Starting phenix.real_space_refine
on Thu Jun  5 03:28:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cy1_46004/06_2025/9cy1_46004.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cy1_46004/06_2025/9cy1_46004.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cy1_46004/06_2025/9cy1_46004.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cy1_46004/06_2025/9cy1_46004.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cy1_46004/06_2025/9cy1_46004.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cy1_46004/06_2025/9cy1_46004.cif"
  }
  resolution = 3.15
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.035
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      39      5.16       5
     C    3286      2.51       5
     N     812      2.21       5
     O     889      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5026
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 529, 4114
          Classifications: {'peptide': 529}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 19, 'TRANS': 509}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 5
    Chain: "B"
      Number of atoms: 912
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 912
          Classifications: {'peptide': 120}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
  Time building chain proxies: 3.53, per 1000 atoms: 0.70
  Number of scatterers: 5026
  At special positions: 0
  Unit cell: (61.544, 103.306, 103.306, 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      39     16.00
     O     889      8.00
     N     812      7.00
     C    3286      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 430 " - pdb=" SG  CYS A 530 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 459 " - pdb=" SG  CYS A 506 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 465 " - pdb=" SG  CYS A 485 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 474 " - pdb=" SG  CYS A 524 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 489 " - pdb=" SG  CYS A 504 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 599 " - pdb=" SG  CYS A 613 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  26 " - pdb=" SG  CYS B 100 " 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: 3.30
  Conformation dependent library (CDL) restraints added in 922.6 milliseconds
  

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1176

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 7 sheets defined
      57.6% alpha, 11.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 51
    Processing helix  chain 'A' and resid 51 through 60
    Processing helix  chain 'A' and resid 62 through 88
      removed outlier: 4.323A  pdb=" N   PHE A  73 " --> pdb=" O   ILE A  69 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   GLU A  74 " --> pdb=" O   ASP A  70 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LEU A  79 " --> pdb=" O   ILE A  75 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   VAL A  80 " --> pdb=" O   GLY A  76 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   VAL A  82 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
      removed outlier: 5.569A  pdb=" N   PHE A  83 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 117
      removed outlier: 3.519A  pdb=" N   ALA A 112 " --> pdb=" O   GLY A 108 " (cutoff:3.500A)
      Proline residue:  A 114  - end of helix
      removed outlier: 3.883A  pdb=" N   PHE A 117 " --> pdb=" O   LEU A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 185
      removed outlier: 3.789A  pdb=" N   VAL A 174 " --> pdb=" O   MET A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 200
      removed outlier: 3.615A  pdb=" N   PHE A 199 " --> pdb=" O   TYR A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 216
    Processing helix  chain 'A' and resid 217 through 232
      removed outlier: 3.732A  pdb=" N   ILE A 221 " --> pdb=" O   MET A 217 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   LYS A 232 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 274
      removed outlier: 3.756A  pdb=" N   ASN A 261 " --> pdb=" O   ALA A 257 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   PHE A 262 " --> pdb=" O   TRP A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 325 through 334
    Processing helix  chain 'A' and resid 335 through 367
      removed outlier: 3.991A  pdb=" N   TYR A 358 " --> pdb=" O   GLY A 354 " (cutoff:3.500A)
      removed outlier: 5.245A  pdb=" N   PHE A 360 " --> pdb=" O   PHE A 356 " (cutoff:3.500A)
      removed outlier: 5.466A  pdb=" N   LYS A 361 " --> pdb=" O   THR A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 401
    Processing helix  chain 'A' and resid 403 through 423
    Processing helix  chain 'A' and resid 424 through 427
    Processing helix  chain 'A' and resid 457 through 461
      removed outlier: 3.647A  pdb=" N   ASN A 460 " --> pdb=" O   SER A 457 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   SER A 461 " --> pdb=" O   TYR A 458 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 457 through 461'
    Processing helix  chain 'A' and resid 527 through 551
      removed outlier: 3.725A  pdb=" N   LYS A 533 " --> pdb=" O   ALA A 529 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   GLY A 551 " --> pdb=" O   PHE A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 563
      removed outlier: 4.241A  pdb=" N   HIS A 555 " --> pdb=" O   GLY A 551 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   VAL A 556 " --> pdb=" O   GLY A 552 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   VAL A 563 " --> pdb=" O   ILE A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 566
      No H-bonds generated for 'chain 'A' and resid 564 through 566'
    Processing helix  chain 'A' and resid 567 through 583
      removed outlier: 3.628A  pdb=" N   HIS A 575 " --> pdb=" O   ALA A 571 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   SER A 576 " --> pdb=" O   LEU A 572 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ARG A 580 " --> pdb=" O   SER A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 596
      removed outlier: 3.720A  pdb=" N   ILE A 589 " --> pdb=" O   ILE A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 617 through 651
      removed outlier: 3.733A  pdb=" N   SER A 636 " --> pdb=" O   LEU A 632 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 95
    Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 436
    Processing sheet with id=AA2, first strand: chain 'A' and resid 489 through 491
      removed outlier: 5.759A  pdb=" N   CYS A 489 " --> pdb=" O   CYS A 504 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   CYS A 504 " --> pdb=" O   CYS A 489 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 599 through 602
      removed outlier: 6.857A  pdb=" N   THR A 615 " --> pdb=" O   ILE A 600 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   TRP A 602 " --> pdb=" O   CYS A 613 " (cutoff:3.500A)
      removed outlier: 7.205A  pdb=" N   CYS A 613 " --> pdb=" O   TRP A 602 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 11
    Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 17
      removed outlier: 6.792A  pdb=" N   VAL B  16 " --> pdb=" O   SER B 118 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 62 through 64
      removed outlier: 6.587A  pdb=" N   TRP B  40 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   ALA B  54 " --> pdb=" O   MET B  38 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   MET B  38 " --> pdb=" O   ALA B  54 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 62 through 64
      removed outlier: 6.587A  pdb=" N   TRP B  40 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   ALA B  54 " --> pdb=" O   MET B  38 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   MET B  38 " --> pdb=" O   ALA B  54 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   THR B 113 " --> pdb=" O   TYR B  98 " (cutoff:3.500A)

    306 hydrogen bonds defined for protein.
    879 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.79

  Time building geometry restraints manager: 3.65 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1481
        1.34 -     1.46: 1294
        1.46 -     1.58: 2319
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 5152
  Sorted by residual:
  bond pdb=" C   VAL A 189 "
       pdb=" N   PRO A 190 "
    ideal  model  delta    sigma   weight residual
    1.334  1.392 -0.058 2.34e-02 1.83e+03 6.18e+00
  bond pdb=" C   ARG A  93 "
       pdb=" N   PRO A  94 "
    ideal  model  delta    sigma   weight residual
    1.335  1.358 -0.023 1.28e-02 6.10e+03 3.33e+00
  bond pdb=" C   ILE A 383 "
       pdb=" N   PRO A 384 "
    ideal  model  delta    sigma   weight residual
    1.335  1.357 -0.023 1.28e-02 6.10e+03 3.10e+00
  bond pdb=" CB  THR A 186 "
       pdb=" CG2 THR A 186 "
    ideal  model  delta    sigma   weight residual
    1.521  1.470  0.051 3.30e-02 9.18e+02 2.43e+00
  bond pdb=" C   LEU A 113 "
       pdb=" N   PRO A 114 "
    ideal  model  delta    sigma   weight residual
    1.335  1.354 -0.019 1.28e-02 6.10e+03 2.19e+00
  ... (remaining 5147 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.95: 6851
        2.95 -     5.90: 101
        5.90 -     8.85: 20
        8.85 -    11.80: 0
       11.80 -    14.75: 1
  Bond angle restraints: 6973
  Sorted by residual:
  angle pdb=" N   VAL B  33 "
        pdb=" CA  VAL B  33 "
        pdb=" C   VAL B  33 "
      ideal   model   delta    sigma   weight residual
     111.91  107.73    4.18 8.90e-01 1.26e+00 2.20e+01
  angle pdb=" C   ASP A 197 "
        pdb=" CA  ASP A 197 "
        pdb=" CB  ASP A 197 "
      ideal   model   delta    sigma   weight residual
     109.72  118.38   -8.66 1.92e+00 2.71e-01 2.03e+01
  angle pdb=" CA  LEU A 344 "
        pdb=" CB  LEU A 344 "
        pdb=" CG  LEU A 344 "
      ideal   model   delta    sigma   weight residual
     116.30  131.05  -14.75 3.50e+00 8.16e-02 1.78e+01
  angle pdb=" C   ALA B  18 "
        pdb=" CA  ALA B  18 "
        pdb=" CB  ALA B  18 "
      ideal   model   delta    sigma   weight residual
     115.89  110.42    5.47 1.32e+00 5.74e-01 1.72e+01
  angle pdb=" CA  TYR A 590 "
        pdb=" CB  TYR A 590 "
        pdb=" CG  TYR A 590 "
      ideal   model   delta    sigma   weight residual
     113.90  121.18   -7.28 1.80e+00 3.09e-01 1.64e+01
  ... (remaining 6968 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.09: 2658
       16.09 -    32.17: 265
       32.17 -    48.25: 55
       48.25 -    64.34: 6
       64.34 -    80.42: 5
  Dihedral angle restraints: 2989
    sinusoidal: 1136
      harmonic: 1853
  Sorted by residual:
  dihedral pdb=" CB  CYS A 430 "
           pdb=" SG  CYS A 430 "
           pdb=" SG  CYS A 530 "
           pdb=" CB  CYS A 530 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -35.14  -50.86     1      1.00e+01 1.00e-02 3.54e+01
  dihedral pdb=" CA  ASN A 617 "
           pdb=" C   ASN A 617 "
           pdb=" N   SER A 618 "
           pdb=" CA  SER A 618 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.39  -19.61     0      5.00e+00 4.00e-02 1.54e+01
  dihedral pdb=" CA  CYS A 530 "
           pdb=" C   CYS A 530 "
           pdb=" N   THR A 531 "
           pdb=" CA  THR A 531 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.21   18.79     0      5.00e+00 4.00e-02 1.41e+01
  ... (remaining 2986 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 633
       0.062 -    0.124: 124
       0.124 -    0.187: 18
       0.187 -    0.249: 4
       0.249 -    0.311: 2
  Chirality restraints: 781
  Sorted by residual:
  chirality pdb=" CB  ILE A  47 "
            pdb=" CA  ILE A  47 "
            pdb=" CG1 ILE A  47 "
            pdb=" CG2 ILE A  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.31 2.00e-01 2.50e+01 2.42e+00
  chirality pdb=" CA  PHE A 117 "
            pdb=" N   PHE A 117 "
            pdb=" C   PHE A 117 "
            pdb=" CB  PHE A 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.79e+00
  chirality pdb=" CB  VAL A  66 "
            pdb=" CA  VAL A  66 "
            pdb=" CG1 VAL A  66 "
            pdb=" CG2 VAL A  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 778 not shown)

  Planarity restraints: 858
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 113 "    0.070 5.00e-02 4.00e+02   1.05e-01 1.77e+01
        pdb=" N   PRO A 114 "   -0.182 5.00e-02 4.00e+02
        pdb=" CA  PRO A 114 "    0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO A 114 "    0.058 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 282 "    0.048 5.00e-02 4.00e+02   7.39e-02 8.74e+00
        pdb=" N   PRO A 283 "   -0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO A 283 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 283 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 115 "   -0.013 2.00e-02 2.50e+03   2.69e-02 7.24e+00
        pdb=" C   VAL B 115 "    0.047 2.00e-02 2.50e+03
        pdb=" O   VAL B 115 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   SER B 116 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 855 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1279
        2.80 -     3.32: 4534
        3.32 -     3.85: 8317
        3.85 -     4.37: 9622
        4.37 -     4.90: 16918
  Nonbonded interactions: 40670
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 425 "
            pdb=" OE1 GLN A 541 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" O   ASN B  34 "
            pdb=" OG  SER B  57 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" OE1 GLN A 348 "
            pdb=" OH  TYR A 640 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   LEU A 346 "
            pdb=" OG  SER A 350 "
     model   vdw
     2.331 3.040
  nonbonded pdb=" OE1 GLN A 365 "
            pdb=" NZ  LYS A 433 "
     model   vdw
     2.350 3.120
  ... (remaining 40665 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             20.230
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     25.260
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:4.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
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      :  0.005   0.058   5159  Z= 0.233
  Angle     :  0.911  14.749   6987  Z= 0.490
  Chirality :  0.054   0.311    781
  Planarity :  0.008   0.105    858
  Dihedral  : 13.400  80.423   1792
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.30), residues: 633
  helix: -0.25 (0.25), residues: 324
  sheet: -0.61 (0.67), residues: 63
  loop : -0.68 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 602 
 HIS   0.006   0.001   HIS A 115 
 PHE   0.040   0.002   PHE A 386 
 TYR   0.033   0.002   TYR A 590 
 ARG   0.012   0.001   ARG A 526 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13698 (  295)
  hydrogen bonds       : angle       7.09302 (  879)
  SS BOND              : bond        0.00379 (    7)
  SS BOND              : angle       1.23131 (   14)
  covalent geometry    : bond        0.00518 ( 5152)
  covalent geometry    : angle       0.90976 ( 6973)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.814 
Fit side-chains
REVERT: A  348 GLN cc_start: 0.7589 (tp40) cc_final: 0.7234 (tt0)
REVERT: A  417 MET cc_start: 0.7379 (tpp) cc_final: 0.7113 (tpp)
REVERT: A  557 MET cc_start: 0.7598 (mmp) cc_final: 0.7231 (mmp)
REVERT: A  577 MET cc_start: 0.7272 (ttt) cc_final: 0.7016 (ttp)
REVERT: A  649 LYS cc_start: 0.7703 (tptm) cc_final: 0.7496 (tttt)
REVERT: B   58 TRP cc_start: 0.6691 (m100) cc_final: 0.6166 (m-10)
REVERT: B  108 TYR cc_start: 0.7153 (m-10) cc_final: 0.6912 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.2115
  time to fit residues: 33.8984
Evaluate side-chains
  99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 48 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 477 ASN
B  86 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.173381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.136282 restraints weight = 5598.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 2.03
r_work: 0.3464 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3335 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5159  Z= 0.144
  Angle     :  0.536   5.378   6987  Z= 0.288
  Chirality :  0.041   0.141    781
  Planarity :  0.005   0.077    858
  Dihedral  :  4.145  20.575    699
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  :  7.89 %
    Favored  : 89.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.32), residues: 633
  helix:  1.18 (0.27), residues: 332
  sheet: -0.19 (0.80), residues: 46
  loop : -0.37 (0.37), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 258 
 HIS   0.003   0.001   HIS B  61 
 PHE   0.022   0.002   PHE A 386 
 TYR   0.026   0.002   TYR A 590 
 ARG   0.003   0.000   ARG B  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04171 (  295)
  hydrogen bonds       : angle       4.73058 (  879)
  SS BOND              : bond        0.00245 (    7)
  SS BOND              : angle       0.93374 (   14)
  covalent geometry    : bond        0.00328 ( 5152)
  covalent geometry    : angle       0.53449 ( 6973)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.590 
Fit side-chains
REVERT: A   25 ASN cc_start: 0.7357 (t0) cc_final: 0.7135 (t0)
REVERT: A   46 ILE cc_start: 0.8534 (tp) cc_final: 0.8277 (tp)
REVERT: A   70 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7744 (m-30)
REVERT: A   90 LYS cc_start: 0.8512 (mtmm) cc_final: 0.8198 (mmtm)
REVERT: A  348 GLN cc_start: 0.7836 (tp40) cc_final: 0.7437 (tt0)
REVERT: A  557 MET cc_start: 0.8130 (mmp) cc_final: 0.7694 (mmp)
REVERT: A  577 MET cc_start: 0.8181 (ttt) cc_final: 0.7923 (ttp)
REVERT: A  645 TYR cc_start: 0.7884 (t80) cc_final: 0.7186 (t80)
REVERT: A  649 LYS cc_start: 0.7899 (tptm) cc_final: 0.7420 (tttt)
REVERT: B   58 TRP cc_start: 0.7011 (m100) cc_final: 0.6136 (m-10)
REVERT: B   87 MET cc_start: 0.7910 (mtp) cc_final: 0.7474 (mtm)
REVERT: B  108 TYR cc_start: 0.8001 (m-10) cc_final: 0.7632 (m-80)
  outliers start: 12
  outliers final: 8
  residues processed: 107
  average time/residue: 0.1805
  time to fit residues: 26.1801
Evaluate side-chains
  101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  542 VAL
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  113 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.171630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.134429 restraints weight = 5671.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 2.04
r_work: 0.3454 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5159  Z= 0.139
  Angle     :  0.510   5.573   6987  Z= 0.273
  Chirality :  0.041   0.236    781
  Planarity :  0.004   0.059    858
  Dihedral  :  3.889  19.943    699
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 10.28 %
    Favored  : 87.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.33), residues: 633
  helix:  1.66 (0.28), residues: 333
  sheet:  0.05 (0.83), residues: 46
  loop : -0.31 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  51 
 HIS   0.003   0.001   HIS B  61 
 PHE   0.016   0.001   PHE A 117 
 TYR   0.026   0.001   TYR A 590 
 ARG   0.003   0.000   ARG B  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03909 (  295)
  hydrogen bonds       : angle       4.42461 (  879)
  SS BOND              : bond        0.00234 (    7)
  SS BOND              : angle       0.79458 (   14)
  covalent geometry    : bond        0.00324 ( 5152)
  covalent geometry    : angle       0.50968 ( 6973)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.601 
Fit side-chains
REVERT: A   25 ASN cc_start: 0.7233 (t0) cc_final: 0.7010 (t0)
REVERT: A   46 ILE cc_start: 0.8591 (tp) cc_final: 0.8350 (tp)
REVERT: A   47 ILE cc_start: 0.8731 (mm) cc_final: 0.8470 (mm)
REVERT: A   60 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8032 (mm-30)
REVERT: A   70 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7858 (m-30)
REVERT: A  173 TYR cc_start: 0.7719 (m-10) cc_final: 0.7494 (m-80)
REVERT: A  348 GLN cc_start: 0.7779 (tp40) cc_final: 0.7360 (tt0)
REVERT: A  477 ASN cc_start: 0.7316 (m110) cc_final: 0.7055 (m110)
REVERT: A  557 MET cc_start: 0.8102 (mmp) cc_final: 0.7659 (mmt)
REVERT: A  645 TYR cc_start: 0.7933 (t80) cc_final: 0.7195 (t80)
REVERT: A  649 LYS cc_start: 0.7871 (tptm) cc_final: 0.7501 (tttm)
REVERT: B   58 TRP cc_start: 0.7043 (m100) cc_final: 0.6102 (m-10)
REVERT: B   87 MET cc_start: 0.8013 (mtp) cc_final: 0.7706 (mtm)
REVERT: B  108 TYR cc_start: 0.8109 (m-10) cc_final: 0.7646 (m-80)
  outliers start: 13
  outliers final: 9
  residues processed: 105
  average time/residue: 0.2096
  time to fit residues: 29.8807
Evaluate side-chains
  107 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  569 SER
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  113 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 36 optimal weight:   20.0000
   chunk 28 optimal weight:    0.8980
   chunk 52 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 1 optimal weight:    0.2980
   chunk 48 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0060
   chunk 16 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.5196

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.173109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.135875 restraints weight = 5727.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 2.04
r_work: 0.3460 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3329 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5159  Z= 0.117
  Angle     :  0.492   5.550   6987  Z= 0.266
  Chirality :  0.039   0.149    781
  Planarity :  0.004   0.052    858
  Dihedral  :  3.802  20.694    699
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 12.84 %
    Favored  : 84.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.33), residues: 633
  helix:  1.99 (0.28), residues: 333
  sheet:  0.21 (0.84), residues: 46
  loop : -0.33 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  51 
 HIS   0.003   0.001   HIS B  61 
 PHE   0.024   0.001   PHE A 386 
 TYR   0.024   0.001   TYR A 590 
 ARG   0.002   0.000   ARG B  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03715 (  295)
  hydrogen bonds       : angle       4.31366 (  879)
  SS BOND              : bond        0.00325 (    7)
  SS BOND              : angle       1.30564 (   14)
  covalent geometry    : bond        0.00264 ( 5152)
  covalent geometry    : angle       0.48857 ( 6973)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 1.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ASN cc_start: 0.7236 (t0) cc_final: 0.7005 (t0)
REVERT: A   46 ILE cc_start: 0.8561 (tp) cc_final: 0.8335 (tp)
REVERT: A   47 ILE cc_start: 0.8703 (mm) cc_final: 0.8437 (mm)
REVERT: A   60 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8040 (mm-30)
REVERT: A   70 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7899 (m-30)
REVERT: A   90 LYS cc_start: 0.8460 (mtmm) cc_final: 0.8108 (mmtm)
REVERT: A  348 GLN cc_start: 0.7726 (tp40) cc_final: 0.7323 (tt0)
REVERT: A  421 PHE cc_start: 0.8221 (m-80) cc_final: 0.7884 (m-80)
REVERT: A  432 ASN cc_start: 0.8034 (m-40) cc_final: 0.7663 (m-40)
REVERT: A  477 ASN cc_start: 0.7486 (m110) cc_final: 0.7199 (m110)
REVERT: A  557 MET cc_start: 0.8083 (mmp) cc_final: 0.7661 (mmp)
REVERT: A  567 LEU cc_start: 0.8619 (mp) cc_final: 0.8388 (mp)
REVERT: A  649 LYS cc_start: 0.7832 (tptm) cc_final: 0.7432 (tttm)
REVERT: B   58 TRP cc_start: 0.7103 (m100) cc_final: 0.6049 (m-10)
REVERT: B   87 MET cc_start: 0.8034 (mtp) cc_final: 0.7676 (mtm)
REVERT: B  108 TYR cc_start: 0.8138 (m-80) cc_final: 0.7589 (m-80)
  outliers start: 13
  outliers final: 8
  residues processed: 114
  average time/residue: 0.2982
  time to fit residues: 49.0190
Evaluate side-chains
  108 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 1.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  569 SER
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  113 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 27 optimal weight:    0.5980
   chunk 53 optimal weight:    9.9990
   chunk 52 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0970
   chunk 61 optimal weight:    0.6980
   chunk 43 optimal weight:    0.5980
   chunk 14 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
A 464 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.172766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.135640 restraints weight = 5706.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 2.03
r_work: 0.3461 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5159  Z= 0.116
  Angle     :  0.496   8.215   6987  Z= 0.265
  Chirality :  0.039   0.134    781
  Planarity :  0.004   0.049    858
  Dihedral  :  3.762  20.761    699
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 13.58 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.33), residues: 633
  helix:  2.18 (0.28), residues: 333
  sheet:  0.21 (0.84), residues: 46
  loop : -0.41 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  51 
 HIS   0.003   0.001   HIS B  61 
 PHE   0.012   0.001   PHE A 117 
 TYR   0.024   0.001   TYR A 590 
 ARG   0.002   0.000   ARG B 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03497 (  295)
  hydrogen bonds       : angle       4.22086 (  879)
  SS BOND              : bond        0.00330 (    7)
  SS BOND              : angle       1.69348 (   14)
  covalent geometry    : bond        0.00269 ( 5152)
  covalent geometry    : angle       0.49047 ( 6973)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 ASN cc_start: 0.7220 (t0) cc_final: 0.6988 (t0)
REVERT: A   46 ILE cc_start: 0.8644 (tp) cc_final: 0.8429 (tp)
REVERT: A   47 ILE cc_start: 0.8691 (mm) cc_final: 0.8420 (mm)
REVERT: A   60 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8002 (mm-30)
REVERT: A   70 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7941 (m-30)
REVERT: A   90 LYS cc_start: 0.8442 (mtmm) cc_final: 0.8069 (mmtm)
REVERT: A  348 GLN cc_start: 0.7685 (tp40) cc_final: 0.7291 (tt0)
REVERT: A  432 ASN cc_start: 0.7990 (m-40) cc_final: 0.7646 (m-40)
REVERT: A  477 ASN cc_start: 0.7499 (m110) cc_final: 0.7244 (m110)
REVERT: A  557 MET cc_start: 0.8031 (mmp) cc_final: 0.7549 (mmt)
REVERT: A  567 LEU cc_start: 0.8683 (mp) cc_final: 0.8449 (mt)
REVERT: A  649 LYS cc_start: 0.7868 (tptm) cc_final: 0.7463 (tttm)
REVERT: B   58 TRP cc_start: 0.7180 (m100) cc_final: 0.6115 (m-10)
REVERT: B   91 LYS cc_start: 0.8047 (mttm) cc_final: 0.7768 (mttm)
REVERT: B  108 TYR cc_start: 0.8195 (m-80) cc_final: 0.7643 (m-80)
  outliers start: 13
  outliers final: 9
  residues processed: 113
  average time/residue: 0.1340
  time to fit residues: 20.8752
Evaluate side-chains
  113 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  569 SER
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  113 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 19 optimal weight:    0.3980
   chunk 3 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0970
   chunk 2 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.5978

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.172073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.134878 restraints weight = 5724.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3598 rms_B_bonded: 2.05
r_work: 0.3454 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3324 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.2702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5159  Z= 0.119
  Angle     :  0.484   5.585   6987  Z= 0.258
  Chirality :  0.039   0.135    781
  Planarity :  0.004   0.047    858
  Dihedral  :  3.719  20.782    699
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 14.68 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.33), residues: 633
  helix:  2.20 (0.28), residues: 333
  sheet:  0.09 (0.83), residues: 46
  loop : -0.45 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  51 
 HIS   0.003   0.001   HIS B  61 
 PHE   0.026   0.001   PHE A 386 
 TYR   0.024   0.001   TYR A 590 
 ARG   0.002   0.000   ARG A  93 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03491 (  295)
  hydrogen bonds       : angle       4.20800 (  879)
  SS BOND              : bond        0.00309 (    7)
  SS BOND              : angle       1.23422 (   14)
  covalent geometry    : bond        0.00278 ( 5152)
  covalent geometry    : angle       0.48094 ( 6973)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.558 
Fit side-chains
REVERT: A   25 ASN cc_start: 0.7253 (t0) cc_final: 0.7024 (t0)
REVERT: A   46 ILE cc_start: 0.8648 (tp) cc_final: 0.8431 (tp)
REVERT: A   47 ILE cc_start: 0.8695 (mm) cc_final: 0.8416 (mm)
REVERT: A   60 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7986 (mm-30)
REVERT: A   70 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7875 (m-30)
REVERT: A   90 LYS cc_start: 0.8367 (mtmm) cc_final: 0.7943 (mmtm)
REVERT: A  348 GLN cc_start: 0.7690 (tp40) cc_final: 0.7292 (tt0)
REVERT: A  432 ASN cc_start: 0.7962 (m-40) cc_final: 0.7677 (m-40)
REVERT: A  477 ASN cc_start: 0.7539 (m110) cc_final: 0.7266 (m110)
REVERT: A  649 LYS cc_start: 0.7870 (tptm) cc_final: 0.7473 (tttm)
REVERT: B   58 TRP cc_start: 0.7176 (m100) cc_final: 0.6111 (m-10)
REVERT: B  108 TYR cc_start: 0.8257 (m-80) cc_final: 0.7734 (m-80)
  outliers start: 16
  outliers final: 13
  residues processed: 107
  average time/residue: 0.1531
  time to fit residues: 22.8545
Evaluate side-chains
  110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  506 CYS
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  569 SER
Chi-restraints excluded: chain A residue  640 TYR
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  113 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 5 optimal weight:    0.1980
   chunk 0 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 39 optimal weight:    8.9990
   chunk 13 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.169638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.132478 restraints weight = 5656.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 2.04
r_work: 0.3428 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.2810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5159  Z= 0.142
  Angle     :  0.513   9.721   6987  Z= 0.267
  Chirality :  0.040   0.138    781
  Planarity :  0.004   0.045    858
  Dihedral  :  3.787  20.737    699
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 15.78 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.33), residues: 633
  helix:  2.10 (0.28), residues: 333
  sheet:  0.02 (0.81), residues: 46
  loop : -0.47 (0.38), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  40 
 HIS   0.003   0.001   HIS B  61 
 PHE   0.026   0.002   PHE A 386 
 TYR   0.024   0.002   TYR A  86 
 ARG   0.002   0.000   ARG A  93 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03689 (  295)
  hydrogen bonds       : angle       4.28213 (  879)
  SS BOND              : bond        0.00248 (    7)
  SS BOND              : angle       1.13582 (   14)
  covalent geometry    : bond        0.00339 ( 5152)
  covalent geometry    : angle       0.51090 ( 6973)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 ASN cc_start: 0.7273 (t0) cc_final: 0.7047 (t0)
REVERT: A   47 ILE cc_start: 0.8699 (mm) cc_final: 0.8395 (mm)
REVERT: A   60 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8002 (mm-30)
REVERT: A   70 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7919 (m-30)
REVERT: A  348 GLN cc_start: 0.7754 (tp40) cc_final: 0.7328 (tt0)
REVERT: A  432 ASN cc_start: 0.7947 (m-40) cc_final: 0.7644 (m-40)
REVERT: A  477 ASN cc_start: 0.7630 (m110) cc_final: 0.7402 (m110)
REVERT: A  557 MET cc_start: 0.8086 (mmp) cc_final: 0.7658 (mmp)
REVERT: A  605 ASN cc_start: 0.6573 (t0) cc_final: 0.5934 (p0)
REVERT: A  649 LYS cc_start: 0.7877 (tptm) cc_final: 0.7483 (tttm)
REVERT: B   58 TRP cc_start: 0.7310 (m100) cc_final: 0.6245 (m-10)
REVERT: B   91 LYS cc_start: 0.8098 (mttm) cc_final: 0.7721 (mttp)
REVERT: B  108 TYR cc_start: 0.8333 (m-80) cc_final: 0.7753 (m-80)
  outliers start: 16
  outliers final: 14
  residues processed: 112
  average time/residue: 0.2107
  time to fit residues: 33.5116
Evaluate side-chains
  116 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 1.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  506 CYS
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  569 SER
Chi-restraints excluded: chain A residue  640 TYR
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  113 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 43 optimal weight:    0.6980
   chunk 35 optimal weight:    0.4980
   chunk 38 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.170022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.132987 restraints weight = 5673.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 2.02
r_work: 0.3433 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3304 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5159  Z= 0.136
  Angle     :  0.508   8.430   6987  Z= 0.264
  Chirality :  0.040   0.138    781
  Planarity :  0.004   0.044    858
  Dihedral  :  3.759  20.743    699
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.70 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.33), residues: 633
  helix:  2.11 (0.28), residues: 333
  sheet: -0.00 (0.81), residues: 46
  loop : -0.53 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  51 
 HIS   0.003   0.001   HIS B  61 
 PHE   0.027   0.001   PHE A 386 
 TYR   0.025   0.002   TYR A  86 
 ARG   0.002   0.000   ARG A  93 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03633 (  295)
  hydrogen bonds       : angle       4.27847 (  879)
  SS BOND              : bond        0.00230 (    7)
  SS BOND              : angle       1.16873 (   14)
  covalent geometry    : bond        0.00325 ( 5152)
  covalent geometry    : angle       0.50596 ( 6973)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.522 
Fit side-chains
REVERT: A   25 ASN cc_start: 0.7188 (t0) cc_final: 0.6966 (t0)
REVERT: A   47 ILE cc_start: 0.8724 (mm) cc_final: 0.8426 (mm)
REVERT: A   60 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8000 (mm-30)
REVERT: A   70 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7909 (m-30)
REVERT: A  348 GLN cc_start: 0.7748 (tp40) cc_final: 0.7317 (tt0)
REVERT: A  421 PHE cc_start: 0.8289 (m-80) cc_final: 0.7971 (m-80)
REVERT: A  432 ASN cc_start: 0.7948 (m-40) cc_final: 0.7666 (m-40)
REVERT: A  477 ASN cc_start: 0.7632 (m110) cc_final: 0.7408 (m110)
REVERT: A  557 MET cc_start: 0.8067 (mmp) cc_final: 0.7849 (mmp)
REVERT: A  567 LEU cc_start: 0.8819 (mp) cc_final: 0.8556 (mt)
REVERT: A  605 ASN cc_start: 0.6608 (t0) cc_final: 0.5959 (p0)
REVERT: A  649 LYS cc_start: 0.7878 (tptm) cc_final: 0.7500 (tttm)
REVERT: B   58 TRP cc_start: 0.7308 (m100) cc_final: 0.6255 (m-10)
REVERT: B  108 TYR cc_start: 0.8341 (m-80) cc_final: 0.7804 (m-80)
  outliers start: 17
  outliers final: 14
  residues processed: 108
  average time/residue: 0.1569
  time to fit residues: 22.9913
Evaluate side-chains
  111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  506 CYS
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  569 SER
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  640 TYR
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  113 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 52 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 1 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   overall best weight:    1.0984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.167977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.130407 restraints weight = 5716.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 2.04
r_work: 0.3402 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3270 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.2991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5159  Z= 0.169
  Angle     :  0.539   8.678   6987  Z= 0.280
  Chirality :  0.041   0.142    781
  Planarity :  0.004   0.044    858
  Dihedral  :  3.855  20.680    699
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 17.06 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.33), residues: 633
  helix:  1.99 (0.28), residues: 333
  sheet: -0.03 (0.81), residues: 46
  loop : -0.54 (0.38), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  51 
 HIS   0.004   0.001   HIS B  61 
 PHE   0.027   0.002   PHE A 386 
 TYR   0.026   0.002   TYR A  86 
 ARG   0.002   0.000   ARG A  93 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03921 (  295)
  hydrogen bonds       : angle       4.38493 (  879)
  SS BOND              : bond        0.00259 (    7)
  SS BOND              : angle       1.13179 (   14)
  covalent geometry    : bond        0.00413 ( 5152)
  covalent geometry    : angle       0.53706 ( 6973)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.692 
Fit side-chains
REVERT: A   25 ASN cc_start: 0.7419 (t0) cc_final: 0.7190 (t0)
REVERT: A   47 ILE cc_start: 0.8719 (mm) cc_final: 0.8403 (mm)
REVERT: A   60 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8023 (mm-30)
REVERT: A   70 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7966 (m-30)
REVERT: A  348 GLN cc_start: 0.7888 (tp40) cc_final: 0.7445 (tt0)
REVERT: A  432 ASN cc_start: 0.8044 (m-40) cc_final: 0.7698 (m-40)
REVERT: A  477 ASN cc_start: 0.7662 (m110) cc_final: 0.7410 (m110)
REVERT: A  557 MET cc_start: 0.8076 (mmp) cc_final: 0.7832 (mmp)
REVERT: A  567 LEU cc_start: 0.8868 (mp) cc_final: 0.8584 (mt)
REVERT: A  649 LYS cc_start: 0.7904 (tptm) cc_final: 0.7514 (tttm)
REVERT: B   58 TRP cc_start: 0.7225 (m100) cc_final: 0.6228 (m-10)
REVERT: B   91 LYS cc_start: 0.8143 (mttm) cc_final: 0.7784 (mttp)
REVERT: B  108 TYR cc_start: 0.8499 (m-80) cc_final: 0.7913 (m-80)
  outliers start: 17
  outliers final: 15
  residues processed: 113
  average time/residue: 0.1789
  time to fit residues: 27.4966
Evaluate side-chains
  115 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  506 CYS
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  569 SER
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  640 TYR
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue   87 MET
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  113 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 13 optimal weight:    0.4980
   chunk 21 optimal weight:    0.1980
   chunk 56 optimal weight:    0.8980
   chunk 37 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 0 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.161836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.127195 restraints weight = 5831.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 1.88
r_work: 0.3187 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.3043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5159  Z= 0.125
  Angle     :  0.504   8.278   6987  Z= 0.263
  Chirality :  0.040   0.137    781
  Planarity :  0.004   0.044    858
  Dihedral  :  3.767  21.016    699
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 17.43 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.33), residues: 633
  helix:  2.09 (0.28), residues: 333
  sheet:  0.01 (0.82), residues: 46
  loop : -0.53 (0.38), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  51 
 HIS   0.003   0.001   HIS B  61 
 PHE   0.027   0.001   PHE A 386 
 TYR   0.023   0.001   TYR A 590 
 ARG   0.001   0.000   ARG A  93 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03621 (  295)
  hydrogen bonds       : angle       4.28099 (  879)
  SS BOND              : bond        0.00210 (    7)
  SS BOND              : angle       1.08390 (   14)
  covalent geometry    : bond        0.00295 ( 5152)
  covalent geometry    : angle       0.50226 ( 6973)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.526 
Fit side-chains
REVERT: A   25 ASN cc_start: 0.7296 (t0) cc_final: 0.7067 (t0)
REVERT: A   47 ILE cc_start: 0.8697 (mm) cc_final: 0.8397 (mm)
REVERT: A   60 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7976 (mm-30)
REVERT: A   70 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7943 (m-30)
REVERT: A  348 GLN cc_start: 0.7793 (tp40) cc_final: 0.7382 (tt0)
REVERT: A  421 PHE cc_start: 0.8270 (m-80) cc_final: 0.8015 (m-80)
REVERT: A  432 ASN cc_start: 0.7864 (m-40) cc_final: 0.7600 (m-40)
REVERT: A  477 ASN cc_start: 0.7690 (m110) cc_final: 0.7427 (m110)
REVERT: A  557 MET cc_start: 0.8020 (mmp) cc_final: 0.7793 (mmp)
REVERT: A  567 LEU cc_start: 0.8784 (mp) cc_final: 0.8518 (mt)
REVERT: A  649 LYS cc_start: 0.7922 (tptm) cc_final: 0.7554 (tttm)
REVERT: B   58 TRP cc_start: 0.7270 (m100) cc_final: 0.6275 (m-10)
REVERT: B   91 LYS cc_start: 0.8101 (mttm) cc_final: 0.7724 (mtmm)
REVERT: B  108 TYR cc_start: 0.8316 (m-80) cc_final: 0.7631 (m-80)
  outliers start: 15
  outliers final: 13
  residues processed: 104
  average time/residue: 0.1422
  time to fit residues: 19.9270
Evaluate side-chains
  107 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  506 CYS
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  640 TYR
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue   87 MET
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  113 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0570
   chunk 36 optimal weight:    8.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.9702

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.160153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.125426 restraints weight = 5924.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 1.91
r_work: 0.3162 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.3141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5159  Z= 0.155
  Angle     :  0.530   8.245   6987  Z= 0.276
  Chirality :  0.040   0.140    781
  Planarity :  0.004   0.043    858
  Dihedral  :  3.799  20.708    699
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 16.88 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.33), residues: 633
  helix:  2.04 (0.28), residues: 333
  sheet: -0.05 (0.81), residues: 46
  loop : -0.53 (0.38), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  51 
 HIS   0.003   0.001   HIS B  61 
 PHE   0.027   0.002   PHE A 386 
 TYR   0.024   0.002   TYR A 590 
 ARG   0.002   0.000   ARG A  93 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03797 (  295)
  hydrogen bonds       : angle       4.34866 (  879)
  SS BOND              : bond        0.00234 (    7)
  SS BOND              : angle       1.07876 (   14)
  covalent geometry    : bond        0.00374 ( 5152)
  covalent geometry    : angle       0.52855 ( 6973)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3781.70 seconds
wall clock time: 69 minutes 26.83 seconds (4166.83 seconds total)