Starting phenix.real_space_refine
on Thu Jul 24 10:18:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dvr_27743/07_2025/8dvr_27743.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dvr_27743/07_2025/8dvr_27743.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dvr_27743/07_2025/8dvr_27743.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dvr_27743/07_2025/8dvr_27743.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dvr_27743/07_2025/8dvr_27743.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dvr_27743/07_2025/8dvr_27743.cif"
  }
  resolution = 3.3
  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
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      24      5.49       5
     S      31      5.16       5
     C    3492      2.51       5
     N     947      2.21       5
     O    1106      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5601
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5123
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 635, 5123
          Classifications: {'peptide': 635}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 27, 'TRANS': 607}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "B"
      Number of atoms: 445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 445
          Classifications: {'RNA': 21}
          Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 11}
          Link IDs: {'rna3p': 20}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   4191  SG  CYS A 810      23.312  29.188  27.887  1.00 29.78           S
  ATOM   4630  SG  CYS A 864      19.045  29.309  28.690  1.00 26.94           S
  ATOM   4669  SG  CYS A 869      21.454  27.047  30.233  1.00 32.07           S

  Time building chain proxies: 5.14, per 1000 atoms: 0.92
  Number of scatterers: 5601
  At special positions: 0
  Unit cell: (79.032, 99.324, 85.44, 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      31     16.00
     P      24     15.00
     O    1106      8.00
     N     947      7.00
     C    3492      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.78
  Conformation dependent library (CDL) restraints added in 785.2 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1001 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 864 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 810 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 869 "


  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1220

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 5 sheets defined
      51.3% alpha, 8.3% beta
      10 base pairs and 14 stacking pairs defined.
    Time for finding SS restraints: 2.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 244 through 256
      removed outlier: 3.515A  pdb=" N   LEU A 250 " --> pdb=" O   TYR A 246 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
      removed outlier: 4.032A  pdb=" N   LYS A 256 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 284
      removed outlier: 3.835A  pdb=" N   LYS A 270 " --> pdb=" O   THR A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 314
    Processing helix  chain 'A' and resid 333 through 340
    Processing helix  chain 'A' and resid 347 through 358
    Processing helix  chain 'A' and resid 362 through 366
      removed outlier: 3.912A  pdb=" N   ILE A 365 " --> pdb=" O   SER A 362 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   PHE A 366 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 362 through 366'
    Processing helix  chain 'A' and resid 374 through 377
    Processing helix  chain 'A' and resid 381 through 396
    Processing helix  chain 'A' and resid 419 through 435
    Processing helix  chain 'A' and resid 448 through 452
      removed outlier: 3.994A  pdb=" N   GLN A 451 " --> pdb=" O   GLU A 448 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   VAL A 452 " --> pdb=" O   LEU A 449 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 448 through 452'
    Processing helix  chain 'A' and resid 469 through 487
    Processing helix  chain 'A' and resid 492 through 497
      removed outlier: 4.511A  pdb=" N   SER A 497 " --> pdb=" O   LEU A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 521
    Processing helix  chain 'A' and resid 529 through 558
      removed outlier: 3.858A  pdb=" N   ARG A 533 " --> pdb=" O   ASP A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 576
      removed outlier: 3.724A  pdb=" N   ALA A 563 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ALA A 576 " --> pdb=" O   SER A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 602
      removed outlier: 3.794A  pdb=" N   GLN A 595 " --> pdb=" O   GLU A 591 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   GLU A 596 " --> pdb=" O   GLU A 592 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   SER A 599 " --> pdb=" O   GLN A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 607
      removed outlier: 4.162A  pdb=" N   GLU A 607 " --> pdb=" O   PRO A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 625
    Processing helix  chain 'A' and resid 636 through 638
      No H-bonds generated for 'chain 'A' and resid 636 through 638'
    Processing helix  chain 'A' and resid 639 through 650
      removed outlier: 3.529A  pdb=" N   LYS A 644 " --> pdb=" O   VAL A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 744 through 771
      removed outlier: 4.107A  pdb=" N   ILE A 748 " --> pdb=" O   ASN A 744 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 794
    Processing helix  chain 'A' and resid 835 through 840
      removed outlier: 3.524A  pdb=" N   LYS A 839 " --> pdb=" O   GLY A 835 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   GLU A 840 " --> pdb=" O   ASP A 836 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 835 through 840'
    Processing helix  chain 'A' and resid 889 through 892
      removed outlier: 3.556A  pdb=" N   PHE A 892 " --> pdb=" O   ILE A 889 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 889 through 892'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 294 through 296
      removed outlier: 7.183A  pdb=" N   LEU A 408 " --> pdb=" O   MET A 369 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   PHE A 371 " --> pdb=" O   LEU A 408 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 461 through 462
      removed outlier: 3.894A  pdb=" N   THR A 742 " --> pdb=" O   ARG A 461 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   ILE A 631 " --> pdb=" O   ILE A 713 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   TYR A 715 " --> pdb=" O   ILE A 631 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   PHE A 633 " --> pdb=" O   TYR A 715 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 816 through 819
      removed outlier: 6.874A  pdb=" N   LEU A 808 " --> pdb=" O   ALA A 817 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 831 through 833
      removed outlier: 4.500A  pdb=" N   ILE A 916 " --> pdb=" O   VAL A 823 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 842 through 846
      removed outlier: 5.749A  pdb=" N   LYS A 858 " --> pdb=" O   LYS A 878 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   LYS A 878 " --> pdb=" O   LYS A 858 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ILE A 862 " --> pdb=" O   GLY A 874 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   GLY A 874 " --> pdb=" O   ILE A 862 " (cutoff:3.500A)

    244 hydrogen bonds defined for protein.
    714 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      25 hydrogen bonds
      50 hydrogen bond angles
      0 basepair planarities
      10 basepair parallelities
      14 stacking parallelities
  Total time for adding SS restraints: 2.65

  Time building geometry restraints manager: 1.89 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1711
        1.34 -     1.46: 902
        1.46 -     1.57: 3057
        1.57 -     1.69: 45
        1.69 -     1.81: 43
  Bond restraints: 5758
  Sorted by residual:
  bond pdb=" C   ILE A 884 "
       pdb=" O   ILE A 884 "
    ideal  model  delta    sigma   weight residual
    1.232  1.241 -0.009 8.90e-03 1.26e+04 9.64e-01
  bond pdb=" N   PRO A 401 "
       pdb=" CA  PRO A 401 "
    ideal  model  delta    sigma   weight residual
    1.469  1.480 -0.011 1.28e-02 6.10e+03 7.60e-01
  bond pdb=" N   GLY A 415 "
       pdb=" CA  GLY A 415 "
    ideal  model  delta    sigma   weight residual
    1.449  1.461 -0.012 1.45e-02 4.76e+03 6.38e-01
  bond pdb=" C   VAL A 414 "
       pdb=" N   GLY A 415 "
    ideal  model  delta    sigma   weight residual
    1.331  1.319  0.011 1.46e-02 4.69e+03 5.79e-01
  bond pdb=" CA  ILE A 916 "
       pdb=" CB  ILE A 916 "
    ideal  model  delta    sigma   weight residual
    1.526  1.537 -0.011 1.55e-02 4.16e+03 4.96e-01
  ... (remaining 5753 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 7739
        1.42 -     2.84: 110
        2.84 -     4.27: 19
        4.27 -     5.69: 3
        5.69 -     7.11: 1
  Bond angle restraints: 7872
  Sorted by residual:
  angle pdb=" N   ILE A 897 "
        pdb=" CA  ILE A 897 "
        pdb=" C   ILE A 897 "
      ideal   model   delta    sigma   weight residual
     111.90  109.07    2.83 8.10e-01 1.52e+00 1.22e+01
  angle pdb=" N   VAL A 414 "
        pdb=" CA  VAL A 414 "
        pdb=" C   VAL A 414 "
      ideal   model   delta    sigma   weight residual
     111.90  109.36    2.54 8.10e-01 1.52e+00 9.82e+00
  angle pdb=" N   ALA A 410 "
        pdb=" CA  ALA A 410 "
        pdb=" C   ALA A 410 "
      ideal   model   delta    sigma   weight residual
     114.04  110.54    3.50 1.24e+00 6.50e-01 7.98e+00
  angle pdb=" C2' GTP B 201 "
        pdb=" C3' GTP B 201 "
        pdb=" C4' GTP B 201 "
      ideal   model   delta    sigma   weight residual
     111.00  103.89    7.11 3.00e+00 1.11e-01 5.62e+00
  angle pdb=" N   ILE A 884 "
        pdb=" CA  ILE A 884 "
        pdb=" C   ILE A 884 "
      ideal   model   delta    sigma   weight residual
     107.61  110.31   -2.70 1.19e+00 7.06e-01 5.14e+00
  ... (remaining 7867 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 3153
       17.86 -    35.71: 265
       35.71 -    53.57: 73
       53.57 -    71.43: 29
       71.43 -    89.28: 15
  Dihedral angle restraints: 3535
    sinusoidal: 1663
      harmonic: 1872
  Sorted by residual:
  dihedral pdb=" C8  GTP B 201 "
           pdb=" C1' GTP B 201 "
           pdb=" N9  GTP B 201 "
           pdb=" O4' GTP B 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59   23.63   80.96     1      2.00e+01 2.50e-03 2.02e+01
  dihedral pdb=" CA  PHE A 853 "
           pdb=" C   PHE A 853 "
           pdb=" N   SER A 854 "
           pdb=" CA  SER A 854 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.24   17.76     0      5.00e+00 4.00e-02 1.26e+01
  dihedral pdb=" CB  GLU A 895 "
           pdb=" CG  GLU A 895 "
           pdb=" CD  GLU A 895 "
           pdb=" OE1 GLU A 895 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.28   89.28     1      3.00e+01 1.11e-03 1.05e+01
  ... (remaining 3532 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 557
       0.024 -    0.049: 201
       0.049 -    0.073: 75
       0.073 -    0.098: 43
       0.098 -    0.122: 17
  Chirality restraints: 893
  Sorted by residual:
  chirality pdb=" CA  ILE A 439 "
            pdb=" N   ILE A 439 "
            pdb=" C   ILE A 439 "
            pdb=" CB  ILE A 439 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.75e-01
  chirality pdb=" CA  ILE A 875 "
            pdb=" N   ILE A 875 "
            pdb=" C   ILE A 875 "
            pdb=" CB  ILE A 875 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.48e-01
  chirality pdb=" CA  ILE A 629 "
            pdb=" N   ILE A 629 "
            pdb=" C   ILE A 629 "
            pdb=" CB  ILE A 629 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.18e-01
  ... (remaining 890 not shown)

  Planarity restraints: 924
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 381 "   -0.016 5.00e-02 4.00e+02   2.41e-02 9.31e-01
        pdb=" N   PRO A 382 "    0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO A 382 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 382 "   -0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 300 "   -0.013 5.00e-02 4.00e+02   1.98e-02 6.26e-01
        pdb=" N   PRO A 301 "    0.034 5.00e-02 4.00e+02
        pdb=" CA  PRO A 301 "   -0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO A 301 "   -0.011 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 884 "    0.013 5.00e-02 4.00e+02   1.96e-02 6.12e-01
        pdb=" N   PRO A 885 "   -0.034 5.00e-02 4.00e+02
        pdb=" CA  PRO A 885 "    0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO A 885 "    0.011 5.00e-02 4.00e+02
  ... (remaining 921 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1363
        2.79 -     3.32: 5223
        3.32 -     3.85: 9434
        3.85 -     4.37: 10722
        4.37 -     4.90: 18061
  Nonbonded interactions: 44803
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 259 "
            pdb=" O   ASP A 435 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" OG  SER A 362 "
            pdb=" OG  SER A 364 "
     model   vdw
     2.325 3.040
  nonbonded pdb=" O   HIS A 557 "
            pdb=" OH  TYR A 715 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" OH  TYR A 622 "
            pdb=" OD1 ASN A 692 "
     model   vdw
     2.349 3.040
  nonbonded pdb=" N   ASP A 580 "
            pdb=" OD1 ASP A 580 "
     model   vdw
     2.355 3.120
  ... (remaining 44798 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.450
  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:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     22.270
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
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      :  0.008   0.524   5762  Z= 0.288
  Angle     :  0.456   7.111   7872  Z= 0.269
  Chirality :  0.035   0.122    893
  Planarity :  0.002   0.024    924
  Dihedral  : 15.720  89.284   2315
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  :  9.46 %
    Favored  : 89.14 %
  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: -2.25 (0.31), residues: 627
  helix:  0.37 (0.28), residues: 280
  sheet: -3.31 (0.51), residues: 81
  loop : -3.00 (0.32), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 512 
 HIS   0.002   0.000   HIS A 847 
 PHE   0.007   0.001   PHE A 856 
 TYR   0.003   0.000   TYR A 390 
 ARG   0.001   0.000   ARG A 575 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12908 (  269)
  hydrogen bonds       : angle       5.04169 (  764)
  metal coordination   : bond        0.35537 (    3)
  covalent geometry    : bond        0.00166 ( 5758)
  covalent geometry    : angle       0.45573 ( 7872)
  Misc. bond           : bond        0.00042 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 135
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
REVERT: A  492 ASP cc_start: 0.7105 (p0) cc_final: 0.6518 (t0)
REVERT: A  759 LYS cc_start: 0.7895 (mtmt) cc_final: 0.7442 (ttpp)
REVERT: A  763 ASP cc_start: 0.7733 (t70) cc_final: 0.7508 (t0)
REVERT: A  789 PHE cc_start: 0.7957 (t80) cc_final: 0.7567 (t80)
REVERT: A  889 ILE cc_start: 0.9123 (tp) cc_final: 0.8588 (tp)
  outliers start: 8
  outliers final: 4
  residues processed: 139
  average time/residue: 0.2621
  time to fit residues: 44.7951
Evaluate side-chains
  93 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 89
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 ASN
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  499 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 37 optimal weight:    0.3980
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN
A 341 ASN
A 354 ASN
A 380 GLN
A 495 ASN
A 517 GLN
A 573 ASN
** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.154772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.127427 restraints weight = 6357.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 1.79
r_work: 0.3359 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.1984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5762  Z= 0.129
  Angle     :  0.509   8.228   7872  Z= 0.250
  Chirality :  0.039   0.182    893
  Planarity :  0.003   0.036    924
  Dihedral  : 13.204  90.567   1015
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 11.73 %
    Favored  : 84.59 %
  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: -1.17 (0.33), residues: 627
  helix:  1.46 (0.30), residues: 288
  sheet: -3.18 (0.51), residues: 84
  loop : -2.63 (0.35), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 873 
 HIS   0.003   0.001   HIS A 281 
 PHE   0.008   0.001   PHE A 371 
 TYR   0.010   0.001   TYR A 383 
 ARG   0.008   0.001   ARG A 811 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03553 (  269)
  hydrogen bonds       : angle       3.82381 (  764)
  metal coordination   : bond        0.00854 (    3)
  covalent geometry    : bond        0.00295 ( 5758)
  covalent geometry    : angle       0.50885 ( 7872)
  Misc. bond           : bond        0.00040 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.642 
Fit side-chains
REVERT: A  255 MET cc_start: 0.8730 (mtt) cc_final: 0.8298 (mtt)
REVERT: A  632 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8232 (tt)
REVERT: A  653 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7938 (pp)
REVERT: A  692 ASN cc_start: 0.8360 (t0) cc_final: 0.8037 (t0)
REVERT: A  759 LYS cc_start: 0.8123 (mtmt) cc_final: 0.7591 (ttpp)
REVERT: A  763 ASP cc_start: 0.8244 (t70) cc_final: 0.7926 (t0)
REVERT: A  872 ASP cc_start: 0.8348 (t0) cc_final: 0.8036 (t0)
  outliers start: 21
  outliers final: 7
  residues processed: 107
  average time/residue: 0.2258
  time to fit residues: 30.3419
Evaluate side-chains
  84 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  903 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 50 optimal weight:    8.9990
   chunk 59 optimal weight:    3.9990
   chunk 41 optimal weight:    0.4980
   chunk 38 optimal weight:    0.0000
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN
A 573 ASN
A 710 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.162650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.134794 restraints weight = 6434.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 1.80
r_work: 0.3330 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5762  Z= 0.096
  Angle     :  0.482   7.855   7872  Z= 0.234
  Chirality :  0.039   0.171    893
  Planarity :  0.003   0.041    924
  Dihedral  : 13.207  90.798   1011
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 14.54 %
    Favored  : 81.61 %
  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: -0.65 (0.34), residues: 627
  helix:  1.93 (0.30), residues: 289
  sheet: -3.03 (0.52), residues: 84
  loop : -2.40 (0.35), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 771 
 HIS   0.002   0.000   HIS A 281 
 PHE   0.012   0.001   PHE A 616 
 TYR   0.006   0.001   TYR A 879 
 ARG   0.006   0.000   ARG A 546 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03251 (  269)
  hydrogen bonds       : angle       3.65102 (  764)
  metal coordination   : bond        0.00119 (    3)
  covalent geometry    : bond        0.00211 ( 5758)
  covalent geometry    : angle       0.48176 ( 7872)
  Misc. bond           : bond        0.00033 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.624 
Fit side-chains
   revert: symmetry clash
REVERT: A  255 MET cc_start: 0.8825 (mtt) cc_final: 0.8512 (mtt)
REVERT: A  492 ASP cc_start: 0.7204 (m-30) cc_final: 0.5918 (t0)
REVERT: A  632 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8209 (tt)
REVERT: A  647 ILE cc_start: 0.8574 (mt) cc_final: 0.8321 (mp)
REVERT: A  653 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7938 (pp)
REVERT: A  759 LYS cc_start: 0.8129 (mtmt) cc_final: 0.7593 (ttpp)
REVERT: A  763 ASP cc_start: 0.8177 (t70) cc_final: 0.7864 (t0)
REVERT: A  872 ASP cc_start: 0.8360 (t0) cc_final: 0.8151 (t0)
  outliers start: 22
  outliers final: 8
  residues processed: 100
  average time/residue: 0.2134
  time to fit residues: 28.4063
Evaluate side-chains
  81 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  340 ASN
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  903 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 54 optimal weight:    0.4980
   chunk 41 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 24 optimal weight:    4.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN
A 573 ASN
A 710 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.155741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.127458 restraints weight = 6484.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 1.79
r_work: 0.3210 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5762  Z= 0.119
  Angle     :  0.511   8.103   7872  Z= 0.250
  Chirality :  0.040   0.193    893
  Planarity :  0.003   0.041    924
  Dihedral  : 13.190  93.292   1011
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 16.81 %
    Favored  : 80.21 %
  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: -0.43 (0.35), residues: 627
  helix:  2.14 (0.31), residues: 285
  sheet: -2.93 (0.52), residues: 84
  loop : -2.25 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 873 
 HIS   0.002   0.000   HIS A 281 
 PHE   0.017   0.001   PHE A 460 
 TYR   0.007   0.001   TYR A 390 
 ARG   0.009   0.001   ARG A 811 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03335 (  269)
  hydrogen bonds       : angle       3.63665 (  764)
  metal coordination   : bond        0.00161 (    3)
  covalent geometry    : bond        0.00270 ( 5758)
  covalent geometry    : angle       0.51106 ( 7872)
  Misc. bond           : bond        0.00023 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.573 
Fit side-chains
REVERT: A  492 ASP cc_start: 0.7403 (m-30) cc_final: 0.5950 (t0)
REVERT: A  632 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8360 (tt)
REVERT: A  647 ILE cc_start: 0.8750 (mt) cc_final: 0.8495 (mp)
REVERT: A  653 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7877 (pp)
REVERT: A  759 LYS cc_start: 0.8194 (mtmt) cc_final: 0.7611 (ttpp)
REVERT: A  763 ASP cc_start: 0.8381 (t70) cc_final: 0.8066 (t0)
  outliers start: 17
  outliers final: 9
  residues processed: 85
  average time/residue: 0.1622
  time to fit residues: 18.7922
Evaluate side-chains
  78 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  903 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 20 optimal weight:    6.9990
   chunk 50 optimal weight:    4.9990
   chunk 13 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 56 optimal weight:    0.0470
   chunk 54 optimal weight:    0.0870
   overall best weight:    0.5056

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

Flipped N/Q/H residues before XYZ refinement:
A 341 ASN
A 573 ASN
A 710 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.159624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.130613 restraints weight = 6394.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 1.85
r_work: 0.3187 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.2864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5762  Z= 0.097
  Angle     :  0.485   7.875   7872  Z= 0.235
  Chirality :  0.039   0.170    893
  Planarity :  0.003   0.040    924
  Dihedral  : 13.192  92.734   1011
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 18.39 %
    Favored  : 79.33 %
  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: -0.21 (0.35), residues: 627
  helix:  2.35 (0.31), residues: 284
  sheet: -2.80 (0.51), residues: 85
  loop : -2.15 (0.35), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 771 
 HIS   0.002   0.000   HIS A 847 
 PHE   0.015   0.001   PHE A 460 
 TYR   0.007   0.001   TYR A 390 
 ARG   0.005   0.000   ARG A 811 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03168 (  269)
  hydrogen bonds       : angle       3.52585 (  764)
  metal coordination   : bond        0.00118 (    3)
  covalent geometry    : bond        0.00216 ( 5758)
  covalent geometry    : angle       0.48508 ( 7872)
  Misc. bond           : bond        0.00035 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
REVERT: A  492 ASP cc_start: 0.7369 (m-30) cc_final: 0.6014 (t0)
REVERT: A  632 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8370 (tt)
REVERT: A  653 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7949 (pp)
REVERT: A  759 LYS cc_start: 0.8216 (mtmt) cc_final: 0.7610 (ttpp)
REVERT: A  763 ASP cc_start: 0.8382 (t70) cc_final: 0.8061 (t0)
  outliers start: 13
  outliers final: 9
  residues processed: 81
  average time/residue: 0.1557
  time to fit residues: 17.6496
Evaluate side-chains
  76 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  903 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 44 optimal weight:   10.0000
   chunk 4 optimal weight:    0.8980
   chunk 0 optimal weight:    9.9990
   chunk 28 optimal weight:    5.9990
   chunk 39 optimal weight:    0.3980
   chunk 35 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 495 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.153885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.124174 restraints weight = 6413.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.96
r_work: 0.3152 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.3225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5762  Z= 0.140
  Angle     :  0.533   8.672   7872  Z= 0.258
  Chirality :  0.040   0.177    893
  Planarity :  0.003   0.038    924
  Dihedral  : 13.223  95.050   1010
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 19.09 %
    Favored  : 77.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.35), residues: 627
  helix:  2.24 (0.30), residues: 293
  sheet: -2.70 (0.52), residues: 85
  loop : -2.09 (0.37), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 873 
 HIS   0.002   0.001   HIS A 281 
 PHE   0.015   0.001   PHE A 616 
 TYR   0.009   0.001   TYR A 566 
 ARG   0.006   0.000   ARG A 811 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03615 (  269)
  hydrogen bonds       : angle       3.68868 (  764)
  metal coordination   : bond        0.00203 (    3)
  covalent geometry    : bond        0.00326 ( 5758)
  covalent geometry    : angle       0.53298 ( 7872)
  Misc. bond           : bond        0.00032 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 67
  time to evaluate  : 1.045 
Fit side-chains
REVERT: A  492 ASP cc_start: 0.7330 (m-30) cc_final: 0.6036 (t0)
REVERT: A  632 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8244 (tt)
REVERT: A  647 ILE cc_start: 0.8803 (mt) cc_final: 0.8583 (mp)
REVERT: A  653 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7938 (pp)
REVERT: A  759 LYS cc_start: 0.8026 (mtmt) cc_final: 0.7552 (ttpp)
REVERT: A  763 ASP cc_start: 0.8255 (t70) cc_final: 0.7952 (t0)
REVERT: A  794 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.6977 (pp30)
  outliers start: 18
  outliers final: 9
  residues processed: 81
  average time/residue: 0.1632
  time to fit residues: 17.8858
Evaluate side-chains
  72 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  794 GLN
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  903 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 573 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.155154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.125440 restraints weight = 6482.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 1.96
r_work: 0.3100 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.3438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5762  Z= 0.151
  Angle     :  0.546   9.076   7872  Z= 0.265
  Chirality :  0.040   0.174    893
  Planarity :  0.003   0.038    924
  Dihedral  : 13.303  95.536   1010
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 20.32 %
    Favored  : 76.36 %
  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: -0.18 (0.34), residues: 627
  helix:  2.09 (0.30), residues: 296
  sheet: -2.57 (0.52), residues: 85
  loop : -2.04 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 771 
 HIS   0.003   0.001   HIS A 871 
 PHE   0.024   0.001   PHE A 616 
 TYR   0.009   0.001   TYR A 566 
 ARG   0.007   0.000   ARG A 811 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03736 (  269)
  hydrogen bonds       : angle       3.75484 (  764)
  metal coordination   : bond        0.00196 (    3)
  covalent geometry    : bond        0.00352 ( 5758)
  covalent geometry    : angle       0.54643 ( 7872)
  Misc. bond           : bond        0.00060 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 66
  time to evaluate  : 0.602 
Fit side-chains
REVERT: A  492 ASP cc_start: 0.7345 (m-30) cc_final: 0.6038 (t0)
REVERT: A  632 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8334 (tt)
REVERT: A  653 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7957 (pp)
REVERT: A  759 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7513 (ttpp)
REVERT: A  763 ASP cc_start: 0.8334 (t70) cc_final: 0.8002 (t0)
REVERT: A  794 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6950 (pp30)
  outliers start: 19
  outliers final: 11
  residues processed: 83
  average time/residue: 0.1660
  time to fit residues: 18.7536
Evaluate side-chains
  77 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  794 GLN
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  903 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 14 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 41 optimal weight:   10.0000
   chunk 57 optimal weight:    0.0980
   chunk 50 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 = 0.3743 r_free = 0.3743 target = 0.156174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.126515 restraints weight = 6356.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 1.93
r_work: 0.3154 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.3407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5762  Z= 0.115
  Angle     :  0.545   8.617   7872  Z= 0.263
  Chirality :  0.041   0.161    893
  Planarity :  0.003   0.039    924
  Dihedral  : 13.320  95.303   1010
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 20.49 %
    Favored  : 76.88 %
  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: -0.03 (0.35), residues: 627
  helix:  2.23 (0.30), residues: 295
  sheet: -2.48 (0.53), residues: 85
  loop : -1.99 (0.37), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 771 
 HIS   0.002   0.000   HIS A 847 
 PHE   0.018   0.001   PHE A 616 
 TYR   0.008   0.001   TYR A 390 
 ARG   0.006   0.000   ARG A 811 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03459 (  269)
  hydrogen bonds       : angle       3.66258 (  764)
  metal coordination   : bond        0.00134 (    3)
  covalent geometry    : bond        0.00262 ( 5758)
  covalent geometry    : angle       0.54514 ( 7872)
  Misc. bond           : bond        0.00059 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.638 
Fit side-chains
REVERT: A  460 PHE cc_start: 0.8528 (m-80) cc_final: 0.8297 (m-80)
REVERT: A  492 ASP cc_start: 0.7294 (m-30) cc_final: 0.6068 (t0)
REVERT: A  526 PRO cc_start: 0.8065 (Cg_endo) cc_final: 0.7782 (Cg_exo)
REVERT: A  632 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8262 (tt)
REVERT: A  647 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8582 (mp)
REVERT: A  653 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7920 (pp)
REVERT: A  759 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7512 (ttpp)
REVERT: A  763 ASP cc_start: 0.8286 (t70) cc_final: 0.7992 (t0)
REVERT: A  794 GLN cc_start: 0.7269 (OUTLIER) cc_final: 0.6965 (pp30)
  outliers start: 15
  outliers final: 10
  residues processed: 79
  average time/residue: 0.1679
  time to fit residues: 17.8687
Evaluate side-chains
  78 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  794 GLN
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  903 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 22 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 51 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 573 ASN

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 = 0.153341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.125203 restraints weight = 6408.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 1.74
r_work: 0.3187 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.3490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5762  Z= 0.125
  Angle     :  0.555   9.005   7872  Z= 0.267
  Chirality :  0.041   0.169    893
  Planarity :  0.003   0.039    924
  Dihedral  : 13.302  95.101   1010
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 20.49 %
    Favored  : 76.71 %
  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:  0.00 (0.35), residues: 627
  helix:  2.21 (0.30), residues: 296
  sheet: -2.40 (0.53), residues: 85
  loop : -1.94 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 512 
 HIS   0.002   0.000   HIS A 847 
 PHE   0.026   0.001   PHE A 616 
 TYR   0.009   0.001   TYR A 390 
 ARG   0.007   0.001   ARG A 811 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03518 (  269)
  hydrogen bonds       : angle       3.66791 (  764)
  metal coordination   : bond        0.00148 (    3)
  covalent geometry    : bond        0.00288 ( 5758)
  covalent geometry    : angle       0.55470 ( 7872)
  Misc. bond           : bond        0.00063 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
REVERT: A  492 ASP cc_start: 0.7314 (m-30) cc_final: 0.6101 (t0)
REVERT: A  526 PRO cc_start: 0.8047 (Cg_endo) cc_final: 0.7767 (Cg_exo)
REVERT: A  632 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8308 (tt)
REVERT: A  647 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8474 (mp)
REVERT: A  653 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7961 (pp)
REVERT: A  759 LYS cc_start: 0.8077 (mtmt) cc_final: 0.7642 (ttpp)
REVERT: A  763 ASP cc_start: 0.8294 (t70) cc_final: 0.8009 (t0)
REVERT: A  794 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6971 (pp30)
  outliers start: 16
  outliers final: 10
  residues processed: 82
  average time/residue: 0.1699
  time to fit residues: 18.7320
Evaluate side-chains
  81 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  794 GLN
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  903 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9990
   chunk 59 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 9 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3746 r_free = 0.3746 target = 0.156530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.127363 restraints weight = 6483.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 1.85
r_work: 0.3154 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.3521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5762  Z= 0.126
  Angle     :  0.552   8.926   7872  Z= 0.266
  Chirality :  0.041   0.167    893
  Planarity :  0.003   0.042    924
  Dihedral  : 13.301  95.272   1010
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 20.67 %
    Favored  : 76.71 %
  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:  0.14 (0.35), residues: 627
  helix:  2.23 (0.30), residues: 296
  sheet: -2.21 (0.56), residues: 79
  loop : -1.82 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 512 
 HIS   0.001   0.000   HIS A 847 
 PHE   0.026   0.001   PHE A 616 
 TYR   0.009   0.001   TYR A 390 
 ARG   0.007   0.000   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03528 (  269)
  hydrogen bonds       : angle       3.66402 (  764)
  metal coordination   : bond        0.00153 (    3)
  covalent geometry    : bond        0.00290 ( 5758)
  covalent geometry    : angle       0.55211 ( 7872)
  Misc. bond           : bond        0.00061 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.640 
Fit side-chains
REVERT: A  492 ASP cc_start: 0.7360 (m-30) cc_final: 0.6156 (t0)
REVERT: A  632 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8283 (tt)
REVERT: A  647 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8477 (mp)
REVERT: A  653 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7971 (pp)
REVERT: A  759 LYS cc_start: 0.8098 (mtmt) cc_final: 0.7650 (ttpp)
REVERT: A  763 ASP cc_start: 0.8294 (t70) cc_final: 0.8025 (t0)
REVERT: A  794 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6960 (pp30)
REVERT: A  883 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7894 (mm-30)
  outliers start: 15
  outliers final: 11
  residues processed: 78
  average time/residue: 0.1801
  time to fit residues: 18.8478
Evaluate side-chains
  80 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  794 GLN
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  903 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 4 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3698 r_free = 0.3698 target = 0.152568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.122987 restraints weight = 6478.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 1.78
r_work: 0.3192 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3046 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.3545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5762  Z= 0.117
  Angle     :  0.544   8.741   7872  Z= 0.262
  Chirality :  0.040   0.172    893
  Planarity :  0.003   0.042    924
  Dihedral  : 13.287  94.978   1010
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 20.84 %
    Favored  : 76.53 %
  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:  0.20 (0.35), residues: 627
  helix:  2.24 (0.30), residues: 297
  sheet: -2.12 (0.57), residues: 79
  loop : -1.78 (0.38), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 512 
 HIS   0.006   0.001   HIS A 786 
 PHE   0.027   0.001   PHE A 616 
 TYR   0.009   0.001   TYR A 390 
 ARG   0.007   0.000   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03446 (  269)
  hydrogen bonds       : angle       3.64127 (  764)
  metal coordination   : bond        0.00140 (    3)
  covalent geometry    : bond        0.00266 ( 5758)
  covalent geometry    : angle       0.54391 ( 7872)
  Misc. bond           : bond        0.00059 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3053.51 seconds
wall clock time: 54 minutes 7.17 seconds (3247.17 seconds total)