Starting phenix.real_space_refine
on Fri Aug 22 13:48:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w5q_37301/08_2025/8w5q_37301.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w5q_37301/08_2025/8w5q_37301.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w5q_37301/08_2025/8w5q_37301.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w5q_37301/08_2025/8w5q_37301.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w5q_37301/08_2025/8w5q_37301.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w5q_37301/08_2025/8w5q_37301.cif"
  }
  resolution = 4.1
  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=   0.009 sd=   0.078
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      11      5.16       5
     C    2250      2.51       5
     N     607      2.21       5
     O     695      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3563
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "L"
      Number of atoms: 765
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 765
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 5, 'TRANS': 92}
    Chain: "H"
      Number of atoms: 907
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 907
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 2, 'TRANS': 112}
    Chain: "C"
      Number of atoms: 935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 935
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 8, 'TRANS': 117}
          Chain breaks: 1
    Chain: "c"
      Number of atoms: 956
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 956
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 8, 'TRANS': 119}
          Chain breaks: 1
  Time building chain proxies: 0.87, per 1000 atoms: 0.24
  Number of scatterers: 3563
  At special positions: 0
  Unit cell: (89.76, 67.32, 81.84, 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      11     16.00
     O     695      8.00
     N     607      7.00
     C    2250      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.04

  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: 0.28
  Conformation dependent library (CDL) restraints added in 132.2 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  910 Ramachandran restraints generated.
    455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  852

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 6 sheets defined
      11.6% alpha, 24.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'C' and resid 101 through 116
      removed outlier: 3.737A  pdb=" N   LEU C 116 " --> pdb=" O   LEU C 112 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 128
    Processing helix  chain 'c' and resid 101 through 117
      removed outlier: 3.536A  pdb=" N   ARG c 105 " --> pdb=" O   THR c 101 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   ALA c 117 " --> pdb=" O   ALA c 113 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 118 through 127
      removed outlier: 3.524A  pdb=" N   GLN c 127 " --> pdb=" O   ASP c 123 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'L' and resid 56 through 57
      removed outlier: 3.503A  pdb=" N   GLN L  48 " --> pdb=" O   GLN L  40 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   TRP L  38 " --> pdb=" O   LEU L  50 " (cutoff:3.500A)
      removed outlier: 5.573A  pdb=" N   PHE L  52 " --> pdb=" O   LEU L  36 " (cutoff:3.500A)
      removed outlier: 7.531A  pdb=" N   LEU L  36 " --> pdb=" O   PHE L  52 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ALA L  37 " --> pdb=" O   GLN L  92 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLN L  92 " --> pdb=" O   ALA L  37 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 66 through 70
    Processing sheet with id=AA3, first strand: chain 'H' and resid 7 through 8
    Processing sheet with id=AA4, first strand: chain 'H' and resid 22 through 23
      removed outlier: 3.595A  pdb=" N   LEU H  23 " --> pdb=" O   LEU H  84 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   SER H  74 " --> pdb=" O   PHE H  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 40 through 41
    Processing sheet with id=AA6, first strand: chain 'C' and resid 6 through 7
      removed outlier: 3.699A  pdb=" N   VAL C   6 " --> pdb=" O   LEU C  21 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   LEU C  21 " --> pdb=" O   VAL C   6 " (cutoff:3.500A)
      removed outlier: 5.345A  pdb=" N   SER C  34 " --> pdb=" O   ARG C  24 " (cutoff:3.500A)
      removed outlier: 5.829A  pdb=" N   CYS C  74 " --> pdb=" O   VAL C  84 " (cutoff:3.500A)
      removed outlier: 5.493A  pdb=" N   VAL C  84 " --> pdb=" O   CYS C  74 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   TYR c  89 " --> pdb=" O   SER C  95 " (cutoff:3.500A)
      removed outlier: 5.421A  pdb=" N   VAL c  84 " --> pdb=" O   CYS c  74 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   CYS c  74 " --> pdb=" O   VAL c  84 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   ARG c  86 " --> pdb=" O   THR c  72 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ASN c  70 " --> pdb=" O   ALA c  88 " (cutoff:3.500A)
      removed outlier: 5.668A  pdb=" N   SER c  34 " --> pdb=" O   ARG c  24 " (cutoff:3.500A)

    111 hydrogen bonds defined for protein.
    291 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: 0.37

  Time building geometry restraints manager: 0.38 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: 1158
        1.34 -     1.46: 821
        1.46 -     1.58: 1641
        1.58 -     1.70: 0
        1.70 -     1.82: 14
  Bond restraints: 3634
  Sorted by residual:
  bond pdb=" CA  LYS H  16 "
       pdb=" C   LYS H  16 "
    ideal  model  delta    sigma   weight residual
    1.519  1.534 -0.015 1.01e-02 9.80e+03 2.31e+00
  bond pdb=" C   LYS H  16 "
       pdb=" N   PRO H  17 "
    ideal  model  delta    sigma   weight residual
    1.334  1.368 -0.034 2.34e-02 1.83e+03 2.12e+00
  bond pdb=" CG  PRO H  17 "
       pdb=" CD  PRO H  17 "
    ideal  model  delta    sigma   weight residual
    1.503  1.456  0.047 3.40e-02 8.65e+02 1.93e+00
  bond pdb=" CB  PRO C  55 "
       pdb=" CG  PRO C  55 "
    ideal  model  delta    sigma   weight residual
    1.492  1.552 -0.060 5.00e-02 4.00e+02 1.43e+00
  bond pdb=" CG  PRO C  55 "
       pdb=" CD  PRO C  55 "
    ideal  model  delta    sigma   weight residual
    1.503  1.463  0.040 3.40e-02 8.65e+02 1.38e+00
  ... (remaining 3629 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.97: 4925
        4.97 -     9.93: 10
        9.93 -    14.90: 1
       14.90 -    19.87: 0
       19.87 -    24.84: 1
  Bond angle restraints: 4937
  Sorted by residual:
  angle pdb=" C   LYS H  16 "
        pdb=" N   PRO H  17 "
        pdb=" CD  PRO H  17 "
      ideal   model   delta    sigma   weight residual
     125.00  100.16   24.84 4.10e+00 5.95e-02 3.67e+01
  angle pdb=" C   ILE L  32 "
        pdb=" N   TYR L  33 "
        pdb=" CA  TYR L  33 "
      ideal   model   delta    sigma   weight residual
     121.54  129.13   -7.59 1.91e+00 2.74e-01 1.58e+01
  angle pdb=" C   PHE H 112 "
        pdb=" N   PHE H 113 "
        pdb=" CA  PHE H 113 "
      ideal   model   delta    sigma   weight residual
     122.62  116.87    5.75 1.56e+00 4.11e-01 1.36e+01
  angle pdb=" N   GLU H 114 "
        pdb=" CA  GLU H 114 "
        pdb=" CB  GLU H 114 "
      ideal   model   delta    sigma   weight residual
     114.17  110.48    3.69 1.14e+00 7.69e-01 1.05e+01
  angle pdb=" CA  LEU C  44 "
        pdb=" CB  LEU C  44 "
        pdb=" CG  LEU C  44 "
      ideal   model   delta    sigma   weight residual
     116.30  127.51  -11.21 3.50e+00 8.16e-02 1.03e+01
  ... (remaining 4932 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.91: 1927
       15.91 -    31.81: 181
       31.81 -    47.72: 43
       47.72 -    63.62: 6
       63.62 -    79.53: 4
  Dihedral angle restraints: 2161
    sinusoidal: 824
      harmonic: 1337
  Sorted by residual:
  dihedral pdb=" CA  LYS H  16 "
           pdb=" C   LYS H  16 "
           pdb=" N   PRO H  17 "
           pdb=" CA  PRO H  17 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -147.68  -32.32     0      5.00e+00 4.00e-02 4.18e+01
  dihedral pdb=" CA  VAL H  51 "
           pdb=" C   VAL H  51 "
           pdb=" N   ALA H  52 "
           pdb=" CA  ALA H  52 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.35  -20.65     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  TYR H 111 "
           pdb=" C   TYR H 111 "
           pdb=" N   PHE H 112 "
           pdb=" CA  PHE H 112 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.62   18.38     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 2158 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 462
       0.057 -    0.113: 75
       0.113 -    0.170: 17
       0.170 -    0.227: 2
       0.227 -    0.283: 1
  Chirality restraints: 557
  Sorted by residual:
  chirality pdb=" CA  PRO H  17 "
            pdb=" N   PRO H  17 "
            pdb=" C   PRO H  17 "
            pdb=" CB  PRO H  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.43    0.28 2.00e-01 2.50e+01 2.01e+00
  chirality pdb=" CB  ILE H  96 "
            pdb=" CA  ILE H  96 "
            pdb=" CG1 ILE H  96 "
            pdb=" CG2 ILE H  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  TYR H 115 "
            pdb=" N   TYR H 115 "
            pdb=" C   TYR H 115 "
            pdb=" CB  TYR H 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.73e-01
  ... (remaining 554 not shown)

  Planarity restraints: 639
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS H  16 "   -0.123 5.00e-02 4.00e+02   1.93e-01 5.98e+01
        pdb=" N   PRO H  17 "    0.334 5.00e-02 4.00e+02
        pdb=" CA  PRO H  17 "   -0.121 5.00e-02 4.00e+02
        pdb=" CD  PRO H  17 "   -0.091 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN c  70 "    0.039 5.00e-02 4.00e+02   6.04e-02 5.83e+00
        pdb=" N   PRO c  71 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO c  71 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO c  71 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER L  10 "   -0.020 5.00e-02 4.00e+02   3.09e-02 1.52e+00
        pdb=" N   PRO L  11 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO L  11 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO L  11 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 636 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 110
        2.69 -     3.25: 3437
        3.25 -     3.80: 5080
        3.80 -     4.35: 6518
        4.35 -     4.90: 10926
  Nonbonded interactions: 26071
  Sorted by model distance:
  nonbonded pdb=" OH  TYR L  39 "
            pdb=" O   PHE H 112 "
     model   vdw
     2.143 3.040
  nonbonded pdb=" OG1 THR C  93 "
            pdb=" OD1 ASP c  91 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" O   PHE L  52 "
            pdb=" OG1 THR L  56 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" N   TYR H  38 "
            pdb=" O   ALA H 100 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" OG  SER H  10 "
            pdb=" O   GLN H 118 "
     model   vdw
     2.263 3.040
  ... (remaining 26066 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
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = (chain 'c' and (resid 1 through 55 or resid 61 through 131))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.370
  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:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.670
  Find NCS groups from input model:        0.040
  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:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
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      :  0.003   0.060   3635  Z= 0.139
  Angle     :  0.810  24.835   4939  Z= 0.391
  Chirality :  0.048   0.283    557
  Planarity :  0.009   0.193    639
  Dihedral  : 13.488  79.527   1306
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 10.55 %
    Favored  : 88.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.35 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.14 (0.38), residues: 455
  helix:  1.78 (0.70), residues: 49
  sheet: -0.59 (0.42), residues: 157
  loop : -2.80 (0.34), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 109 
 TYR   0.020   0.001   TYR H 107 
 PHE   0.016   0.001   PHE L 101 
 TRP   0.011   0.001   TRP H  39 
 HIS   0.001   0.000   HIS L  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 3634)
  covalent geometry    : angle       0.80969 ( 4937)
  SS BOND              : bond        0.00461 (    1)
  SS BOND              : angle       1.46088 (    2)
  hydrogen bonds       : bond        0.18220 (  111)
  hydrogen bonds       : angle       7.73289 (  291)

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

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

  910 Ramachandran restraints generated.
    455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  910 Ramachandran restraints generated.
    455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   36 LEU cc_start: 0.8148 (pt) cc_final: 0.7795 (pt)
REVERT: C   35 LEU cc_start: 0.8771 (mm) cc_final: 0.8227 (mt)
REVERT: C   37 GLN cc_start: 0.8270 (tt0) cc_final: 0.7351 (tm-30)
REVERT: c   14 ASP cc_start: 0.8290 (p0) cc_final: 0.7808 (p0)
REVERT: c   68 ILE cc_start: 0.9241 (mt) cc_final: 0.8794 (tt)
REVERT: c  102 ASP cc_start: 0.8233 (p0) cc_final: 0.7889 (p0)
REVERT: c  122 ILE cc_start: 0.9016 (pt) cc_final: 0.8795 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.0805
  time to fit residues: 16.0145
Evaluate side-chains
  114 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    8.9990
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:    7.9990
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0770
   chunk 37 optimal weight:    6.9990
   overall best weight:    2.7542

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

Flipped N/Q/H residues before XYZ refinement:
H   6 GLN
** c  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
c  69 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.067033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.056302 restraints weight = 18785.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.057903 restraints weight = 11114.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.059017 restraints weight = 7585.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.059788 restraints weight = 5712.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.060415 restraints weight = 4636.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.3821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3635  Z= 0.153
  Angle     :  0.737   9.114   4939  Z= 0.370
  Chirality :  0.048   0.221    557
  Planarity :  0.006   0.105    639
  Dihedral  :  5.449  27.598    505
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 14.56
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  9.45 %
    Favored  : 89.89 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  5.74 %
    Favored  : 93.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.23 (0.37), residues: 455
  helix:  0.54 (0.71), residues: 50
  sheet: -0.54 (0.41), residues: 155
  loop : -2.66 (0.34), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 105 
 TYR   0.015   0.002   TYR H  53 
 PHE   0.012   0.002   PHE L  94 
 TRP   0.008   0.001   TRP H  50 
 HIS   0.000   0.000   HIS L  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 3634)
  covalent geometry    : angle       0.73632 ( 4937)
  SS BOND              : bond        0.00203 (    1)
  SS BOND              : angle       1.31066 (    2)
  hydrogen bonds       : bond        0.03778 (  111)
  hydrogen bonds       : angle       6.00138 (  291)

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

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

  910 Ramachandran restraints generated.
    455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  910 Ramachandran restraints generated.
    455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 128
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   55 LYS cc_start: 0.9759 (mtmm) cc_final: 0.9360 (mttm)
REVERT: H   65 ASP cc_start: 0.8969 (t0) cc_final: 0.8666 (t0)
REVERT: C    5 THR cc_start: 0.8723 (p) cc_final: 0.8302 (p)
REVERT: C   13 LYS cc_start: 0.8715 (ttmm) cc_final: 0.7622 (ttmm)
REVERT: C   37 GLN cc_start: 0.8718 (tt0) cc_final: 0.8167 (tm-30)
REVERT: C   63 LYS cc_start: 0.9054 (tmtt) cc_final: 0.8637 (tmtt)
REVERT: C  100 SER cc_start: 0.9431 (p) cc_final: 0.8905 (p)
REVERT: C  104 GLU cc_start: 0.9207 (pt0) cc_final: 0.8875 (pp20)
REVERT: C  123 ASP cc_start: 0.9132 (t0) cc_final: 0.8774 (t0)
REVERT: c   14 ASP cc_start: 0.9128 (p0) cc_final: 0.8544 (p0)
REVERT: c   21 LEU cc_start: 0.9058 (pp) cc_final: 0.8514 (pp)
REVERT: c   37 GLN cc_start: 0.8601 (pp30) cc_final: 0.8281 (pp30)
REVERT: c  102 ASP cc_start: 0.9455 (p0) cc_final: 0.9238 (p0)
REVERT: c  127 GLN cc_start: 0.9182 (mp10) cc_final: 0.8866 (mp10)
  outliers start: 2
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0691
  time to fit residues: 10.7261
Evaluate side-chains
  105 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 12 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 36 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 40 optimal weight:    5.9990
   chunk 39 optimal weight:    7.9990
   chunk 27 optimal weight:    9.9990
   chunk 38 optimal weight:    7.9990
   chunk 25 optimal weight:   10.0000
   chunk 41 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  22 ASN
** c  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
c  69 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.061106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.050901 restraints weight = 19291.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.052469 restraints weight = 11095.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.053568 restraints weight = 7468.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.054297 restraints weight = 5578.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.054869 restraints weight = 4500.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.4823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   3635  Z= 0.237
  Angle     :  0.756   8.738   4939  Z= 0.396
  Chirality :  0.046   0.209    557
  Planarity :  0.006   0.087    639
  Dihedral  :  5.603  28.442    505
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 15.69
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 10.11 %
    Favored  : 89.01 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  7.83 %
    Favored  : 91.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.43 (0.37), residues: 455
  helix:  0.31 (0.74), residues: 49
  sheet: -0.84 (0.40), residues: 162
  loop : -2.67 (0.35), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG L  41 
 TYR   0.022   0.002   TYR H 111 
 PHE   0.013   0.002   PHE L 101 
 TRP   0.018   0.003   TRP H 116 
 HIS   0.003   0.002   HIS L  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 ( 3634)
  covalent geometry    : angle       0.75513 ( 4937)
  SS BOND              : bond        0.00680 (    1)
  SS BOND              : angle       1.51454 (    2)
  hydrogen bonds       : bond        0.03800 (  111)
  hydrogen bonds       : angle       5.77575 (  291)

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

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

  910 Ramachandran restraints generated.
    455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  910 Ramachandran restraints generated.
    455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   52 PHE cc_start: 0.8788 (m-80) cc_final: 0.8377 (m-10)
REVERT: L   55 LYS cc_start: 0.9712 (mtmm) cc_final: 0.9461 (mtmm)
REVERT: L   74 TYR cc_start: 0.8268 (m-80) cc_final: 0.7960 (m-80)
REVERT: H   35 TYR cc_start: 0.9086 (m-80) cc_final: 0.8571 (m-80)
REVERT: H   62 TYR cc_start: 0.9100 (m-80) cc_final: 0.8641 (m-80)
REVERT: H   68 LYS cc_start: 0.9195 (mmpt) cc_final: 0.8964 (mmtt)
REVERT: H  116 TRP cc_start: 0.7263 (t-100) cc_final: 0.7031 (t-100)
REVERT: C   14 ASP cc_start: 0.9489 (p0) cc_final: 0.9247 (p0)
REVERT: C   37 GLN cc_start: 0.8974 (tt0) cc_final: 0.8284 (tm-30)
REVERT: C   63 LYS cc_start: 0.9050 (tmtt) cc_final: 0.8732 (tmtt)
REVERT: C   79 SER cc_start: 0.7653 (t) cc_final: 0.7314 (t)
REVERT: C  100 SER cc_start: 0.9448 (p) cc_final: 0.8671 (p)
REVERT: C  123 ASP cc_start: 0.9144 (t0) cc_final: 0.8737 (t0)
REVERT: c   13 LYS cc_start: 0.9660 (tttt) cc_final: 0.9459 (tttp)
REVERT: c   14 ASP cc_start: 0.9078 (p0) cc_final: 0.8702 (p0)
REVERT: c   37 GLN cc_start: 0.8611 (pp30) cc_final: 0.8240 (pp30)
REVERT: c   69 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8139 (tp40)
REVERT: c  102 ASP cc_start: 0.9548 (p0) cc_final: 0.9180 (p0)
REVERT: c  121 LEU cc_start: 0.9559 (mm) cc_final: 0.9266 (mm)
REVERT: c  123 ASP cc_start: 0.9328 (t0) cc_final: 0.9111 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 123
  average time/residue: 0.0801
  time to fit residues: 11.6185
Evaluate side-chains
  93 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 22 optimal weight:    0.7980
   chunk 23 optimal weight:   20.0000
   chunk 0 optimal weight:   30.0000
   chunk 19 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 43 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 39 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 10 optimal weight:   30.0000
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
C  22 ASN
C  87 GLN
c  37 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.062290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.052096 restraints weight = 19348.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.053551 restraints weight = 11393.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.054589 restraints weight = 7816.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.055272 restraints weight = 5917.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.055819 restraints weight = 4827.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.5127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3635  Z= 0.142
  Angle     :  0.730   8.734   4939  Z= 0.369
  Chirality :  0.048   0.226    557
  Planarity :  0.006   0.115    639
  Dihedral  :  5.323  29.346    505
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 14.56
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  8.57 %
    Favored  : 90.55 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  3.92 %
    Favored  : 95.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.26 (0.37), residues: 455
  helix:  0.37 (0.72), residues: 49
  sheet: -0.56 (0.41), residues: 159
  loop : -2.65 (0.34), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  90 
 TYR   0.011   0.001   TYR L  39 
 PHE   0.016   0.002   PHE L 101 
 TRP   0.011   0.002   TRP H  50 
 HIS   0.002   0.001   HIS L  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 3634)
  covalent geometry    : angle       0.72991 ( 4937)
  SS BOND              : bond        0.00494 (    1)
  SS BOND              : angle       1.03088 (    2)
  hydrogen bonds       : bond        0.03428 (  111)
  hydrogen bonds       : angle       5.47021 (  291)

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

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

  910 Ramachandran restraints generated.
    455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  910 Ramachandran restraints generated.
    455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 131
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   24 ILE cc_start: 0.8184 (pt) cc_final: 0.7903 (mp)
REVERT: H   35 TYR cc_start: 0.8943 (m-80) cc_final: 0.8455 (m-80)
REVERT: H   62 TYR cc_start: 0.8910 (m-80) cc_final: 0.8422 (m-80)
REVERT: H  116 TRP cc_start: 0.7312 (t-100) cc_final: 0.6973 (t-100)
REVERT: C    5 THR cc_start: 0.9435 (p) cc_final: 0.8412 (p)
REVERT: C   14 ASP cc_start: 0.9189 (p0) cc_final: 0.8970 (p0)
REVERT: C   16 LYS cc_start: 0.8997 (mmpt) cc_final: 0.8693 (mmmt)
REVERT: C   37 GLN cc_start: 0.8968 (tt0) cc_final: 0.8260 (tm-30)
REVERT: C   63 LYS cc_start: 0.9082 (tmtt) cc_final: 0.8572 (ttpp)
REVERT: C   79 SER cc_start: 0.7565 (t) cc_final: 0.7237 (t)
REVERT: C  123 ASP cc_start: 0.9225 (t0) cc_final: 0.8724 (t0)
REVERT: c   14 ASP cc_start: 0.9164 (p0) cc_final: 0.8632 (p0)
REVERT: c   37 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8238 (pp30)
REVERT: c  104 GLU cc_start: 0.9312 (pt0) cc_final: 0.8933 (pm20)
REVERT: c  111 GLU cc_start: 0.9316 (pt0) cc_final: 0.8863 (pt0)
REVERT: c  121 LEU cc_start: 0.9572 (mm) cc_final: 0.9168 (mm)
REVERT: c  123 ASP cc_start: 0.9294 (t0) cc_final: 0.9021 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 131
  average time/residue: 0.0746
  time to fit residues: 11.5073
Evaluate side-chains
  100 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 9 optimal weight:    7.9990
   chunk 14 optimal weight:    7.9990
   chunk 31 optimal weight:    0.6980
   chunk 4 optimal weight:    5.9990
   chunk 2 optimal weight:    9.9990
   chunk 34 optimal weight:    6.9990
   chunk 1 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 20 optimal weight:   10.0000
   chunk 42 optimal weight:    6.9990
   chunk 23 optimal weight:   20.0000
   overall best weight:    5.7388

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

Flipped N/Q/H residues before XYZ refinement:
C  87 GLN
c  69 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.058935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.049286 restraints weight = 20102.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.050713 restraints weight = 11670.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.051714 restraints weight = 7935.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.052376 restraints weight = 5961.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.052888 restraints weight = 4834.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.5697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   3635  Z= 0.233
  Angle     :  0.772   9.743   4939  Z= 0.397
  Chirality :  0.048   0.230    557
  Planarity :  0.006   0.122    639
  Dihedral  :  5.616  28.051    505
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 15.69
  Ramachandran Plot:
    Outliers :  1.10 %
    Allowed  : 10.55 %
    Favored  : 88.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.40 (0.37), residues: 455
  helix: -0.27 (0.69), residues: 50
  sheet: -0.59 (0.41), residues: 162
  loop : -2.70 (0.36), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  90 
 TYR   0.014   0.002   TYR L  89 
 PHE   0.014   0.002   PHE L 101 
 TRP   0.014   0.003   TRP H 116 
 HIS   0.002   0.002   HIS L  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00519 ( 3634)
  covalent geometry    : angle       0.77241 ( 4937)
  SS BOND              : bond        0.00311 (    1)
  SS BOND              : angle       0.91444 (    2)
  hydrogen bonds       : bond        0.03651 (  111)
  hydrogen bonds       : angle       5.51462 (  291)

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

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

  910 Ramachandran restraints generated.
    455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  910 Ramachandran restraints generated.
    455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L    7 MET cc_start: 0.7914 (pmm) cc_final: 0.7376 (pmm)
REVERT: L   41 ARG cc_start: 0.9452 (tpt90) cc_final: 0.9063 (tpt170)
REVERT: H   86 MET cc_start: 0.9000 (mpp) cc_final: 0.8786 (mpp)
REVERT: H  103 ARG cc_start: 0.8644 (mmm160) cc_final: 0.7885 (mmm160)
REVERT: H  116 TRP cc_start: 0.7489 (t-100) cc_final: 0.6778 (t-100)
REVERT: C   13 LYS cc_start: 0.9053 (ptpt) cc_final: 0.8419 (mttp)
REVERT: C   14 ASP cc_start: 0.9306 (p0) cc_final: 0.9048 (p0)
REVERT: C   37 GLN cc_start: 0.9024 (tt0) cc_final: 0.8663 (tm-30)
REVERT: C   63 LYS cc_start: 0.9096 (tmtt) cc_final: 0.8593 (ttpp)
REVERT: C  123 ASP cc_start: 0.9249 (t0) cc_final: 0.8794 (t0)
REVERT: c   37 GLN cc_start: 0.9075 (tm-30) cc_final: 0.8781 (tm-30)
REVERT: c   96 PHE cc_start: 0.9079 (m-80) cc_final: 0.8795 (m-80)
REVERT: c  100 SER cc_start: 0.9064 (p) cc_final: 0.8792 (p)
REVERT: c  104 GLU cc_start: 0.9347 (pt0) cc_final: 0.9104 (pm20)
REVERT: c  111 GLU cc_start: 0.9418 (pt0) cc_final: 0.9013 (pt0)
REVERT: c  121 LEU cc_start: 0.9611 (mm) cc_final: 0.9249 (mm)
REVERT: c  123 ASP cc_start: 0.9346 (t0) cc_final: 0.9037 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.0891
  time to fit residues: 11.5720
Evaluate side-chains
  87 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 26 optimal weight:   10.0000
   chunk 34 optimal weight:    7.9990
   chunk 30 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   chunk 7 optimal weight:   20.0000
   chunk 32 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9990
   chunk 16 optimal weight:    6.9990
   chunk 28 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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 = 0.3177 r_free = 0.3177 target = 0.059262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.049602 restraints weight = 19868.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.051010 restraints weight = 11672.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.051964 restraints weight = 7971.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.052654 restraints weight = 6007.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.053150 restraints weight = 4864.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.5808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3635  Z= 0.190
  Angle     :  0.754  10.012   4939  Z= 0.383
  Chirality :  0.048   0.217    557
  Planarity :  0.005   0.100    639
  Dihedral  :  5.456  28.071    505
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  1.10 %
    Allowed  : 10.11 %
    Favored  : 88.79 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  2.87 %
    Favored  : 96.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.35 (0.38), residues: 455
  helix: -0.43 (0.70), residues: 51
  sheet: -0.53 (0.42), residues: 159
  loop : -2.62 (0.36), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  47 
 TYR   0.012   0.002   TYR H  38 
 PHE   0.020   0.001   PHE L 101 
 TRP   0.008   0.002   TRP L  99 
 HIS   0.003   0.002   HIS L  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 3634)
  covalent geometry    : angle       0.75347 ( 4937)
  SS BOND              : bond        0.00382 (    1)
  SS BOND              : angle       0.94204 (    2)
  hydrogen bonds       : bond        0.03458 (  111)
  hydrogen bonds       : angle       5.35581 (  291)

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

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

  910 Ramachandran restraints generated.
    455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  910 Ramachandran restraints generated.
    455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   24 ILE cc_start: 0.8422 (pt) cc_final: 0.8188 (mp)
REVERT: L   41 ARG cc_start: 0.9463 (tpt90) cc_final: 0.9154 (tpt170)
REVERT: H  116 TRP cc_start: 0.7296 (t-100) cc_final: 0.6824 (t-100)
REVERT: C    5 THR cc_start: 0.9332 (p) cc_final: 0.8362 (p)
REVERT: C   13 LYS cc_start: 0.8986 (ptpt) cc_final: 0.8381 (mtmm)
REVERT: C   14 ASP cc_start: 0.9474 (p0) cc_final: 0.9025 (p0)
REVERT: C   37 GLN cc_start: 0.8982 (tt0) cc_final: 0.8475 (tm-30)
REVERT: C   63 LYS cc_start: 0.9080 (tmtt) cc_final: 0.8592 (ttpp)
REVERT: C  123 ASP cc_start: 0.9227 (t0) cc_final: 0.8730 (t0)
REVERT: c   37 GLN cc_start: 0.9117 (tm-30) cc_final: 0.8733 (tm-30)
REVERT: c   68 ILE cc_start: 0.9736 (mt) cc_final: 0.9508 (mt)
REVERT: c  100 SER cc_start: 0.9210 (p) cc_final: 0.8960 (p)
REVERT: c  104 GLU cc_start: 0.9324 (pt0) cc_final: 0.9086 (pm20)
REVERT: c  111 GLU cc_start: 0.9452 (pt0) cc_final: 0.9095 (pt0)
REVERT: c  122 ILE cc_start: 0.9144 (tt) cc_final: 0.8589 (tt)
REVERT: c  123 ASP cc_start: 0.9302 (t0) cc_final: 0.9005 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 106
  average time/residue: 0.0714
  time to fit residues: 8.8288
Evaluate side-chains
  83 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 18 optimal weight:    9.9990
   chunk 24 optimal weight:    6.9990
   chunk 40 optimal weight:    7.9990
   chunk 29 optimal weight:    4.9990
   chunk 28 optimal weight:    7.9990
   chunk 31 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 32 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 37 optimal weight:    9.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
C  87 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.058171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.048558 restraints weight = 20172.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.049958 restraints weight = 11742.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.050953 restraints weight = 8011.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.051619 restraints weight = 6021.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.052131 restraints weight = 4896.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.6084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   3635  Z= 0.233
  Angle     :  0.809  14.978   4939  Z= 0.403
  Chirality :  0.049   0.261    557
  Planarity :  0.007   0.155    639
  Dihedral  :  5.684  31.466    505
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 15.69
  Ramachandran Plot:
    Outliers :  1.10 %
    Allowed  : 10.55 %
    Favored  : 88.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.35 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.45 (0.37), residues: 455
  helix: -0.33 (0.68), residues: 50
  sheet: -0.63 (0.41), residues: 162
  loop : -2.72 (0.36), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  75 
 TYR   0.020   0.002   TYR H  38 
 PHE   0.021   0.002   PHE L  94 
 TRP   0.011   0.002   TRP L  99 
 HIS   0.004   0.003   HIS L  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 ( 3634)
  covalent geometry    : angle       0.80885 ( 4937)
  SS BOND              : bond        0.00358 (    1)
  SS BOND              : angle       0.89633 (    2)
  hydrogen bonds       : bond        0.03597 (  111)
  hydrogen bonds       : angle       5.40404 (  291)

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

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

  910 Ramachandran restraints generated.
    455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  910 Ramachandran restraints generated.
    455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   41 ARG cc_start: 0.9397 (tpt90) cc_final: 0.9044 (tpt170)
REVERT: H   49 GLU cc_start: 0.8705 (pm20) cc_final: 0.8154 (pm20)
REVERT: H  116 TRP cc_start: 0.7458 (t-100) cc_final: 0.6862 (t-100)
REVERT: C    5 THR cc_start: 0.9372 (p) cc_final: 0.8319 (p)
REVERT: C   13 LYS cc_start: 0.8917 (ptpt) cc_final: 0.8214 (mttp)
REVERT: C   14 ASP cc_start: 0.9471 (p0) cc_final: 0.8982 (p0)
REVERT: C   37 GLN cc_start: 0.9018 (tt0) cc_final: 0.8618 (tm-30)
REVERT: C   63 LYS cc_start: 0.9149 (tmtt) cc_final: 0.8718 (ttpp)
REVERT: C   68 ILE cc_start: 0.9521 (mt) cc_final: 0.9318 (mp)
REVERT: C  123 ASP cc_start: 0.9189 (t0) cc_final: 0.8725 (t0)
REVERT: c   13 LYS cc_start: 0.9576 (tttt) cc_final: 0.9291 (tttp)
REVERT: c   37 GLN cc_start: 0.9130 (tm-30) cc_final: 0.8711 (tm-30)
REVERT: c   68 ILE cc_start: 0.9754 (mt) cc_final: 0.9465 (mt)
REVERT: c   96 PHE cc_start: 0.9082 (m-80) cc_final: 0.8868 (m-80)
REVERT: c  122 ILE cc_start: 0.8895 (tt) cc_final: 0.8196 (tt)
REVERT: c  123 ASP cc_start: 0.9244 (t0) cc_final: 0.9035 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.0793
  time to fit residues: 9.2306
Evaluate side-chains
  76 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   chunk 32 optimal weight:   20.0000
   chunk 13 optimal weight:    4.9990
   chunk 41 optimal weight:    0.2980
   chunk 35 optimal weight:    7.9990
   chunk 11 optimal weight:    6.9990
   chunk 20 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 6 optimal weight:   20.0000
   overall best weight:    4.4588

-------------------------------------------------------------------------------
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 = 0.3186 r_free = 0.3186 target = 0.059438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.049894 restraints weight = 20049.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.051310 restraints weight = 11879.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.052262 restraints weight = 8085.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.052958 restraints weight = 6103.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.053466 restraints weight = 4945.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.6154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3635  Z= 0.191
  Angle     :  0.767  11.056   4939  Z= 0.389
  Chirality :  0.050   0.279    557
  Planarity :  0.006   0.130    639
  Dihedral  :  5.589  31.433    505
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 14.70
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 10.33 %
    Favored  : 88.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.35 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.50 (0.37), residues: 455
  helix: -0.53 (0.70), residues: 51
  sheet: -0.65 (0.40), residues: 162
  loop : -2.74 (0.36), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG c  47 
 TYR   0.014   0.002   TYR H  38 
 PHE   0.017   0.002   PHE L  94 
 TRP   0.009   0.002   TRP H  39 
 HIS   0.003   0.002   HIS L  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 3634)
  covalent geometry    : angle       0.76706 ( 4937)
  SS BOND              : bond        0.00390 (    1)
  SS BOND              : angle       0.85411 (    2)
  hydrogen bonds       : bond        0.03594 (  111)
  hydrogen bonds       : angle       5.33938 (  291)

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

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

  910 Ramachandran restraints generated.
    455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  910 Ramachandran restraints generated.
    455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   49 GLU cc_start: 0.8714 (pm20) cc_final: 0.8139 (pm20)
REVERT: H  116 TRP cc_start: 0.7380 (t-100) cc_final: 0.6801 (t-100)
REVERT: C   13 LYS cc_start: 0.8887 (ptpt) cc_final: 0.8431 (ptpt)
REVERT: C   14 ASP cc_start: 0.9448 (p0) cc_final: 0.9103 (p0)
REVERT: C   37 GLN cc_start: 0.9007 (tt0) cc_final: 0.8566 (tm-30)
REVERT: C   63 LYS cc_start: 0.9110 (tmtt) cc_final: 0.8707 (ttpp)
REVERT: C  115 LEU cc_start: 0.9719 (tp) cc_final: 0.9517 (tp)
REVERT: C  123 ASP cc_start: 0.9221 (t0) cc_final: 0.8712 (t0)
REVERT: c   13 LYS cc_start: 0.9303 (tttt) cc_final: 0.9066 (tttp)
REVERT: c   14 ASP cc_start: 0.8771 (p0) cc_final: 0.8458 (p0)
REVERT: c   37 GLN cc_start: 0.9162 (tm-30) cc_final: 0.8639 (tm-30)
REVERT: c   68 ILE cc_start: 0.9740 (mt) cc_final: 0.9497 (mt)
REVERT: c  104 GLU cc_start: 0.9363 (pm20) cc_final: 0.8828 (pm20)
REVERT: c  122 ILE cc_start: 0.9011 (tt) cc_final: 0.8145 (tt)
REVERT: c  123 ASP cc_start: 0.9176 (t0) cc_final: 0.8940 (t0)
REVERT: c  126 ASP cc_start: 0.8707 (m-30) cc_final: 0.8296 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.0773
  time to fit residues: 9.3594
Evaluate side-chains
  81 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 3 optimal weight:    9.9990
   chunk 5 optimal weight:    7.9990
   chunk 22 optimal weight:    7.9990
   chunk 10 optimal weight:   30.0000
   chunk 12 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9980
   chunk 33 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    5.9990
   overall best weight:    4.3386

-------------------------------------------------------------------------------
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 = 0.3170 r_free = 0.3170 target = 0.058941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.049298 restraints weight = 19471.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.050768 restraints weight = 10894.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.051800 restraints weight = 7260.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.052551 restraints weight = 5397.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.053085 restraints weight = 4290.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.6271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3635  Z= 0.187
  Angle     :  0.779  11.352   4939  Z= 0.396
  Chirality :  0.050   0.247    557
  Planarity :  0.004   0.041    639
  Dihedral  :  5.747  44.890    505
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 15.41
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 10.11 %
    Favored  : 89.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.35 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.41 (0.38), residues: 455
  helix: -0.52 (0.69), residues: 51
  sheet: -0.56 (0.40), residues: 159
  loop : -2.67 (0.37), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  47 
 TYR   0.016   0.002   TYR L  33 
 PHE   0.020   0.002   PHE c 107 
 TRP   0.010   0.002   TRP H  39 
 HIS   0.004   0.002   HIS L  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 3634)
  covalent geometry    : angle       0.77911 ( 4937)
  SS BOND              : bond        0.00397 (    1)
  SS BOND              : angle       0.88875 (    2)
  hydrogen bonds       : bond        0.03484 (  111)
  hydrogen bonds       : angle       5.33382 (  291)

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

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

  910 Ramachandran restraints generated.
    455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  910 Ramachandran restraints generated.
    455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   65 ASP cc_start: 0.8697 (t0) cc_final: 0.8481 (t0)
REVERT: H   86 MET cc_start: 0.9016 (mpp) cc_final: 0.8782 (mpp)
REVERT: H  116 TRP cc_start: 0.7485 (t-100) cc_final: 0.6810 (t-100)
REVERT: C   13 LYS cc_start: 0.8903 (ptpt) cc_final: 0.8474 (ptpt)
REVERT: C   14 ASP cc_start: 0.9463 (p0) cc_final: 0.9131 (p0)
REVERT: C   37 GLN cc_start: 0.9047 (tt0) cc_final: 0.8541 (tm-30)
REVERT: C   63 LYS cc_start: 0.9067 (tmtt) cc_final: 0.8588 (ttpp)
REVERT: C   65 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8057 (tm-30)
REVERT: C  123 ASP cc_start: 0.9230 (t0) cc_final: 0.8782 (t0)
REVERT: c   13 LYS cc_start: 0.9493 (tttt) cc_final: 0.9146 (tttp)
REVERT: c   14 ASP cc_start: 0.8821 (p0) cc_final: 0.8521 (p0)
REVERT: c   37 GLN cc_start: 0.9148 (tm-30) cc_final: 0.8674 (tm-30)
REVERT: c   68 ILE cc_start: 0.9728 (mt) cc_final: 0.9525 (mt)
REVERT: c  104 GLU cc_start: 0.9322 (pm20) cc_final: 0.8541 (pm20)
REVERT: c  122 ILE cc_start: 0.8955 (tt) cc_final: 0.8040 (tt)
REVERT: c  123 ASP cc_start: 0.9261 (t0) cc_final: 0.9004 (t0)
REVERT: c  126 ASP cc_start: 0.8558 (m-30) cc_final: 0.8346 (m-30)
REVERT: c  127 GLN cc_start: 0.9037 (mp10) cc_final: 0.8834 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.0778
  time to fit residues: 9.1348
Evaluate side-chains
  82 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0040
   chunk 24 optimal weight:   10.0000
   chunk 37 optimal weight:    9.9990
   chunk 17 optimal weight:   20.0000
   chunk 29 optimal weight:    2.9990
   chunk 6 optimal weight:   20.0000
   chunk 15 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   overall best weight:    2.8000

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

Flipped N/Q/H residues before XYZ refinement:
C  10 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.059796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.050131 restraints weight = 19626.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.051604 restraints weight = 11358.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.052646 restraints weight = 7586.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.053388 restraints weight = 5609.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.053913 restraints weight = 4470.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.6364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3635  Z= 0.155
  Angle     :  0.784  11.430   4939  Z= 0.398
  Chirality :  0.050   0.229    557
  Planarity :  0.004   0.038    639
  Dihedral  :  5.602  38.614    505
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 14.85
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 11.43 %
    Favored  : 87.91 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  0.26 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.35 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.30 (0.38), residues: 455
  helix: -0.30 (0.70), residues: 51
  sheet: -0.46 (0.41), residues: 159
  loop : -2.66 (0.37), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  47 
 TYR   0.010   0.001   TYR L  39 
 PHE   0.022   0.002   PHE c 107 
 TRP   0.008   0.001   TRP H  39 
 HIS   0.003   0.002   HIS L  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 3634)
  covalent geometry    : angle       0.78375 ( 4937)
  SS BOND              : bond        0.00661 (    1)
  SS BOND              : angle       1.81354 (    2)
  hydrogen bonds       : bond        0.03462 (  111)
  hydrogen bonds       : angle       5.24846 (  291)

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

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

  910 Ramachandran restraints generated.
    455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  910 Ramachandran restraints generated.
    455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   86 MET cc_start: 0.8983 (mpp) cc_final: 0.8711 (mpp)
REVERT: H  116 TRP cc_start: 0.7481 (t-100) cc_final: 0.6801 (t-100)
REVERT: C    5 THR cc_start: 0.9358 (p) cc_final: 0.8371 (p)
REVERT: C   13 LYS cc_start: 0.8857 (ptpt) cc_final: 0.7653 (mttp)
REVERT: C   14 ASP cc_start: 0.9421 (p0) cc_final: 0.8928 (p0)
REVERT: C   37 GLN cc_start: 0.8860 (tt0) cc_final: 0.8202 (tm-30)
REVERT: C   63 LYS cc_start: 0.9037 (tmtt) cc_final: 0.8560 (ttpp)
REVERT: C   65 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7866 (tm-30)
REVERT: C  115 LEU cc_start: 0.9720 (tp) cc_final: 0.9460 (tt)
REVERT: C  123 ASP cc_start: 0.9270 (t0) cc_final: 0.8824 (t0)
REVERT: c   13 LYS cc_start: 0.9443 (tttt) cc_final: 0.9241 (tttp)
REVERT: c   14 ASP cc_start: 0.8825 (p0) cc_final: 0.8501 (p0)
REVERT: c   37 GLN cc_start: 0.9156 (tm-30) cc_final: 0.8810 (tm-30)
REVERT: c   68 ILE cc_start: 0.9727 (mt) cc_final: 0.9483 (mt)
REVERT: c  102 ASP cc_start: 0.9581 (p0) cc_final: 0.9362 (p0)
REVERT: c  104 GLU cc_start: 0.9365 (pm20) cc_final: 0.8885 (pm20)
REVERT: c  122 ILE cc_start: 0.8941 (tt) cc_final: 0.8067 (tt)
REVERT: c  123 ASP cc_start: 0.9258 (t0) cc_final: 0.9008 (t0)
REVERT: c  126 ASP cc_start: 0.8732 (m-30) cc_final: 0.8351 (m-30)
REVERT: c  127 GLN cc_start: 0.9007 (mp10) cc_final: 0.8771 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 101
  average time/residue: 0.0701
  time to fit residues: 8.4395
Evaluate side-chains
  86 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 28 optimal weight:   10.0000
   chunk 32 optimal weight:   20.0000
   chunk 39 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9990
   chunk 4 optimal weight:    0.2980
   chunk 9 optimal weight:    0.5980
   chunk 35 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   chunk 17 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
C  10 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.061700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.051825 restraints weight = 18962.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.053350 restraints weight = 10693.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.054403 restraints weight = 7131.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.055170 restraints weight = 5275.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.055637 restraints weight = 4194.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.6394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3635  Z= 0.141
  Angle     :  0.811  11.218   4939  Z= 0.405
  Chirality :  0.050   0.216    557
  Planarity :  0.004   0.039    639
  Dihedral  :  5.193  32.853    505
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  9.45 %
    Favored  : 89.89 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  0.00 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.35 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.09 (0.39), residues: 455
  helix:  0.32 (0.75), residues: 49
  sheet: -0.12 (0.43), residues: 153
  loop : -2.71 (0.36), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG c 105 
 TYR   0.014   0.001   TYR L  90 
 PHE   0.025   0.002   PHE c 107 
 TRP   0.007   0.001   TRP L  95 
 HIS   0.003   0.002   HIS L  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 3634)
  covalent geometry    : angle       0.81040 ( 4937)
  SS BOND              : bond        0.00379 (    1)
  SS BOND              : angle       1.68933 (    2)
  hydrogen bonds       : bond        0.03501 (  111)
  hydrogen bonds       : angle       5.10965 (  291)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 665.00 seconds
wall clock time: 12 minutes 8.14 seconds (728.14 seconds total)