Starting phenix.real_space_refine
on Fri Aug 22 18:42:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h3s_32829/08_2025/8h3s_32829.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h3s_32829/08_2025/8h3s_32829.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h3s_32829/08_2025/8h3s_32829.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h3s_32829/08_2025/8h3s_32829.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8h3s_32829/08_2025/8h3s_32829.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h3s_32829/08_2025/8h3s_32829.map"
  }
  resolution = 4.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.001
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: 4
    Type Number    sf(0)   Gaussians
     S      45      5.16       5
     C    4353      2.51       5
     N    1178      2.21       5
     O    1325      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6901
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 449, 3510
          Classifications: {'peptide': 449}
          Link IDs: {'PTRANS': 29, 'TRANS': 419}
    Chain: "B"
      Number of atoms: 1714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1714
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 203}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 1677
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1677
          Classifications: {'peptide': 221}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 209}
          Chain breaks: 1
  Time building chain proxies: 1.30, per 1000 atoms: 0.19
  Number of scatterers: 6901
  At special positions: 0
  Unit cell: (83.3, 85, 146.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      45     16.00
     O    1325      8.00
     N    1178      7.00
     C    4353      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 347 " - pdb=" SG  CYS A 354 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 422 " - pdb=" SG  CYS A 502 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 650 " - pdb=" SG  CYS A 668 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 662 " - pdb=" SG  CYS A 677 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 716 " - pdb=" SG  CYS A 767 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 772 " - pdb=" SG  CYS B 896 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 810 " - pdb=" SG  CYS B 826 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 910 " - pdb=" SG  CYS B 977 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 941 " - pdb=" SG  CYS B 956 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  48 " - pdb=" SG  CYS C  64 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 139 " - pdb=" SG  CYS C 206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 171 " - pdb=" SG  CYS C 185 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.37
  Conformation dependent library (CDL) restraints added in 321.9 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1622

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 15 sheets defined
      7.4% alpha, 20.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 340 through 346
    Processing helix  chain 'A' and resid 708 through 719
    Processing helix  chain 'B' and resid 937 through 945
    Processing helix  chain 'B' and resid 1007 through 1009
      No H-bonds generated for 'chain 'B' and resid 1007 through 1009'
    Processing helix  chain 'B' and resid 1010 through 1019
      removed outlier: 4.145A  pdb=" N   PHE B1017 " --> pdb=" O   TRP B1013 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   HIS B1019 " --> pdb=" O   GLN B1015 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 65
    Processing helix  chain 'C' and resid 167 through 175
    Processing helix  chain 'C' and resid 235 through 245
    Processing sheet with id=AA1, first strand: chain 'A' and resid 367 through 370
      removed outlier: 3.827A  pdb=" N   GLU A 367 " --> pdb=" O   SER A 395 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 405 through 410
      removed outlier: 3.670A  pdb=" N   LEU A 437 " --> pdb=" O   LYS A 454 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   LYS A 454 " --> pdb=" O   LEU A 437 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ILE A 439 " --> pdb=" O   PHE A 452 " (cutoff:3.500A)
      removed outlier: 4.835A  pdb=" N   PHE A 452 " --> pdb=" O   ILE A 439 " (cutoff:3.500A)
      removed outlier: 8.444A  pdb=" N   ILE A 441 " --> pdb=" O   THR A 450 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   THR A 450 " --> pdb=" O   ILE A 441 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 463 through 467
      removed outlier: 5.123A  pdb=" N   TRP A 426 " --> pdb=" O   ASP A 494 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   ASP A 494 " --> pdb=" O   TRP A 426 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 553 through 557
      removed outlier: 3.790A  pdb=" N   LEU A 615 " --> pdb=" O   GLU A 581 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLU A 581 " --> pdb=" O   LEU A 615 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   VAL A 580 " --> pdb=" O   VAL A 595 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   VAL A 595 " --> pdb=" O   VAL A 580 " (cutoff:3.500A)
      removed outlier: 7.576A  pdb=" N   ILE A 582 " --> pdb=" O   LEU A 593 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 571 through 572
    Processing sheet with id=AA6, first strand: chain 'A' and resid 688 through 689
      removed outlier: 3.898A  pdb=" N   GLY A 689 " --> pdb=" O   LEU A 765 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ARG A 764 " --> pdb=" O   LYS A 728 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   LYS A 728 " --> pdb=" O   ARG A 764 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 693 through 694
    Processing sheet with id=AA8, first strand: chain 'A' and resid 740 through 741
    Processing sheet with id=AA9, first strand: chain 'B' and resid 789 through 790
    Processing sheet with id=AB1, first strand: chain 'B' and resid 799 through 804
      removed outlier: 3.847A  pdb=" N   VAL B 800 " --> pdb=" O   ALA B 812 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ALA B 812 " --> pdb=" O   VAL B 800 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   CYS B 810 " --> pdb=" O   LEU B 802 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   TYR B 804 " --> pdb=" O   LEU B 808 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   LEU B 808 " --> pdb=" O   TYR B 804 " (cutoff:3.500A)
      removed outlier: 7.297A  pdb=" N   GLY B 811 " --> pdb=" O   ALA B 823 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   ALA B 823 " --> pdb=" O   GLY B 811 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   GLU B 861 " --> pdb=" O   HIS B 881 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ILE B 859 " --> pdb=" O   TRP B 837 " (cutoff:3.500A)
      removed outlier: 5.597A  pdb=" N   TRP B 837 " --> pdb=" O   ILE B 859 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLY B 801 " --> pdb=" O   ILE B 840 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 910 through 911
    Processing sheet with id=AB3, first strand: chain 'B' and resid 954 through 956
    Processing sheet with id=AB4, first strand: chain 'B' and resid 974 through 978
      removed outlier: 3.766A  pdb=" N   GLY B 987 " --> pdb=" O   LEU B 975 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   CYS B 977 " --> pdb=" O   LEU B 985 " (cutoff:3.500A)
      removed outlier: 5.640A  pdb=" N   LEU B 985 " --> pdb=" O   CYS B 977 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 46 through 49
      removed outlier: 4.284A  pdb=" N   CYS C  48 " --> pdb=" O   LEU C  41 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   LYS C 112 " --> pdb=" O   ALA C  91 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   ILE C  93 " --> pdb=" O   LEU C 110 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   LEU C 110 " --> pdb=" O   ILE C  93 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 159 through 164
      removed outlier: 3.684A  pdb=" N   SER C 142 " --> pdb=" O   PRO C 203 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   VAL C 204 " --> pdb=" O   GLN C 211 " (cutoff:3.500A)
      removed outlier: 7.386A  pdb=" N   VAL C 228 " --> pdb=" O   SER C 215 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   GLY C 227 " --> pdb=" O   VAL C 186 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   VAL C 186 " --> pdb=" O   GLY C 227 " (cutoff:3.500A)

    131 hydrogen bonds defined for protein.
    336 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.03

  Time building geometry restraints manager: 0.56 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2300
        1.35 -     1.46: 1626
        1.46 -     1.58: 3091
        1.58 -     1.70: 0
        1.70 -     1.82: 56
  Bond restraints: 7073
  Sorted by residual:
  bond pdb=" N   VAL A 513 "
       pdb=" CA  VAL A 513 "
    ideal  model  delta    sigma   weight residual
    1.465  1.494 -0.029 1.02e-02 9.61e+03 8.18e+00
  bond pdb=" N   THR A 511 "
       pdb=" CA  THR A 511 "
    ideal  model  delta    sigma   weight residual
    1.461  1.488 -0.026 1.20e-02 6.94e+03 4.86e+00
  bond pdb=" N   LEU A 512 "
       pdb=" CA  LEU A 512 "
    ideal  model  delta    sigma   weight residual
    1.462  1.489 -0.027 1.26e-02 6.30e+03 4.66e+00
  bond pdb=" CA  THR A 511 "
       pdb=" C   THR A 511 "
    ideal  model  delta    sigma   weight residual
    1.519  1.532 -0.013 1.14e-02 7.69e+03 1.25e+00
  bond pdb=" CA  VAL A 513 "
       pdb=" CB  VAL A 513 "
    ideal  model  delta    sigma   weight residual
    1.526  1.541 -0.015 1.55e-02 4.16e+03 9.99e-01
  ... (remaining 7068 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.30: 9412
        1.30 -     2.59: 170
        2.59 -     3.89: 41
        3.89 -     5.18: 2
        5.18 -     6.48: 1
  Bond angle restraints: 9626
  Sorted by residual:
  angle pdb=" N   ASP A 460 "
        pdb=" CA  ASP A 460 "
        pdb=" C   ASP A 460 "
      ideal   model   delta    sigma   weight residual
     114.39  110.79    3.60 1.45e+00 4.76e-01 6.15e+00
  angle pdb=" C   SER A 545 "
        pdb=" N   TYR A 546 "
        pdb=" CA  TYR A 546 "
      ideal   model   delta    sigma   weight residual
     120.97  114.49    6.48 2.84e+00 1.24e-01 5.20e+00
  angle pdb=" CA  LEU A 512 "
        pdb=" C   LEU A 512 "
        pdb=" O   LEU A 512 "
      ideal   model   delta    sigma   weight residual
     120.92  118.68    2.24 1.04e+00 9.25e-01 4.65e+00
  angle pdb=" C   VAL A 513 "
        pdb=" N   PRO A 514 "
        pdb=" CA  PRO A 514 "
      ideal   model   delta    sigma   weight residual
     119.84  122.37   -2.53 1.25e+00 6.40e-01 4.11e+00
  angle pdb=" N   PHE A 542 "
        pdb=" CA  PHE A 542 "
        pdb=" C   PHE A 542 "
      ideal   model   delta    sigma   weight residual
     113.16  115.82   -2.66 1.42e+00 4.96e-01 3.50e+00
  ... (remaining 9621 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.30: 4014
       17.30 -    34.59: 166
       34.59 -    51.89: 24
       51.89 -    69.18: 6
       69.18 -    86.48: 4
  Dihedral angle restraints: 4214
    sinusoidal: 1679
      harmonic: 2535
  Sorted by residual:
  dihedral pdb=" CA  GLU A 532 "
           pdb=" C   GLU A 532 "
           pdb=" N   PRO A 533 "
           pdb=" CA  PRO A 533 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.37  -23.63     0      5.00e+00 4.00e-02 2.23e+01
  dihedral pdb=" CB  CYS A 716 "
           pdb=" SG  CYS A 716 "
           pdb=" SG  CYS A 767 "
           pdb=" CB  CYS A 767 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  127.85  -34.85     1      1.00e+01 1.00e-02 1.72e+01
  dihedral pdb=" CA  SER A 539 "
           pdb=" C   SER A 539 "
           pdb=" N   THR A 540 "
           pdb=" CA  THR A 540 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.42   17.58     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 4211 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 593
       0.025 -    0.050: 269
       0.050 -    0.075: 73
       0.075 -    0.101: 53
       0.101 -    0.126: 50
  Chirality restraints: 1038
  Sorted by residual:
  chirality pdb=" CA  VAL A 513 "
            pdb=" N   VAL A 513 "
            pdb=" C   VAL A 513 "
            pdb=" CB  VAL A 513 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.95e-01
  chirality pdb=" CA  ILE A 490 "
            pdb=" N   ILE A 490 "
            pdb=" C   ILE A 490 "
            pdb=" CB  ILE A 490 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.92e-01
  chirality pdb=" CA  VAL B 988 "
            pdb=" N   VAL B 988 "
            pdb=" C   VAL B 988 "
            pdb=" CB  VAL B 988 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.58e-01
  ... (remaining 1035 not shown)

  Planarity restraints: 1276
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 515 "    0.029 5.00e-02 4.00e+02   4.38e-02 3.07e+00
        pdb=" N   PRO A 516 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 516 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 516 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 517 "    0.024 5.00e-02 4.00e+02   3.62e-02 2.10e+00
        pdb=" N   PRO A 518 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 518 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 518 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 542 "    0.019 5.00e-02 4.00e+02   2.84e-02 1.29e+00
        pdb=" N   PRO A 543 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO A 543 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 543 "    0.016 5.00e-02 4.00e+02
  ... (remaining 1273 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 541
        2.74 -     3.28: 6922
        3.28 -     3.82: 11384
        3.82 -     4.36: 13020
        4.36 -     4.90: 22240
  Nonbonded interactions: 54107
  Sorted by model distance:
  nonbonded pdb=" O   GLU A 574 "
            pdb=" OG1 THR A 597 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OD1 ASP A 584 "
            pdb=" OG1 THR A 609 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   SER A 375 "
            pdb=" OG1 THR A 378 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OD2 ASP A 383 "
            pdb=" OG1 THR A 385 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   ILE C 243 "
            pdb=" OG  SER C 247 "
     model   vdw
     2.301 3.040
  ... (remaining 54102 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:             0.930
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.640
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6579
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      :  0.002   0.044   7085  Z= 0.103
  Angle     :  0.445   6.478   9650  Z= 0.246
  Chirality :  0.041   0.126   1038
  Planarity :  0.003   0.044   1276
  Dihedral  :  9.515  86.476   2556
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  :  5.77 %
    Favored  : 91.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.26 (0.24), residues: 876
  helix: -2.90 (0.45), residues: 58
  sheet: -2.77 (0.33), residues: 196
  loop : -3.05 (0.22), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B1000 
 TYR   0.005   0.000   TYR A 546 
 PHE   0.006   0.001   PHE A 475 
 TRP   0.005   0.000   TRP A 366 
 HIS   0.001   0.000   HIS A 700 

Details of bonding type rmsd
  covalent geometry    : bond        0.00178 ( 7073)
  covalent geometry    : angle       0.44487 ( 9626)
  SS BOND              : bond        0.00144 (   12)
  SS BOND              : angle       0.48588 (   24)
  hydrogen bonds       : bond        0.28779 (  131)
  hydrogen bonds       : angle      11.70257 (  336)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 176
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7236 (tm-30)
REVERT: A  419 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8170 (pm20)
REVERT: A  437 LEU cc_start: 0.8326 (pt) cc_final: 0.7838 (pp)
REVERT: A  520 LEU cc_start: 0.8906 (mp) cc_final: 0.8388 (pp)
REVERT: A  582 ILE cc_start: 0.8552 (mt) cc_final: 0.8197 (tt)
REVERT: A  714 ASP cc_start: 0.8561 (m-30) cc_final: 0.8144 (m-30)
REVERT: B  867 HIS cc_start: 0.9104 (m-70) cc_final: 0.8869 (t-90)
REVERT: B  975 LEU cc_start: 0.9317 (tp) cc_final: 0.9049 (tp)
REVERT: B 1017 PHE cc_start: 0.8326 (m-80) cc_final: 0.8008 (m-80)
REVERT: C   30 CYS cc_start: 0.4856 (t) cc_final: 0.4322 (p)
  outliers start: 21
  outliers final: 4
  residues processed: 192
  average time/residue: 0.0983
  time to fit residues: 23.6806
Evaluate side-chains
  95 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.0070
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    8.9990
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    1.0000

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

Flipped N/Q/H residues before XYZ refinement:
A 341 ASN
A 435 HIS
A 453 GLN
A 548 ASN
** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 713 ASN
A 766 GLN
A 768 ASN
A 769 HIS
** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 938 ASN
B 943 GLN
B 978 GLN
** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 234 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.077032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.060968 restraints weight = 63792.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.062025 restraints weight = 54251.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.062830 restraints weight = 47677.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.063517 restraints weight = 43043.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.064076 restraints weight = 39509.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6799
moved from start:          0.3332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7085  Z= 0.138
  Angle     :  0.618   8.045   9650  Z= 0.319
  Chirality :  0.046   0.161   1038
  Planarity :  0.004   0.049   1276
  Dihedral  :  3.893  24.955    943
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 13.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.02 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.41 %
    Favored  : 96.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.77 (0.25), residues: 876
  helix: -2.05 (0.48), residues: 65
  sheet: -2.33 (0.35), residues: 185
  loop : -2.81 (0.22), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 403 
 TYR   0.009   0.001   TYR A 458 
 PHE   0.016   0.001   PHE A 542 
 TRP   0.015   0.001   TRP B 983 
 HIS   0.002   0.001   HIS A 700 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7073)
  covalent geometry    : angle       0.61266 ( 9626)
  SS BOND              : bond        0.00535 (   12)
  SS BOND              : angle       1.69794 (   24)
  hydrogen bonds       : bond        0.04558 (  131)
  hydrogen bonds       : angle       8.56469 (  336)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  437 LEU cc_start: 0.8828 (pt) cc_final: 0.8562 (pt)
REVERT: A  520 LEU cc_start: 0.8832 (mp) cc_final: 0.8238 (pp)
REVERT: A  564 ILE cc_start: 0.8487 (mp) cc_final: 0.8027 (mp)
REVERT: A  568 PHE cc_start: 0.7327 (m-80) cc_final: 0.7026 (m-80)
REVERT: A  615 LEU cc_start: 0.9505 (mp) cc_final: 0.9234 (mp)
REVERT: B  867 HIS cc_start: 0.9083 (m-70) cc_final: 0.8821 (t70)
REVERT: B 1017 PHE cc_start: 0.8714 (m-80) cc_final: 0.8319 (m-80)
REVERT: C   30 CYS cc_start: 0.4178 (t) cc_final: 0.3735 (p)
REVERT: C  109 MET cc_start: 0.7440 (ttp) cc_final: 0.6923 (ttp)
  outliers start: 1
  outliers final: 0
  residues processed: 106
  average time/residue: 0.0810
  time to fit residues: 11.1633
Evaluate side-chains
  66 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 63 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9990
   chunk 71 optimal weight:    9.9990
   chunk 19 optimal weight:    7.9990
   chunk 10 optimal weight:    9.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 453 GLN
** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 665 HIS
B 875 ASN
** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.073552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.057979 restraints weight = 65338.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.058910 restraints weight = 56709.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.059625 restraints weight = 50550.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.060211 restraints weight = 46123.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.060567 restraints weight = 42752.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6939
moved from start:          0.4197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7085  Z= 0.130
  Angle     :  0.590   6.797   9650  Z= 0.304
  Chirality :  0.045   0.145   1038
  Planarity :  0.004   0.053   1276
  Dihedral  :  4.143  25.406    943
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 14.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.27 %
    Favored  : 89.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.37 (0.26), residues: 876
  helix: -1.20 (0.56), residues: 63
  sheet: -2.05 (0.36), residues: 181
  loop : -2.59 (0.23), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 368 
 TYR   0.012   0.001   TYR C 229 
 PHE   0.014   0.002   PHE A 731 
 TRP   0.013   0.001   TRP B 983 
 HIS   0.006   0.001   HIS A 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7073)
  covalent geometry    : angle       0.58807 ( 9626)
  SS BOND              : bond        0.00593 (   12)
  SS BOND              : angle       1.07699 (   24)
  hydrogen bonds       : bond        0.03337 (  131)
  hydrogen bonds       : angle       7.74805 (  336)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  437 LEU cc_start: 0.8796 (pt) cc_final: 0.8538 (pt)
REVERT: A  627 PHE cc_start: 0.8377 (p90) cc_final: 0.8122 (p90)
REVERT: B  845 MET cc_start: 0.9047 (tpt) cc_final: 0.8744 (tpp)
REVERT: B  867 HIS cc_start: 0.9021 (m-70) cc_final: 0.8713 (t70)
REVERT: B 1017 PHE cc_start: 0.8655 (m-80) cc_final: 0.8342 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.0941
  time to fit residues: 10.9931
Evaluate side-chains
  57 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 13 optimal weight:   10.0000
   chunk 27 optimal weight:    8.9990
   chunk 18 optimal weight:    0.9980
   chunk 20 optimal weight:    5.9990
   chunk 14 optimal weight:    8.9990
   chunk 62 optimal weight:    6.9990
   chunk 30 optimal weight:    7.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    1.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 453 GLN
** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 944 GLN
** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 234 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.070489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.054738 restraints weight = 67624.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.055658 restraints weight = 59091.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.056340 restraints weight = 52757.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.056932 restraints weight = 48250.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.057368 restraints weight = 44736.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
moved from start:          0.4884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7085  Z= 0.135
  Angle     :  0.598   6.322   9650  Z= 0.309
  Chirality :  0.044   0.144   1038
  Planarity :  0.005   0.102   1276
  Dihedral  :  4.395  27.292    943
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 15.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.62 %
    Favored  : 89.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.25 (0.26), residues: 876
  helix: -1.16 (0.61), residues: 56
  sheet: -2.04 (0.36), residues: 178
  loop : -2.46 (0.23), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 908 
 TYR   0.027   0.001   TYR B1004 
 PHE   0.011   0.001   PHE B 904 
 TRP   0.009   0.001   TRP B1013 
 HIS   0.003   0.001   HIS A 384 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 7073)
  covalent geometry    : angle       0.59438 ( 9626)
  SS BOND              : bond        0.00432 (   12)
  SS BOND              : angle       1.44290 (   24)
  hydrogen bonds       : bond        0.03025 (  131)
  hydrogen bonds       : angle       7.39957 (  336)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  437 LEU cc_start: 0.8817 (pt) cc_final: 0.8533 (pt)
REVERT: A  579 VAL cc_start: 0.8549 (m) cc_final: 0.8313 (m)
REVERT: A  612 MET cc_start: 0.7851 (mmp) cc_final: 0.7643 (mmm)
REVERT: B  845 MET cc_start: 0.9055 (tpt) cc_final: 0.8785 (tpp)
REVERT: B  867 HIS cc_start: 0.9027 (m-70) cc_final: 0.8743 (t70)
REVERT: B  900 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8779 (tm-30)
REVERT: B 1017 PHE cc_start: 0.8644 (m-80) cc_final: 0.8253 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.0833
  time to fit residues: 8.8957
Evaluate side-chains
  59 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 79 optimal weight:   30.0000
   chunk 68 optimal weight:    9.9990
   chunk 38 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   chunk 75 optimal weight:   20.0000
   chunk 30 optimal weight:    0.0970
   chunk 74 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 8 optimal weight:    7.9990
   overall best weight:    3.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 453 GLN
A 457 ASN
A 463 ASN
** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  76 HIS
** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.064049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.048908 restraints weight = 73333.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.049756 restraints weight = 63316.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.050420 restraints weight = 56414.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.050955 restraints weight = 51362.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.051359 restraints weight = 47578.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.6214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7085  Z= 0.202
  Angle     :  0.703   6.713   9650  Z= 0.367
  Chirality :  0.046   0.149   1038
  Planarity :  0.006   0.097   1276
  Dihedral  :  5.227  31.078    943
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 26.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.10 %
    Favored  : 87.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.85 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.23 (0.26), residues: 876
  helix: -1.29 (0.59), residues: 56
  sheet: -2.15 (0.37), residues: 178
  loop : -2.40 (0.23), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 694 
 TYR   0.012   0.002   TYR C  65 
 PHE   0.018   0.002   PHE A 479 
 TRP   0.025   0.002   TRP B1013 
 HIS   0.006   0.002   HIS A 567 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 7073)
  covalent geometry    : angle       0.69717 ( 9626)
  SS BOND              : bond        0.00521 (   12)
  SS BOND              : angle       1.88230 (   24)
  hydrogen bonds       : bond        0.03674 (  131)
  hydrogen bonds       : angle       7.31438 (  336)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  566 LEU cc_start: 0.9477 (tp) cc_final: 0.9274 (tp)
REVERT: B  845 MET cc_start: 0.9158 (tpt) cc_final: 0.8915 (tpp)
REVERT: B  910 CYS cc_start: 0.7125 (p) cc_final: 0.6823 (p)
REVERT: B 1017 PHE cc_start: 0.8702 (m-80) cc_final: 0.8348 (m-80)
REVERT: C   30 CYS cc_start: 0.4020 (t) cc_final: 0.3792 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.0877
  time to fit residues: 8.5858
Evaluate side-chains
  58 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 44 optimal weight:   20.0000
   chunk 38 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 8 optimal weight:    4.9990
   chunk 71 optimal weight:    4.9990
   chunk 84 optimal weight:    9.9990
   chunk 68 optimal weight:   10.0000
   chunk 75 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 453 GLN
** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 234 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.063238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.048305 restraints weight = 73018.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.049134 restraints weight = 64178.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.049730 restraints weight = 57277.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.050241 restraints weight = 52493.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.050645 restraints weight = 48812.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7287
moved from start:          0.6685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7085  Z= 0.173
  Angle     :  0.655   6.365   9650  Z= 0.343
  Chirality :  0.046   0.209   1038
  Planarity :  0.005   0.065   1276
  Dihedral  :  5.314  29.992    943
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 23.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.10 %
    Favored  : 87.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.18 (0.27), residues: 876
  helix: -1.39 (0.61), residues: 56
  sheet: -1.94 (0.36), residues: 200
  loop : -2.40 (0.24), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 679 
 TYR   0.015   0.002   TYR C 229 
 PHE   0.014   0.002   PHE B 991 
 TRP   0.011   0.002   TRP A 699 
 HIS   0.006   0.001   HIS B 867 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 7073)
  covalent geometry    : angle       0.65158 ( 9626)
  SS BOND              : bond        0.00461 (   12)
  SS BOND              : angle       1.50051 (   24)
  hydrogen bonds       : bond        0.03367 (  131)
  hydrogen bonds       : angle       7.38181 (  336)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  506 LEU cc_start: 0.8607 (mt) cc_final: 0.8321 (pp)
REVERT: A  507 TYR cc_start: 0.8956 (m-80) cc_final: 0.8598 (m-80)
REVERT: A  566 LEU cc_start: 0.9534 (tp) cc_final: 0.9331 (tp)
REVERT: A  579 VAL cc_start: 0.8865 (p) cc_final: 0.8453 (m)
REVERT: A  636 HIS cc_start: 0.8763 (m-70) cc_final: 0.8307 (p-80)
REVERT: B  845 MET cc_start: 0.9180 (tpt) cc_final: 0.8938 (tpp)
REVERT: B  867 HIS cc_start: 0.8194 (t70) cc_final: 0.7848 (t70)
REVERT: B 1017 PHE cc_start: 0.8705 (m-80) cc_final: 0.8338 (m-80)
REVERT: C   41 LEU cc_start: 0.9034 (mt) cc_final: 0.8826 (mt)
REVERT: C  229 TYR cc_start: 0.8082 (m-80) cc_final: 0.7853 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.0934
  time to fit residues: 8.8472
Evaluate side-chains
  57 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   chunk 22 optimal weight:    0.8980
   chunk 9 optimal weight:    6.9990
   chunk 37 optimal weight:    9.9990
   chunk 46 optimal weight:   20.0000
   chunk 35 optimal weight:    8.9990
   chunk 19 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 50 optimal weight:    9.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.060708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.046297 restraints weight = 74472.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.047023 restraints weight = 65152.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.047564 restraints weight = 58595.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.048029 restraints weight = 53992.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.048383 restraints weight = 50472.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.7339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7085  Z= 0.186
  Angle     :  0.678   7.883   9650  Z= 0.355
  Chirality :  0.046   0.167   1038
  Planarity :  0.006   0.061   1276
  Dihedral  :  5.598  31.290    943
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 26.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.36 %
    Favored  : 86.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.85 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.30 (0.27), residues: 876
  helix: -1.44 (0.61), residues: 56
  sheet: -2.14 (0.35), residues: 206
  loop : -2.44 (0.24), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 679 
 TYR   0.015   0.002   TYR C 229 
 PHE   0.014   0.002   PHE A 479 
 TRP   0.015   0.002   TRP A 699 
 HIS   0.005   0.001   HIS B 867 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 7073)
  covalent geometry    : angle       0.67169 ( 9626)
  SS BOND              : bond        0.00487 (   12)
  SS BOND              : angle       1.95424 (   24)
  hydrogen bonds       : bond        0.03556 (  131)
  hydrogen bonds       : angle       7.46787 (  336)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  490 ILE cc_start: 0.9348 (mt) cc_final: 0.8886 (mm)
REVERT: A  506 LEU cc_start: 0.8605 (mt) cc_final: 0.8285 (pp)
REVERT: A  507 TYR cc_start: 0.9038 (m-80) cc_final: 0.8614 (m-80)
REVERT: A  579 VAL cc_start: 0.8906 (p) cc_final: 0.8517 (m)
REVERT: A  612 MET cc_start: 0.8227 (mmp) cc_final: 0.7617 (mmm)
REVERT: A  636 HIS cc_start: 0.8896 (m-70) cc_final: 0.8415 (p-80)
REVERT: A  765 LEU cc_start: 0.9064 (tp) cc_final: 0.8826 (tp)
REVERT: B  845 MET cc_start: 0.9235 (tpt) cc_final: 0.9002 (tpp)
REVERT: B  867 HIS cc_start: 0.8225 (t70) cc_final: 0.7950 (t70)
REVERT: B 1017 PHE cc_start: 0.8745 (m-80) cc_final: 0.8319 (m-80)
REVERT: C  229 TYR cc_start: 0.8105 (m-80) cc_final: 0.7879 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.0917
  time to fit residues: 9.1300
Evaluate side-chains
  60 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 62 optimal weight:    9.9990
   chunk 58 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   chunk 21 optimal weight:    7.9990
   chunk 51 optimal weight:    6.9990
   chunk 36 optimal weight:    6.9990
   chunk 17 optimal weight:    0.5980
   chunk 61 optimal weight:   10.0000
   chunk 18 optimal weight:    5.9990
   overall best weight:    4.3188

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

Flipped N/Q/H residues before XYZ refinement:
A 453 GLN
** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 717 GLN
** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 867 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.058030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.043921 restraints weight = 78354.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.044668 restraints weight = 68654.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.045220 restraints weight = 61370.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.045690 restraints weight = 56119.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.045962 restraints weight = 52215.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.8173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   7085  Z= 0.220
  Angle     :  0.764   8.979   9650  Z= 0.400
  Chirality :  0.048   0.195   1038
  Planarity :  0.007   0.159   1276
  Dihedral  :  6.230  30.801    943
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 32.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.84 %
    Favored  : 85.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.85 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.52 (0.26), residues: 876
  helix: -1.57 (0.59), residues: 54
  sheet: -2.39 (0.33), residues: 202
  loop : -2.56 (0.24), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 830 
 TYR   0.017   0.003   TYR B 804 
 PHE   0.029   0.002   PHE B1010 
 TRP   0.017   0.003   TRP B 819 
 HIS   0.008   0.002   HIS A 428 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 ( 7073)
  covalent geometry    : angle       0.75767 ( 9626)
  SS BOND              : bond        0.00535 (   12)
  SS BOND              : angle       2.11183 (   24)
  hydrogen bonds       : bond        0.04082 (  131)
  hydrogen bonds       : angle       7.89522 (  336)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  579 VAL cc_start: 0.8897 (p) cc_final: 0.8648 (m)
REVERT: A  612 MET cc_start: 0.8539 (mmp) cc_final: 0.8257 (mmm)
REVERT: A  636 HIS cc_start: 0.8924 (m-70) cc_final: 0.8512 (p-80)
REVERT: A  765 LEU cc_start: 0.9079 (tp) cc_final: 0.8809 (tp)
REVERT: B  845 MET cc_start: 0.9270 (tpt) cc_final: 0.9057 (tpp)
REVERT: B 1017 PHE cc_start: 0.8699 (m-80) cc_final: 0.8326 (m-80)
REVERT: C  229 TYR cc_start: 0.8082 (m-80) cc_final: 0.7843 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.0893
  time to fit residues: 8.1449
Evaluate side-chains
  49 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 35 optimal weight:   10.0000
   chunk 73 optimal weight:    6.9990
   chunk 57 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 70 optimal weight:    5.9990
   chunk 84 optimal weight:    8.9990
   chunk 43 optimal weight:    5.9990
   chunk 82 optimal weight:    8.9990
   chunk 45 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    2.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 790 ASN
** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 234 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.058848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.044661 restraints weight = 77207.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.045350 restraints weight = 67852.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.045887 restraints weight = 61304.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.046316 restraints weight = 56432.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.046555 restraints weight = 52799.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.8286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   7085  Z= 0.171
  Angle     :  0.704   8.686   9650  Z= 0.368
  Chirality :  0.048   0.189   1038
  Planarity :  0.006   0.113   1276
  Dihedral  :  5.995  29.266    943
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 26.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.36 %
    Favored  : 86.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.46 (0.27), residues: 876
  helix: -1.53 (0.60), residues: 56
  sheet: -2.49 (0.33), residues: 207
  loop : -2.45 (0.25), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 679 
 TYR   0.021   0.002   TYR B 804 
 PHE   0.016   0.002   PHE A 382 
 TRP   0.022   0.002   TRP A 356 
 HIS   0.004   0.001   HIS B 867 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 7073)
  covalent geometry    : angle       0.69516 ( 9626)
  SS BOND              : bond        0.00446 (   12)
  SS BOND              : angle       2.32191 (   24)
  hydrogen bonds       : bond        0.03331 (  131)
  hydrogen bonds       : angle       7.45999 (  336)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  490 ILE cc_start: 0.9490 (mt) cc_final: 0.9166 (mt)
REVERT: A  579 VAL cc_start: 0.8865 (p) cc_final: 0.8586 (m)
REVERT: A  612 MET cc_start: 0.8456 (mmp) cc_final: 0.8201 (mmm)
REVERT: A  636 HIS cc_start: 0.8927 (m-70) cc_final: 0.8488 (p-80)
REVERT: A  765 LEU cc_start: 0.9074 (tp) cc_final: 0.8869 (tp)
REVERT: B  845 MET cc_start: 0.9274 (tpt) cc_final: 0.9063 (tpp)
REVERT: C  229 TYR cc_start: 0.8116 (m-80) cc_final: 0.7880 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.0910
  time to fit residues: 8.1930
Evaluate side-chains
  52 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 44 optimal weight:    7.9990
   chunk 60 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 69 optimal weight:    5.9990
   chunk 28 optimal weight:    8.9990
   chunk 23 optimal weight:    3.9990
   chunk 74 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.058282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.044133 restraints weight = 76800.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.044846 restraints weight = 67154.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.045416 restraints weight = 60376.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.045846 restraints weight = 55372.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 15)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.046103 restraints weight = 51760.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.8534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7085  Z= 0.179
  Angle     :  0.745   9.379   9650  Z= 0.386
  Chirality :  0.048   0.211   1038
  Planarity :  0.006   0.114   1276
  Dihedral  :  6.264  30.024    943
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 28.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.16 %
    Favored  : 85.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.85 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.42 (0.27), residues: 876
  helix: -1.28 (0.63), residues: 56
  sheet: -2.42 (0.32), residues: 219
  loop : -2.45 (0.25), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 679 
 TYR   0.022   0.002   TYR B 804 
 PHE   0.026   0.002   PHE B1010 
 TRP   0.027   0.002   TRP B1013 
 HIS   0.009   0.002   HIS B1019 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 7073)
  covalent geometry    : angle       0.73304 ( 9626)
  SS BOND              : bond        0.00471 (   12)
  SS BOND              : angle       2.77890 (   24)
  hydrogen bonds       : bond        0.03638 (  131)
  hydrogen bonds       : angle       7.66293 (  336)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  579 VAL cc_start: 0.8896 (p) cc_final: 0.8637 (m)
REVERT: A  636 HIS cc_start: 0.8941 (m-70) cc_final: 0.8494 (p-80)
REVERT: B  845 MET cc_start: 0.9197 (tpt) cc_final: 0.8994 (tpp)
REVERT: B  976 MET cc_start: 0.7712 (ptt) cc_final: 0.6309 (ptt)
REVERT: B 1013 TRP cc_start: 0.6827 (t60) cc_final: 0.6278 (t60)
REVERT: B 1017 PHE cc_start: 0.7007 (p90) cc_final: 0.6145 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.0863
  time to fit residues: 8.1491
Evaluate side-chains
  54 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 43 optimal weight:    8.9990
   chunk 21 optimal weight:    7.9990
   chunk 68 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 75 optimal weight:   20.0000
   chunk 17 optimal weight:    7.9990
   chunk 72 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 67 optimal weight:    8.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 929 GLN
** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.057199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.043268 restraints weight = 77830.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.043958 restraints weight = 68111.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.044502 restraints weight = 61161.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.044918 restraints weight = 56232.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.045164 restraints weight = 52601.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
moved from start:          0.8914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7085  Z= 0.192
  Angle     :  0.753   8.470   9650  Z= 0.392
  Chirality :  0.049   0.174   1038
  Planarity :  0.006   0.111   1276
  Dihedral  :  6.410  32.736    943
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 30.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.27 %
    Favored  : 85.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.85 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.52 (0.26), residues: 876
  helix: -1.30 (0.62), residues: 56
  sheet: -2.52 (0.33), residues: 205
  loop : -2.52 (0.24), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 807 
 TYR   0.025   0.003   TYR B 804 
 PHE   0.024   0.002   PHE B1010 
 TRP   0.027   0.002   TRP B 819 
 HIS   0.008   0.002   HIS A 428 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 7073)
  covalent geometry    : angle       0.74346 ( 9626)
  SS BOND              : bond        0.00461 (   12)
  SS BOND              : angle       2.56173 (   24)
  hydrogen bonds       : bond        0.03537 (  131)
  hydrogen bonds       : angle       7.55761 (  336)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1230.02 seconds
wall clock time: 21 minutes 55.43 seconds (1315.43 seconds total)