   0.008   0.001   HIS A 623 
 PHE   0.013   0.001   PHE A 685 
 TYR   0.010   0.001   TYR A 715 
 ARG   0.008   0.000   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03157 (  266)
  hydrogen bonds       : angle       3.48236 (  754)
  metal coordination   : bond        0.00123 (    3)
  covalent geometry    : bond        0.00238 ( 6158)
  covalent geometry    : angle       0.48720 ( 8421)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.733 
Fit side-chains
REVERT: A  454 TYR cc_start: 0.7245 (OUTLIER) cc_final: 0.6829 (m-80)
REVERT: A  754 ASN cc_start: 0.7788 (m-40) cc_final: 0.7529 (m-40)
REVERT: A  758 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8008 (tm-30)
REVERT: A  889 ILE cc_start: 0.9285 (tp) cc_final: 0.8998 (tp)
REVERT: A  895 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7420 (tm-30)
  outliers start: 18
  outliers final: 13
  residues processed: 75
  average time/residue: 0.1351
  time to fit residues: 15.0625
Evaluate side-chains
  71 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  454 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  673 MET
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  853 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 69 optimal weight:    3.9990
   chunk 13 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 623 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.122882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.100699 restraints weight = 8326.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.103927 restraints weight = 4870.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.105959 restraints weight = 3496.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.3390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6161  Z= 0.121
  Angle     :  0.507   6.909   8421  Z= 0.250
  Chirality :  0.039   0.249    956
  Planarity :  0.003   0.032    994
  Dihedral  : 14.158  73.599   1105
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 16.61 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.33), residues: 680
  helix:  2.16 (0.30), residues: 305
  sheet: -2.83 (0.49), residues: 93
  loop : -2.32 (0.33), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 512 
 HIS   0.008   0.001   HIS A 623 
 PHE   0.011   0.001   PHE A 853 
 TYR   0.023   0.001   TYR A 622 
 ARG   0.007   0.000   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03219 (  266)
  hydrogen bonds       : angle       3.50177 (  754)
  metal coordination   : bond        0.00164 (    3)
  covalent geometry    : bond        0.00283 ( 6158)
  covalent geometry    : angle       0.50676 ( 8421)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 63
  time to evaluate  : 0.671 
Fit side-chains
REVERT: A  454 TYR cc_start: 0.7286 (OUTLIER) cc_final: 0.6841 (m-80)
REVERT: A  758 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8057 (tm-30)
REVERT: A  889 ILE cc_start: 0.9292 (tp) cc_final: 0.9021 (tp)
REVERT: A  895 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7477 (tm-30)
  outliers start: 23
  outliers final: 17
  residues processed: 76
  average time/residue: 0.1645
  time to fit residues: 18.5692
Evaluate side-chains
  75 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 57
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  454 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  615 CYS
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  673 MET
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  709 CYS
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  742 THR
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  853 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 1 optimal weight:    0.1980
   chunk 4 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    1.2388

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

Flipped N/Q/H residues before XYZ refinement:
A 623 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.119523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.097179 restraints weight = 8479.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.100275 restraints weight = 4963.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.102429 restraints weight = 3593.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.3605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6161  Z= 0.176
  Angle     :  0.551   7.756   8421  Z= 0.274
  Chirality :  0.041   0.265    956
  Planarity :  0.003   0.035    994
  Dihedral  : 14.099  73.496   1105
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 17.60 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.33), residues: 680
  helix:  2.05 (0.30), residues: 306
  sheet: -2.94 (0.45), residues: 103
  loop : -2.29 (0.34), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 512 
 HIS   0.009   0.001   HIS A 623 
 PHE   0.018   0.001   PHE A 853 
 TYR   0.026   0.002   TYR A 622 
 ARG   0.007   0.001   ARG A 811 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03660 (  266)
  hydrogen bonds       : angle       3.67605 (  754)
  metal coordination   : bond        0.00238 (    3)
  covalent geometry    : bond        0.00417 ( 6158)
  covalent geometry    : angle       0.55137 ( 8421)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 56
  time to evaluate  : 0.652 
Fit side-chains
REVERT: A  454 TYR cc_start: 0.7362 (OUTLIER) cc_final: 0.6856 (m-80)
REVERT: A  620 GLU cc_start: 0.8340 (tp30) cc_final: 0.7807 (tp30)
REVERT: A  754 ASN cc_start: 0.7865 (m-40) cc_final: 0.7590 (m-40)
REVERT: A  758 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8071 (tm-30)
REVERT: A  889 ILE cc_start: 0.9272 (tp) cc_final: 0.9026 (tp)
  outliers start: 24
  outliers final: 15
  residues processed: 72
  average time/residue: 0.1675
  time to fit residues: 17.0170
Evaluate side-chains
  70 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 54
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  454 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  615 CYS
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  673 MET
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  742 THR
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  775 VAL
Chi-restraints excluded: chain A residue  853 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 63 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 57 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 41 optimal weight:    0.6980
   chunk 49 optimal weight:    5.9990
   chunk 9 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   chunk 2 optimal weight:    0.0570
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
A 623 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.122693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.100511 restraints weight = 8339.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.103749 restraints weight = 4868.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.105922 restraints weight = 3485.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.3530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6161  Z= 0.109
  Angle     :  0.509   8.011   8421  Z= 0.250
  Chirality :  0.039   0.285    956
  Planarity :  0.003   0.033    994
  Dihedral  : 14.161  73.624   1105
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 17.93 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.34), residues: 680
  helix:  2.21 (0.30), residues: 306
  sheet: -2.68 (0.47), residues: 103
  loop : -2.19 (0.35), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 512 
 HIS   0.009   0.001   HIS A 623 
 PHE   0.010   0.001   PHE A 523 
 TYR   0.023   0.001   TYR A 622 
 ARG   0.006   0.000   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03201 (  266)
  hydrogen bonds       : angle       3.54104 (  754)
  metal coordination   : bond        0.00118 (    3)
  covalent geometry    : bond        0.00252 ( 6158)
  covalent geometry    : angle       0.50877 ( 8421)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 64
  time to evaluate  : 0.631 
Fit side-chains
REVERT: A  454 TYR cc_start: 0.7369 (OUTLIER) cc_final: 0.6835 (m-80)
REVERT: A  754 ASN cc_start: 0.7745 (m-40) cc_final: 0.7468 (m-40)
REVERT: A  758 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8036 (tm-30)
REVERT: A  889 ILE cc_start: 0.9286 (tp) cc_final: 0.9019 (tp)
REVERT: A  895 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7533 (tm-30)
  outliers start: 19
  outliers final: 13
  residues processed: 75
  average time/residue: 0.1362
  time to fit residues: 14.8814
Evaluate side-chains
  74 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  454 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  615 CYS
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  673 MET
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  742 THR
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  853 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 69 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.8786

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

Flipped N/Q/H residues before XYZ refinement:
A 623 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.119526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.098006 restraints weight = 8443.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.101130 restraints weight = 4823.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.103295 restraints weight = 3427.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.3597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6161  Z= 0.136
  Angle     :  0.545   8.537   8421  Z= 0.267
  Chirality :  0.040   0.285    956
  Planarity :  0.003   0.033    994
  Dihedral  : 14.083  73.575   1105
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 17.43 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.34), residues: 680
  helix:  2.16 (0.30), residues: 306
  sheet: -2.58 (0.46), residues: 108
  loop : -2.20 (0.36), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 512 
 HIS   0.010   0.001   HIS A 623 
 PHE   0.013   0.001   PHE A 853 
 TYR   0.022   0.001   TYR A 622 
 ARG   0.006   0.000   ARG A 811 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03348 (  266)
  hydrogen bonds       : angle       3.59786 (  754)
  metal coordination   : bond        0.00177 (    3)
  covalent geometry    : bond        0.00317 ( 6158)
  covalent geometry    : angle       0.54487 ( 8421)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 60
  time to evaluate  : 1.321 
Fit side-chains
REVERT: A  454 TYR cc_start: 0.7387 (OUTLIER) cc_final: 0.6847 (m-80)
REVERT: A  754 ASN cc_start: 0.7772 (m-40) cc_final: 0.7488 (m-40)
REVERT: A  758 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8068 (tm-30)
REVERT: A  822 ASP cc_start: 0.9080 (OUTLIER) cc_final: 0.8174 (p0)
REVERT: A  889 ILE cc_start: 0.9292 (tp) cc_final: 0.9030 (tp)
REVERT: A  895 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7563 (tm-30)
  outliers start: 22
  outliers final: 14
  residues processed: 74
  average time/residue: 0.2147
  time to fit residues: 24.4684
Evaluate side-chains
  71 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 GLN
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  454 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  615 CYS
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  673 MET
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  742 THR
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  822 ASP
Chi-restraints excluded: chain A residue  853 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 69 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 623 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.117680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.095253 restraints weight = 8621.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.098423 restraints weight = 5079.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.100499 restraints weight = 3652.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.3813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   6161  Z= 0.209
  Angle     :  0.611  10.092   8421  Z= 0.302
  Chirality :  0.043   0.296    956
  Planarity :  0.004   0.040    994
  Dihedral  : 14.067  73.490   1105
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.38 %
    Favored  : 91.62 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 18.26 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.33), residues: 680
  helix:  1.93 (0.30), residues: 307
  sheet: -2.88 (0.44), residues: 109
  loop : -2.35 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 512 
 HIS   0.009   0.001   HIS A 623 
 PHE   0.021   0.002   PHE A 853 
 TYR   0.026   0.002   TYR A 622 
 ARG   0.008   0.001   ARG A 811 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03853 (  266)
  hydrogen bonds       : angle       3.83514 (  754)
  metal coordination   : bond        0.00290 (    3)
  covalent geometry    : bond        0.00494 ( 6158)
  covalent geometry    : angle       0.61079 ( 8421)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 58
  time to evaluate  : 1.322 
Fit side-chains
REVERT: A  454 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.6821 (m-80)
REVERT: A  754 ASN cc_start: 0.7883 (m-40) cc_final: 0.7594 (m-40)
REVERT: A  758 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8076 (tm-30)
REVERT: A  822 ASP cc_start: 0.9147 (OUTLIER) cc_final: 0.8111 (p0)
REVERT: A  889 ILE cc_start: 0.9282 (tp) cc_final: 0.9029 (tp)
  outliers start: 21
  outliers final: 15
  residues processed: 70
  average time/residue: 0.2027
  time to fit residues: 21.7917
Evaluate side-chains
  72 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 55
  time to evaluate  : 1.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 GLN
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  454 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  673 MET
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  742 THR
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  775 VAL
Chi-restraints excluded: chain A residue  822 ASP
Chi-restraints excluded: chain A residue  853 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 51 optimal weight:    0.6980
   chunk 39 optimal weight:    0.3980
   chunk 18 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 341 ASN
A 623 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.121003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.098778 restraints weight = 8615.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.101959 restraints weight = 4973.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.104165 restraints weight = 3556.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.3694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6161  Z= 0.123
  Angle     :  0.546   9.044   8421  Z= 0.269
  Chirality :  0.040   0.303    956
  Planarity :  0.003   0.034    994
  Dihedral  : 14.158  73.633   1105
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.82 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 18.91 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.34), residues: 680
  helix:  2.13 (0.30), residues: 307
  sheet: -2.88 (0.46), residues: 98
  loop : -2.09 (0.35), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 512 
 HIS   0.010   0.001   HIS A 623 
 PHE   0.012   0.001   PHE A 853 
 TYR   0.026   0.001   TYR A 622 
 ARG   0.006   0.000   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03322 (  266)
  hydrogen bonds       : angle       3.65440 (  754)
  metal coordination   : bond        0.00162 (    3)
  covalent geometry    : bond        0.00287 ( 6158)
  covalent geometry    : angle       0.54568 ( 8421)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2385.81 seconds
wall clock time: 44 minutes 16.37 seconds (2656.37 seconds total)