Starting phenix.real_space_refine
on Tue Aug  4 16:06:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rh6_53959/08_2026/9rh6_53959.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rh6_53959/08_2026/9rh6_53959.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rh6_53959/08_2026/9rh6_53959.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rh6_53959/08_2026/9rh6_53959.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rh6_53959/08_2026/9rh6_53959.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rh6_53959/08_2026/9rh6_53959.cif"
  }
  resolution = 3.4
  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      19      5.16       5
     C    3019      2.51       5
     N     757      2.21       5
     O     837      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4632
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 387, 2909
          Classifications: {'peptide': 387}
          Link IDs: {'PTRANS': 15, 'TRANS': 371}
    Chain: "B"
      Number of atoms: 907
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 907
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 4, 'TRANS': 113}
    Chain: "C"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 816
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101}
  Time building chain proxies: 0.91, per 1000 atoms: 0.20
  Number of scatterers: 4632
  At special positions: 0
  Unit cell: (67.797, 76.167, 102.114, 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      19     16.00
     O     837      8.00
     N     757      7.00
     C    3019      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  88 " 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: 0.31
  Conformation dependent library (CDL) restraints added in 155.5 milliseconds
  

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1110

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 7 sheets defined
      52.4% alpha, 19.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 31
      removed outlier: 4.160A  pdb=" N   GLY A  15 " --> pdb=" O   ASP A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 43
      removed outlier: 4.595A  pdb=" N   GLY A  36 " --> pdb=" O   GLY A  32 " (cutoff:3.500A)
      removed outlier: 4.807A  pdb=" N   TRP A  37 " --> pdb=" O   ALA A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 85
      removed outlier: 3.518A  pdb=" N   MET A  84 " --> pdb=" O   LYS A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 117
      removed outlier: 4.780A  pdb=" N   PHE A  96 " --> pdb=" O   ARG A  92 " (cutoff:3.500A)
      Proline residue:  A  97  - end of helix
      removed outlier: 3.566A  pdb=" N   VAL A 107 " --> pdb=" O   GLY A 103 " (cutoff:3.500A)
      Proline residue:  A 108  - end of helix
      removed outlier: 3.975A  pdb=" N   PHE A 115 " --> pdb=" O   LEU A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 126
      removed outlier: 3.528A  pdb=" N   GLU A 124 " --> pdb=" O   ILE A 121 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   TRP A 126 " --> pdb=" O   ARG A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 145
      removed outlier: 4.033A  pdb=" N   LEU A 144 " --> pdb=" O   VAL A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 148
      No H-bonds generated for 'chain 'A' and resid 146 through 148'
    Processing helix  chain 'A' and resid 149 through 175
    Processing helix  chain 'A' and resid 180 through 200
    Processing helix  chain 'A' and resid 204 through 219
      removed outlier: 3.627A  pdb=" N   TYR A 208 " --> pdb=" O   ARG A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 237
      removed outlier: 3.844A  pdb=" N   GLY A 230 " --> pdb=" O   ALA A 226 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   VAL A 231 " --> pdb=" O   THR A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 262
      Proline residue:  A 257  - end of helix
    Processing helix  chain 'A' and resid 262 through 272
    Processing helix  chain 'A' and resid 282 through 285
    Processing helix  chain 'A' and resid 286 through 298
    Processing helix  chain 'A' and resid 298 through 314
    Processing helix  chain 'A' and resid 324 through 335
    Processing helix  chain 'A' and resid 338 through 351
    Processing helix  chain 'A' and resid 354 through 384
      removed outlier: 3.887A  pdb=" N   VAL A 382 " --> pdb=" O   SER A 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 32
      removed outlier: 3.970A  pdb=" N   TYR B  32 " --> pdb=" O   PHE B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 83
    Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 50
    Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 6
    Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.352A  pdb=" N   MET B  34 " --> pdb=" O   ALA B  50 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ALA B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   TRP B  36 " --> pdb=" O   ILE B  48 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.651A  pdb=" N   CYS B  96 " --> pdb=" O   TRP B 108 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   TRP B 108 " --> pdb=" O   CYS B  96 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   LYS B  98 " --> pdb=" O   ASP B 106 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 5
      removed outlier: 3.584A  pdb=" N   SER C  65 " --> pdb=" O   SER C  72 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   THR C  74 " --> pdb=" O   SER C  63 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12
      removed outlier: 3.521A  pdb=" N   ILE C  48 " --> pdb=" O   TRP C  35 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   GLN C  37 " --> pdb=" O   ARG C  46 " (cutoff:3.500A)
      removed outlier: 5.448A  pdb=" N   ARG C  46 " --> pdb=" O   GLN C  37 " (cutoff:3.500A)

    292 hydrogen bonds defined for protein.
    810 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: 0.46

  Time building geometry restraints manager: 0.42 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: 1431
        1.34 -     1.46: 882
        1.46 -     1.58: 2392
        1.58 -     1.69: 0
        1.69 -     1.81: 31
  Bond restraints: 4736
  Sorted by residual:
  bond pdb=" N   VAL A 353 "
       pdb=" CA  VAL A 353 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.25e-02 6.40e+03 8.15e+00
  bond pdb=" N   ILE A 106 "
       pdb=" CA  ILE A 106 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.20e-02 6.94e+03 7.89e+00
  bond pdb=" N   VAL A 107 "
       pdb=" CA  VAL A 107 "
    ideal  model  delta    sigma   weight residual
    1.463  1.495 -0.033 1.18e-02 7.18e+03 7.68e+00
  bond pdb=" N   GLU B  99 "
       pdb=" CA  GLU B  99 "
    ideal  model  delta    sigma   weight residual
    1.455  1.492 -0.037 1.33e-02 5.65e+03 7.58e+00
  bond pdb=" N   HIS A   3 "
       pdb=" CA  HIS A   3 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.29e-02 6.01e+03 7.38e+00
  ... (remaining 4731 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 6113
        1.32 -     2.65: 245
        2.65 -     3.97: 61
        3.97 -     5.29: 14
        5.29 -     6.61: 8
  Bond angle restraints: 6441
  Sorted by residual:
  angle pdb=" N   ASN B 103 "
        pdb=" CA  ASN B 103 "
        pdb=" C   ASN B 103 "
      ideal   model   delta    sigma   weight residual
     109.06  115.67   -6.61 1.70e+00 3.46e-01 1.51e+01
  angle pdb=" N   GLU B 100 "
        pdb=" CA  GLU B 100 "
        pdb=" C   GLU B 100 "
      ideal   model   delta    sigma   weight residual
     110.20  104.27    5.93 1.58e+00 4.01e-01 1.41e+01
  angle pdb=" C   VAL A 353 "
        pdb=" CA  VAL A 353 "
        pdb=" CB  VAL A 353 "
      ideal   model   delta    sigma   weight residual
     111.29  105.15    6.14 1.64e+00 3.72e-01 1.40e+01
  angle pdb=" CA  ASP A 354 "
        pdb=" CB  ASP A 354 "
        pdb=" CG  ASP A 354 "
      ideal   model   delta    sigma   weight residual
     112.60  116.16   -3.56 1.00e+00 1.00e+00 1.27e+01
  angle pdb=" CA  LYS A 240 "
        pdb=" C   LYS A 240 "
        pdb=" O   LYS A 240 "
      ideal   model   delta    sigma   weight residual
     121.19  117.31    3.88 1.10e+00 8.26e-01 1.24e+01
  ... (remaining 6436 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.51: 2520
       16.51 -    33.01: 173
       33.01 -    49.52: 65
       49.52 -    66.02: 12
       66.02 -    82.53: 2
  Dihedral angle restraints: 2772
    sinusoidal: 1031
      harmonic: 1741
  Sorted by residual:
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  96 "
           pdb=" CB  CYS B  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   54.82   38.18     1      1.00e+01 1.00e-02 2.05e+01
  dihedral pdb=" CA  TYR C  49 "
           pdb=" C   TYR C  49 "
           pdb=" N   ALA C  50 "
           pdb=" CA  ALA C  50 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.02  -18.98     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CB  CYS C  23 "
           pdb=" SG  CYS C  23 "
           pdb=" SG  CYS C  88 "
           pdb=" CB  CYS C  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   62.46   30.54     1      1.00e+01 1.00e-02 1.33e+01
  ... (remaining 2769 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 556
       0.039 -    0.078: 140
       0.078 -    0.118: 46
       0.118 -    0.157: 14
       0.157 -    0.196: 5
  Chirality restraints: 761
  Sorted by residual:
  chirality pdb=" CA  VAL A 353 "
            pdb=" N   VAL A 353 "
            pdb=" C   VAL A 353 "
            pdb=" CB  VAL A 353 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 9.60e-01
  chirality pdb=" CA  THR C   7 "
            pdb=" N   THR C   7 "
            pdb=" C   THR C   7 "
            pdb=" CB  THR C   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.33    0.19 2.00e-01 2.50e+01 9.21e-01
  chirality pdb=" CA  LYS A 240 "
            pdb=" N   LYS A 240 "
            pdb=" C   LYS A 240 "
            pdb=" CB  LYS A 240 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.62e-01
  ... (remaining 758 not shown)

  Planarity restraints: 793
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 245 "   -0.026 9.50e-02 1.11e+02   2.76e-02 7.90e+00
        pdb=" NE  ARG A 245 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 245 "   -0.048 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 245 "    0.016 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 245 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A  57 "   -0.010 2.00e-02 2.50e+03   2.04e-02 4.18e+00
        pdb=" C   LYS A  57 "    0.035 2.00e-02 2.50e+03
        pdb=" O   LYS A  57 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ASN A  58 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 240 "    0.009 2.00e-02 2.50e+03   1.80e-02 3.25e+00
        pdb=" C   LYS A 240 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   LYS A 240 "    0.012 2.00e-02 2.50e+03
        pdb=" N   GLU A 241 "    0.011 2.00e-02 2.50e+03
  ... (remaining 790 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 1247
        2.81 -     3.33: 4367
        3.33 -     3.85: 7817
        3.85 -     4.38: 9099
        4.38 -     4.90: 15660
  Nonbonded interactions: 38190
  Sorted by model distance:
  nonbonded pdb=" O   PRO C   8 "
            pdb=" OG1 THR C 102 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OH  TYR A  38 "
            pdb=" O   PHE A 269 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" OD2 ASP B  73 "
            pdb=" OG  SER B  76 "
     model   vdw
     2.331 3.040
  nonbonded pdb=" ND2 ASN A 198 "
            pdb=" O   PHE A 236 "
     model   vdw
     2.349 3.120
  nonbonded pdb=" NE2 GLN A 327 "
            pdb=" OH  TYR C  32 "
     model   vdw
     2.365 3.120
  ... (remaining 38185 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.760
  Find NCS groups from input model:        0.020
  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:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
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      :  0.004   0.037   4738  Z= 0.234
  Angle     :  0.693   6.613   6445  Z= 0.423
  Chirality :  0.044   0.196    761
  Planarity :  0.004   0.065    793
  Dihedral  : 13.415  82.530   1656
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  8.76 %
    Favored  : 91.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 are not related in a simple way.
  whole:  0.90 (0.34), residues: 605
  helix:  0.87 (0.29), residues: 281
  sheet:  1.22 (0.45), residues: 130
  loop : -0.08 (0.47), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.048   0.002   ARG A 245 
 TYR   0.011   0.001   TYR C  49 
 PHE   0.010   0.001   PHE A 136 
 TRP   0.014   0.002   TRP A 379 
 HIS   0.004   0.001   HIS A   5 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00363 /  0.23 ( 4736)
  covalent geometry    : angle       0.69315 /  0.42 ( 6441)
  SS BOND              : bond        0.00238 /  0.12 (    2)
  SS BOND              : angle       0.67978 /  0.35 (    4)
  hydrogen bonds       : bond        0.20874 / 13.87 (  281)
  hydrogen bonds       : angle       8.09295 /  5.90 (  810)

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A   28 MET cc_start: 0.8638 (mmm) cc_final: 0.8056 (mmt)
REVERT: A   44 THR cc_start: 0.8934 (m) cc_final: 0.8502 (p)
REVERT: A   65 ASP cc_start: 0.8997 (m-30) cc_final: 0.8737 (m-30)
REVERT: A   84 MET cc_start: 0.7590 (mtt) cc_final: 0.7363 (mtp)
REVERT: A  121 ILE cc_start: 0.8584 (mt) cc_final: 0.8270 (pt)
REVERT: A  274 VAL cc_start: 0.9163 (m) cc_final: 0.8880 (p)
REVERT: A  354 ASP cc_start: 0.7923 (t70) cc_final: 0.7634 (t0)
REVERT: A  355 PRO cc_start: 0.8595 (Cg_exo) cc_final: 0.8325 (Cg_endo)
REVERT: A  379 TRP cc_start: 0.7871 (t-100) cc_final: 0.7482 (t-100)
REVERT: B   60 TYR cc_start: 0.6753 (m-80) cc_final: 0.6510 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 78
  average time/residue: 0.0689
  time to fit residues: 7.0796
Evaluate side-chains
  64 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 63
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 177 ASN
A 198 ASN
A 253 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.201884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.138435 restraints weight = 5244.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 2.03
r_work: 0.3060 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4738  Z= 0.133
  Angle     :  0.534   6.366   6445  Z= 0.278
  Chirality :  0.040   0.182    761
  Planarity :  0.004   0.025    793
  Dihedral  :  4.956  58.220    654
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  9.57 %
    Favored  : 89.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 are not related in a simple way.
  whole:  1.71 (0.34), residues: 605
  helix:  1.99 (0.30), residues: 286
  sheet:  1.27 (0.47), residues: 118
  loop : -0.17 (0.44), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 245 
 TYR   0.012   0.001   TYR C  49 
 PHE   0.015   0.001   PHE A  71 
 TRP   0.010   0.001   TRP B  36 
 HIS   0.004   0.001   HIS A   5 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.13 ( 4736)
  covalent geometry    : angle       0.53390 /  0.28 ( 6441)
  SS BOND              : bond        0.00270 /  0.13 (    2)
  SS BOND              : angle       0.51520 /  0.26 (    4)
  hydrogen bonds       : bond        0.04317 /  3.04 (  281)
  hydrogen bonds       : angle       5.35693 /  3.80 (  810)

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A   28 MET cc_start: 0.8785 (mmm) cc_final: 0.8185 (mmt)
REVERT: A   44 THR cc_start: 0.9010 (m) cc_final: 0.8624 (p)
REVERT: A  121 ILE cc_start: 0.8727 (mt) cc_final: 0.8373 (pt)
REVERT: B   33 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6550 (pt0)
REVERT: B  104 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7359 (m-30)
  outliers start: 6
  outliers final: 3
  residues processed: 72
  average time/residue: 0.0541
  time to fit residues: 5.1095
Evaluate side-chains
  67 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  177 ASN
Chi-restraints excluded: chain A residue  198 ASN
Chi-restraints excluded: chain B residue   33 GLU
Chi-restraints excluded: chain B residue  104 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 54 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 45 optimal weight:   20.0000
   chunk 33 optimal weight:    0.7980
   chunk 57 optimal weight:   20.0000
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A   5 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.203610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.141799 restraints weight = 5160.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 2.30
r_work: 0.3040 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2916 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4738  Z= 0.118
  Angle     :  0.502   8.387   6445  Z= 0.259
  Chirality :  0.039   0.178    761
  Planarity :  0.003   0.024    793
  Dihedral  :  4.490  46.828    654
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 11.81 %
    Favored  : 86.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 are not related in a simple way.
  whole:  1.91 (0.35), residues: 605
  helix:  2.22 (0.31), residues: 286
  sheet:  1.42 (0.48), residues: 118
  loop : -0.22 (0.44), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 385 
 TYR   0.009   0.001   TYR C  49 
 PHE   0.009   0.001   PHE A  71 
 TRP   0.011   0.001   TRP A 216 
 HIS   0.004   0.001   HIS A 256 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.12 ( 4736)
  covalent geometry    : angle       0.50214 /  0.26 ( 6441)
  SS BOND              : bond        0.00141 /  0.07 (    2)
  SS BOND              : angle       0.23300 /  0.12 (    4)
  hydrogen bonds       : bond        0.03672 /  2.61 (  281)
  hydrogen bonds       : angle       4.98292 /  3.52 (  810)

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A   28 MET cc_start: 0.8693 (mmm) cc_final: 0.8050 (mmt)
REVERT: A   44 THR cc_start: 0.9022 (m) cc_final: 0.8541 (p)
REVERT: A  121 ILE cc_start: 0.8787 (mt) cc_final: 0.8402 (pt)
REVERT: A  221 LYS cc_start: 0.9065 (mtpt) cc_final: 0.8847 (mmtp)
REVERT: B   33 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6584 (mp0)
REVERT: B  104 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7428 (m-30)
REVERT: C   33 LEU cc_start: 0.9006 (tt) cc_final: 0.8683 (tt)
  outliers start: 7
  outliers final: 3
  residues processed: 70
  average time/residue: 0.0580
  time to fit residues: 5.3985
Evaluate side-chains
  67 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain B residue   33 GLU
Chi-restraints excluded: chain B residue  103 ASN
Chi-restraints excluded: chain B residue  104 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 47 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 27 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 49 optimal weight:    8.9990
   chunk 37 optimal weight:    1.9990
   chunk 38 optimal weight:    8.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A   5 HIS
A 198 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.193345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.131075 restraints weight = 5178.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 2.21
r_work: 0.2918 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2788 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8774
moved from start:          0.2869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   4738  Z= 0.219
  Angle     :  0.594   6.236   6445  Z= 0.302
  Chirality :  0.043   0.173    761
  Planarity :  0.004   0.028    793
  Dihedral  :  4.557  29.768    654
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 11.61 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 are not related in a simple way.
  whole:  1.56 (0.35), residues: 605
  helix:  1.82 (0.31), residues: 285
  sheet:  1.34 (0.47), residues: 118
  loop : -0.25 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  92 
 TYR   0.014   0.002   TYR C  49 
 PHE   0.014   0.002   PHE A  72 
 TRP   0.010   0.002   TRP B  36 
 HIS   0.004   0.002   HIS A 253 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00533 /  0.22 ( 4736)
  covalent geometry    : angle       0.59426 /  0.30 ( 6441)
  SS BOND              : bond        0.00065 /  0.03 (    2)
  SS BOND              : angle       0.31225 /  0.15 (    4)
  hydrogen bonds       : bond        0.04145 /  2.86 (  281)
  hydrogen bonds       : angle       5.02904 /  3.57 (  810)

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A    5 HIS cc_start: 0.7955 (OUTLIER) cc_final: 0.7470 (m90)
REVERT: A   44 THR cc_start: 0.9110 (m) cc_final: 0.8466 (p)
REVERT: A  121 ILE cc_start: 0.9003 (mt) cc_final: 0.8712 (pt)
REVERT: A  381 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7992 (mtp85)
REVERT: B   34 MET cc_start: 0.6328 (tpp) cc_final: 0.6046 (tpp)
REVERT: B   81 MET cc_start: 0.4400 (mtm) cc_final: 0.3983 (mpp)
REVERT: B  104 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7618 (m-30)
REVERT: C   33 LEU cc_start: 0.9037 (tt) cc_final: 0.8586 (tt)
  outliers start: 15
  outliers final: 9
  residues processed: 76
  average time/residue: 0.0646
  time to fit residues: 6.4544
Evaluate side-chains
  69 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 HIS
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  198 ASN
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain A residue  381 ARG
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue  103 ASN
Chi-restraints excluded: chain B residue  104 ASP
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   54 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 52 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 50 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9980
   chunk 47 optimal weight:   20.0000
   chunk 20 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    1.3382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A   5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 256 HIS ** 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 = 0.4106 r_free = 0.4106 target = 0.194902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.131805 restraints weight = 5168.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.02
r_work: 0.2942 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2820 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8730
moved from start:          0.2983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4738  Z= 0.150
  Angle     :  0.511   5.276   6445  Z= 0.263
  Chirality :  0.040   0.173    761
  Planarity :  0.003   0.029    793
  Dihedral  :  4.227  18.100    651
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 13.44 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 are not related in a simple way.
  whole:  1.67 (0.34), residues: 605
  helix:  1.98 (0.30), residues: 285
  sheet:  1.43 (0.47), residues: 118
  loop : -0.33 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 250 
 TYR   0.011   0.001   TYR C  49 
 PHE   0.011   0.001   PHE A  72 
 TRP   0.010   0.001   TRP A 216 
 HIS   0.010   0.001   HIS A   5 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00365 /  0.15 ( 4736)
  covalent geometry    : angle       0.51143 /  0.26 ( 6441)
  SS BOND              : bond        0.00068 /  0.03 (    2)
  SS BOND              : angle       0.19279 /  0.10 (    4)
  hydrogen bonds       : bond        0.03577 /  2.52 (  281)
  hydrogen bonds       : angle       4.83711 /  3.42 (  810)

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A   28 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8359 (mmt)
REVERT: A   44 THR cc_start: 0.9107 (m) cc_final: 0.8472 (p)
REVERT: A  121 ILE cc_start: 0.8991 (mt) cc_final: 0.8685 (pt)
REVERT: A  250 ARG cc_start: 0.8516 (ttm-80) cc_final: 0.8020 (mtt180)
REVERT: A  381 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7927 (mtp85)
REVERT: B   34 MET cc_start: 0.6199 (tpp) cc_final: 0.5944 (tpp)
REVERT: B  104 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7581 (m-30)
REVERT: C   33 LEU cc_start: 0.9013 (tt) cc_final: 0.8539 (tt)
  outliers start: 11
  outliers final: 5
  residues processed: 68
  average time/residue: 0.0472
  time to fit residues: 4.3367
Evaluate side-chains
  67 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  381 ARG
Chi-restraints excluded: chain B residue  103 ASN
Chi-restraints excluded: chain B residue  104 ASP
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue   54 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 54 optimal weight:    0.1980
   chunk 39 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 33 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.8582

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.197305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.134101 restraints weight = 5260.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 2.06
r_work: 0.2973 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2849 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8707
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4738  Z= 0.114
  Angle     :  0.479   5.743   6445  Z= 0.246
  Chirality :  0.039   0.172    761
  Planarity :  0.003   0.028    793
  Dihedral  :  4.013  17.295    651
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 13.24 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 are not related in a simple way.
  whole:  1.90 (0.35), residues: 605
  helix:  2.26 (0.30), residues: 285
  sheet:  1.38 (0.47), residues: 118
  loop : -0.26 (0.45), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 250 
 TYR   0.010   0.001   TYR C  91 
 PHE   0.008   0.001   PHE A  71 
 TRP   0.011   0.001   TRP B  36 
 HIS   0.002   0.001   HIS A 256 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.11 ( 4736)
  covalent geometry    : angle       0.47918 /  0.25 ( 6441)
  SS BOND              : bond        0.00094 /  0.05 (    2)
  SS BOND              : angle       0.24490 /  0.13 (    4)
  hydrogen bonds       : bond        0.03169 /  2.25 (  281)
  hydrogen bonds       : angle       4.66088 /  3.28 (  810)

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.099 
Fit side-chains
REVERT: A   28 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8353 (mmt)
REVERT: A   44 THR cc_start: 0.9072 (m) cc_final: 0.8498 (p)
REVERT: A  121 ILE cc_start: 0.8989 (mt) cc_final: 0.8677 (pt)
REVERT: B   34 MET cc_start: 0.6217 (tpp) cc_final: 0.5967 (tpp)
REVERT: B   81 MET cc_start: 0.4534 (mtp) cc_final: 0.4267 (mpp)
REVERT: B  104 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7608 (m-30)
REVERT: C   33 LEU cc_start: 0.8976 (tt) cc_final: 0.8517 (tt)
  outliers start: 12
  outliers final: 7
  residues processed: 67
  average time/residue: 0.0380
  time to fit residues: 3.5901
Evaluate side-chains
  63 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain B residue  103 ASN
Chi-restraints excluded: chain B residue  104 ASP
Chi-restraints excluded: chain C residue    7 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 45 optimal weight:    7.9990
   chunk 48 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 10 optimal weight:    4.9990
   chunk 0 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   overall best weight:    1.1182

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.195486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.131656 restraints weight = 5168.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.10
r_work: 0.2946 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2823 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8723
moved from start:          0.3279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4738  Z= 0.131
  Angle     :  0.491   5.637   6445  Z= 0.249
  Chirality :  0.039   0.171    761
  Planarity :  0.003   0.028    793
  Dihedral  :  3.989  17.456    651
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 13.65 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 are not related in a simple way.
  whole:  1.97 (0.35), residues: 605
  helix:  2.30 (0.31), residues: 285
  sheet:  1.43 (0.48), residues: 118
  loop : -0.20 (0.45), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 250 
 TYR   0.011   0.001   TYR B  60 
 PHE   0.010   0.001   PHE A  72 
 TRP   0.009   0.001   TRP A 216 
 HIS   0.003   0.001   HIS A 256 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.13 ( 4736)
  covalent geometry    : angle       0.49066 /  0.25 ( 6441)
  SS BOND              : bond        0.00081 /  0.04 (    2)
  SS BOND              : angle       0.30172 /  0.16 (    4)
  hydrogen bonds       : bond        0.03289 /  2.32 (  281)
  hydrogen bonds       : angle       4.66866 /  3.29 (  810)

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 0.092 
Fit side-chains
REVERT: A   28 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8329 (mmt)
REVERT: A   44 THR cc_start: 0.9095 (m) cc_final: 0.8442 (p)
REVERT: A  121 ILE cc_start: 0.9000 (mt) cc_final: 0.8687 (pt)
REVERT: A  381 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7998 (mtp85)
REVERT: B   34 MET cc_start: 0.6288 (tpp) cc_final: 0.6035 (tpp)
REVERT: B   81 MET cc_start: 0.4463 (mtp) cc_final: 0.4182 (mpp)
REVERT: B  104 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7654 (m-30)
REVERT: C   33 LEU cc_start: 0.9004 (tt) cc_final: 0.8532 (tt)
  outliers start: 16
  outliers final: 11
  residues processed: 67
  average time/residue: 0.0465
  time to fit residues: 4.1233
Evaluate side-chains
  69 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  381 ARG
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  103 ASN
Chi-restraints excluded: chain B residue  104 ASP
Chi-restraints excluded: chain C residue    7 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 47 optimal weight:   30.0000
   chunk 11 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.7582

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.197027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.133578 restraints weight = 5228.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 2.13
r_work: 0.2966 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2842 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8706
moved from start:          0.3352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4738  Z= 0.106
  Angle     :  0.471   5.407   6445  Z= 0.240
  Chirality :  0.038   0.171    761
  Planarity :  0.003   0.028    793
  Dihedral  :  3.896  17.028    651
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 14.46 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 are not related in a simple way.
  whole:  2.09 (0.35), residues: 605
  helix:  2.39 (0.30), residues: 286
  sheet:  1.44 (0.47), residues: 118
  loop : -0.12 (0.46), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 250 
 TYR   0.008   0.001   TYR C  49 
 PHE   0.008   0.001   PHE A  72 
 TRP   0.009   0.001   TRP A 216 
 HIS   0.002   0.001   HIS A 256 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.11 ( 4736)
  covalent geometry    : angle       0.47132 /  0.24 ( 6441)
  SS BOND              : bond        0.00091 /  0.04 (    2)
  SS BOND              : angle       0.29334 /  0.15 (    4)
  hydrogen bonds       : bond        0.03062 /  2.18 (  281)
  hydrogen bonds       : angle       4.58573 /  3.23 (  810)

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.098 
Fit side-chains
REVERT: A   28 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8341 (mmt)
REVERT: A   44 THR cc_start: 0.9090 (m) cc_final: 0.8422 (p)
REVERT: A  121 ILE cc_start: 0.8994 (mt) cc_final: 0.8653 (pt)
REVERT: A  154 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8548 (mp)
REVERT: A  177 ASN cc_start: 0.7601 (p0) cc_final: 0.7372 (p0)
REVERT: B   34 MET cc_start: 0.6218 (tpp) cc_final: 0.5976 (tpp)
REVERT: C   33 LEU cc_start: 0.8989 (tt) cc_final: 0.8541 (tt)
  outliers start: 14
  outliers final: 9
  residues processed: 65
  average time/residue: 0.0451
  time to fit residues: 3.9909
Evaluate side-chains
  64 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  103 ASN
Chi-restraints excluded: chain C residue    7 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 42 optimal weight:    5.9990
   chunk 43 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 53 optimal weight:    6.9990
   chunk 33 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.0982

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.195652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.132158 restraints weight = 5165.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 2.11
r_work: 0.2956 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2833 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8720
moved from start:          0.3467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4738  Z= 0.129
  Angle     :  0.485   5.282   6445  Z= 0.248
  Chirality :  0.039   0.171    761
  Planarity :  0.003   0.027    793
  Dihedral  :  3.883  17.433    651
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 15.48 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 are not related in a simple way.
  whole:  2.05 (0.35), residues: 605
  helix:  2.36 (0.30), residues: 285
  sheet:  1.40 (0.47), residues: 118
  loop : -0.11 (0.45), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 250 
 TYR   0.011   0.001   TYR B  60 
 PHE   0.010   0.001   PHE A  72 
 TRP   0.009   0.001   TRP A 216 
 HIS   0.003   0.001   HIS A 256 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.13 ( 4736)
  covalent geometry    : angle       0.48549 /  0.25 ( 6441)
  SS BOND              : bond        0.00087 /  0.04 (    2)
  SS BOND              : angle       0.20795 /  0.11 (    4)
  hydrogen bonds       : bond        0.03217 /  2.27 (  281)
  hydrogen bonds       : angle       4.61618 /  3.26 (  810)

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 0.097 
Fit side-chains
REVERT: A   28 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8310 (mmt)
REVERT: A   44 THR cc_start: 0.9106 (m) cc_final: 0.8438 (p)
REVERT: A  121 ILE cc_start: 0.9004 (mt) cc_final: 0.8681 (pt)
REVERT: A  154 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8570 (mp)
REVERT: A  177 ASN cc_start: 0.7616 (p0) cc_final: 0.7395 (p0)
REVERT: C   33 LEU cc_start: 0.8978 (tt) cc_final: 0.8530 (tt)
  outliers start: 11
  outliers final: 9
  residues processed: 61
  average time/residue: 0.0413
  time to fit residues: 3.5288
Evaluate side-chains
  64 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  103 ASN
Chi-restraints excluded: chain C residue    7 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 48 optimal weight:    7.9990
   chunk 31 optimal weight:    0.8980
   chunk 42 optimal weight:    6.9990
   chunk 41 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 54 optimal weight:    8.9990
   chunk 33 optimal weight:    0.8980
   chunk 44 optimal weight:    7.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.8180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.196691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.133469 restraints weight = 5174.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 2.12
r_work: 0.2977 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2854 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8702
moved from start:          0.3520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4738  Z= 0.110
  Angle     :  0.473   5.185   6445  Z= 0.241
  Chirality :  0.038   0.170    761
  Planarity :  0.003   0.027    793
  Dihedral  :  3.841  17.080    651
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 15.89 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 are not related in a simple way.
  whole:  2.11 (0.35), residues: 605
  helix:  2.41 (0.30), residues: 286
  sheet:  1.39 (0.48), residues: 118
  loop : -0.08 (0.46), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 250 
 TYR   0.008   0.001   TYR C  49 
 PHE   0.008   0.001   PHE A  72 
 TRP   0.009   0.001   TRP A 216 
 HIS   0.002   0.001   HIS A 256 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.11 ( 4736)
  covalent geometry    : angle       0.47302 /  0.24 ( 6441)
  SS BOND              : bond        0.00092 /  0.04 (    2)
  SS BOND              : angle       0.21673 /  0.12 (    4)
  hydrogen bonds       : bond        0.03069 /  2.18 (  281)
  hydrogen bonds       : angle       4.55592 /  3.21 (  810)

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 0.096 
Fit side-chains
REVERT: A   28 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8303 (mmt)
REVERT: A   44 THR cc_start: 0.9096 (m) cc_final: 0.8426 (p)
REVERT: A  121 ILE cc_start: 0.8991 (mt) cc_final: 0.8661 (pt)
REVERT: A  154 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8538 (mp)
REVERT: A  177 ASN cc_start: 0.7559 (p0) cc_final: 0.7351 (p0)
REVERT: C   33 LEU cc_start: 0.8951 (tt) cc_final: 0.8519 (tt)
  outliers start: 11
  outliers final: 7
  residues processed: 61
  average time/residue: 0.0345
  time to fit residues: 3.0792
Evaluate side-chains
  62 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain B residue   87 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 52 optimal weight:    6.9990
   chunk 40 optimal weight:    6.9990
   chunk 25 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0980
   chunk 24 optimal weight:    0.0870
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.4958

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 116 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.198425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.136591 restraints weight = 5244.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 2.48
r_work: 0.3025 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8674
moved from start:          0.3645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4738  Z= 0.092
  Angle     :  0.454   5.159   6445  Z= 0.232
  Chirality :  0.037   0.119    761
  Planarity :  0.003   0.027    793
  Dihedral  :  3.736  16.644    651
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 16.50 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 are not related in a simple way.
  whole:  2.19 (0.35), residues: 605
  helix:  2.49 (0.30), residues: 287
  sheet:  1.41 (0.48), residues: 118
  loop : -0.05 (0.46), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 250 
 TYR   0.012   0.001   TYR B  60 
 PHE   0.008   0.001   PHE A  71 
 TRP   0.009   0.001   TRP A 216 
 HIS   0.002   0.001   HIS A   3 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00209 /  0.09 ( 4736)
  covalent geometry    : angle       0.45370 /  0.23 ( 6441)
  SS BOND              : bond        0.00071 /  0.03 (    2)
  SS BOND              : angle       0.24149 /  0.13 (    4)
  hydrogen bonds       : bond        0.02863 /  2.05 (  281)
  hydrogen bonds       : angle       4.44471 /  3.12 (  810)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1104.45 seconds
wall clock time: 19 minutes 36.67 seconds (1176.67 seconds total)