Starting phenix.real_space_refine
on Fri May  9 19:33:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w5q_37301/05_2025/8w5q_37301.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w5q_37301/05_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_37301/05_2025/8w5q_37301.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w5q_37301/05_2025/8w5q_37301.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w5q_37301/05_2025/8w5q_37301.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w5q_37301/05_2025/8w5q_37301.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.009 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 2.89, per 1000 atoms: 0.81
  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: 0.75
  Conformation dependent library (CDL) restraints added in 412.0 milliseconds
  

  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: 0.34
  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: 0.79

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 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:             0.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.870
  Find NCS groups from input model:        0.090
  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:3.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.030
-------------------------------------------------------------------------------
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 : 11.88
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.14 (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
 TRP   0.011   0.001   TRP H  39 
 HIS   0.001   0.000   HIS L  93 
 PHE   0.016   0.001   PHE L 101 
 TYR   0.020   0.001   TYR H 107 
 ARG   0.002   0.000   ARG C 109 

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

*********************** 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  : 0.429 
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: 0.2013
  time to fit residues: 40.0127
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  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 33 optimal weight:   20.0000
   chunk 18 optimal weight:   10.0000
   chunk 11 optimal weight:    6.9990
   chunk 22 optimal weight:    5.9990
   chunk 17 optimal weight:    8.9990
   chunk 34 optimal weight:    4.9990
   chunk 13 optimal weight:    7.9990
   chunk 20 optimal weight:   20.0000
   chunk 25 optimal weight:   10.0000
   chunk 39 optimal weight:   20.0000
   overall best weight:    5.3188

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.063525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.053018 restraints weight = 19071.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.054539 restraints weight = 11304.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.055608 restraints weight = 7750.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.4199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   3635  Z= 0.231
  Angle     :  0.785  11.085   4939  Z= 0.398
  Chirality :  0.048   0.223    557
  Planarity :  0.007   0.108    639
  Dihedral  :  5.773  28.271    505
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 18.38
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  9.89 %
    Favored  : 89.23 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  7.05 %
    Favored  : 92.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.35 (0.37), residues: 455
  helix:  0.45 (0.73), residues: 49
  sheet: -0.78 (0.40), residues: 162
  loop : -2.64 (0.35), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H 116 
 HIS   0.001   0.001   HIS L  93 
 PHE   0.017   0.002   PHE L  52 
 TYR   0.019   0.002   TYR H 111 
 ARG   0.003   0.001   ARG H  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04001 (  111)
  hydrogen bonds       : angle       6.13452 (  291)
  SS BOND              : bond        0.00263 (    1)
  SS BOND              : angle       1.34240 (    2)
  covalent geometry    : bond        0.00509 ( 3634)
  covalent geometry    : angle       0.78438 ( 4937)

*********************** 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
  126 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 123
  time to evaluate  : 0.380 
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: C   37 GLN cc_start: 0.8860 (tt0) cc_final: 0.8256 (tm-30)
REVERT: C   63 LYS cc_start: 0.9148 (tmtt) cc_final: 0.8705 (tmtt)
REVERT: C  100 SER cc_start: 0.9479 (p) cc_final: 0.8647 (p)
REVERT: C  104 GLU cc_start: 0.9319 (pt0) cc_final: 0.8948 (pp20)
REVERT: C  123 ASP cc_start: 0.9124 (t0) cc_final: 0.8735 (t0)
REVERT: c    3 LEU cc_start: 0.9245 (mp) cc_final: 0.8250 (mp)
REVERT: c    6 VAL cc_start: 0.9612 (t) cc_final: 0.9313 (p)
REVERT: c   14 ASP cc_start: 0.9139 (p0) cc_final: 0.8675 (p0)
REVERT: c   21 LEU cc_start: 0.9196 (pp) cc_final: 0.8683 (pp)
REVERT: c   37 GLN cc_start: 0.8642 (pp30) cc_final: 0.8318 (pp30)
REVERT: c  127 GLN cc_start: 0.9181 (mp10) cc_final: 0.8939 (mp10)
  outliers start: 3
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1633
  time to fit residues: 24.3283
Evaluate side-chains
  102 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 18 optimal weight:   20.0000
   chunk 24 optimal weight:    6.9990
   chunk 7 optimal weight:   30.0000
   chunk 35 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 37 optimal weight:    9.9990
   chunk 32 optimal weight:    4.9990
   chunk 21 optimal weight:   10.0000
   chunk 41 optimal weight:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
H   6 GLN
C  22 ASN
** c  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
c  69 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.060414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.050657 restraints weight = 18972.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.052153 restraints weight = 10810.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.053202 restraints weight = 7256.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.4795

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= 0.194
  Angle     :  0.714   8.149   4939  Z= 0.370
  Chirality :  0.046   0.207    557
  Planarity :  0.006   0.087    639
  Dihedral  :  5.522  27.845    505
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 14.70
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  9.23 %
    Favored  : 90.11 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  5.74 %
    Favored  : 93.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.33 (0.37), residues: 455
  helix:  0.50 (0.73), residues: 48
  sheet: -0.77 (0.40), residues: 162
  loop : -2.63 (0.35), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP H 116 
 HIS   0.002   0.001   HIS L  93 
 PHE   0.013   0.002   PHE L 101 
 TYR   0.018   0.002   TYR H  35 
 ARG   0.002   0.000   ARG C 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03632 (  111)
  hydrogen bonds       : angle       5.59733 (  291)
  SS BOND              : bond        0.00615 (    1)
  SS BOND              : angle       1.30597 (    2)
  covalent geometry    : bond        0.00426 ( 3634)
  covalent geometry    : angle       0.71350 ( 4937)

*********************** 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
  129 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   52 PHE cc_start: 0.8715 (m-80) cc_final: 0.8371 (m-10)
REVERT: H   35 TYR cc_start: 0.9039 (m-80) cc_final: 0.8519 (m-80)
REVERT: H   62 TYR cc_start: 0.8851 (m-80) cc_final: 0.8492 (m-80)
REVERT: H  116 TRP cc_start: 0.7463 (t-100) cc_final: 0.7151 (t-100)
REVERT: C   13 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8418 (ptpt)
REVERT: C   14 ASP cc_start: 0.9440 (p0) cc_final: 0.9224 (p0)
REVERT: C   37 GLN cc_start: 0.8977 (tt0) cc_final: 0.8342 (tm-30)
REVERT: C   63 LYS cc_start: 0.9070 (tmtt) cc_final: 0.8764 (tmtt)
REVERT: C   79 SER cc_start: 0.7595 (t) cc_final: 0.7252 (t)
REVERT: C  100 SER cc_start: 0.9459 (p) cc_final: 0.9124 (p)
REVERT: C  104 GLU cc_start: 0.8980 (pt0) cc_final: 0.8596 (pt0)
REVERT: C  123 ASP cc_start: 0.9165 (t0) cc_final: 0.8795 (t0)
REVERT: c    3 LEU cc_start: 0.9052 (mp) cc_final: 0.8396 (mt)
REVERT: c   13 LYS cc_start: 0.9660 (tttt) cc_final: 0.9442 (tttp)
REVERT: c   14 ASP cc_start: 0.9056 (p0) cc_final: 0.8711 (p0)
REVERT: c   37 GLN cc_start: 0.8459 (pp30) cc_final: 0.8137 (pp30)
REVERT: c  111 GLU cc_start: 0.9526 (pt0) cc_final: 0.9237 (pt0)
REVERT: c  121 LEU cc_start: 0.9553 (mm) cc_final: 0.9237 (mm)
REVERT: c  122 ILE cc_start: 0.9111 (tt) cc_final: 0.8325 (tt)
REVERT: c  123 ASP cc_start: 0.9353 (t0) cc_final: 0.9147 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 128
  average time/residue: 0.1861
  time to fit residues: 28.0318
Evaluate side-chains
  102 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 20 optimal weight:    0.5980
   chunk 35 optimal weight:    8.9990
   chunk 28 optimal weight:    9.9990
   chunk 14 optimal weight:    0.4980
   chunk 0 optimal weight:   30.0000
   chunk 6 optimal weight:    8.9990
   chunk 22 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 18 optimal weight:    8.9990
   chunk 5 optimal weight:   10.0000
   overall best weight:    4.2186

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
c  69 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.059509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.049720 restraints weight = 19784.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.051184 restraints weight = 11240.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.052199 restraints weight = 7528.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.5292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3635  Z= 0.178
  Angle     :  0.715   8.819   4939  Z= 0.366
  Chirality :  0.047   0.224    557
  Planarity :  0.006   0.117    639
  Dihedral  :  5.513  28.704    505
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 15.13
  Ramachandran Plot:
    Outliers :  1.10 %
    Allowed  :  9.45 %
    Favored  : 89.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.26 (0.37), residues: 455
  helix:  0.22 (0.74), residues: 49
  sheet: -0.65 (0.40), residues: 160
  loop : -2.56 (0.36), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H 116 
 HIS   0.002   0.001   HIS L  93 
 PHE   0.015   0.002   PHE L 101 
 TYR   0.012   0.002   TYR H  35 
 ARG   0.002   0.000   ARG c 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03555 (  111)
  hydrogen bonds       : angle       5.51635 (  291)
  SS BOND              : bond        0.00535 (    1)
  SS BOND              : angle       1.17249 (    2)
  covalent geometry    : bond        0.00396 ( 3634)
  covalent geometry    : angle       0.71450 ( 4937)

*********************** 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
  119 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.416 
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   41 ARG cc_start: 0.9419 (tpt90) cc_final: 0.9074 (tpt170)
REVERT: H   62 TYR cc_start: 0.8867 (m-80) cc_final: 0.8517 (m-80)
REVERT: H  116 TRP cc_start: 0.7420 (t-100) cc_final: 0.7105 (t-100)
REVERT: C   13 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8130 (mttp)
REVERT: C   14 ASP cc_start: 0.9438 (p0) cc_final: 0.9141 (p0)
REVERT: C   37 GLN cc_start: 0.9065 (tt0) cc_final: 0.8338 (tm-30)
REVERT: C   63 LYS cc_start: 0.9128 (tmtt) cc_final: 0.8817 (tmtt)
REVERT: C   79 SER cc_start: 0.7684 (t) cc_final: 0.7377 (t)
REVERT: C  100 SER cc_start: 0.9469 (p) cc_final: 0.9122 (p)
REVERT: C  104 GLU cc_start: 0.9049 (pt0) cc_final: 0.8635 (pt0)
REVERT: C  123 ASP cc_start: 0.9194 (t0) cc_final: 0.8794 (t0)
REVERT: c    3 LEU cc_start: 0.9135 (mp) cc_final: 0.8479 (mt)
REVERT: c   14 ASP cc_start: 0.9027 (p0) cc_final: 0.8711 (p0)
REVERT: c   37 GLN cc_start: 0.8605 (pp30) cc_final: 0.8296 (pp30)
REVERT: c  111 GLU cc_start: 0.9517 (pt0) cc_final: 0.9232 (pt0)
REVERT: c  121 LEU cc_start: 0.9582 (mm) cc_final: 0.9299 (mm)
REVERT: c  122 ILE cc_start: 0.8765 (tt) cc_final: 0.8198 (tt)
REVERT: c  126 ASP cc_start: 0.8443 (m-30) cc_final: 0.8118 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.1807
  time to fit residues: 25.4102
Evaluate side-chains
  92 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 32 optimal weight:   20.0000
   chunk 15 optimal weight:    9.9990
   chunk 39 optimal weight:   10.0000
   chunk 27 optimal weight:    0.2980
   chunk 21 optimal weight:    9.9990
   chunk 28 optimal weight:   10.0000
   chunk 24 optimal weight:   20.0000
   chunk 36 optimal weight:    9.9990
   chunk 20 optimal weight:    0.0030
   chunk 41 optimal weight:    9.9990
   chunk 11 optimal weight:   50.0000
   overall best weight:    6.0596

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.058619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.048955 restraints weight = 20105.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.050395 restraints weight = 11261.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.051379 restraints weight = 7549.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.5674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   3635  Z= 0.241
  Angle     :  0.767   9.896   4939  Z= 0.394
  Chirality :  0.048   0.225    557
  Planarity :  0.007   0.126    639
  Dihedral  :  5.747  27.472    505
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 15.69
  Ramachandran Plot:
    Outliers :  1.32 %
    Allowed  : 10.55 %
    Favored  : 88.13 %
  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 : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.38), residues: 455
  helix:  0.15 (0.74), residues: 48
  sheet: -0.60 (0.40), residues: 160
  loop : -2.59 (0.37), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP H 116 
 HIS   0.003   0.002   HIS L  93 
 PHE   0.018   0.002   PHE L 101 
 TYR   0.015   0.002   TYR L  39 
 ARG   0.002   0.000   ARG H 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03728 (  111)
  hydrogen bonds       : angle       5.45942 (  291)
  SS BOND              : bond        0.00479 (    1)
  SS BOND              : angle       0.94277 (    2)
  covalent geometry    : bond        0.00534 ( 3634)
  covalent geometry    : angle       0.76685 ( 4937)

*********************** 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
  114 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   41 ARG cc_start: 0.9511 (tpt90) cc_final: 0.8985 (tpt170)
REVERT: H   86 MET cc_start: 0.9039 (mpp) cc_final: 0.8815 (mpp)
REVERT: H  116 TRP cc_start: 0.7492 (t-100) cc_final: 0.6810 (t-100)
REVERT: C   14 ASP cc_start: 0.9393 (p0) cc_final: 0.9069 (p0)
REVERT: C   37 GLN cc_start: 0.9072 (tt0) cc_final: 0.8419 (tm-30)
REVERT: C   63 LYS cc_start: 0.9136 (tmtt) cc_final: 0.8558 (ttpp)
REVERT: C   65 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7708 (tm-30)
REVERT: C   68 ILE cc_start: 0.9472 (mt) cc_final: 0.9258 (mp)
REVERT: C  100 SER cc_start: 0.9438 (p) cc_final: 0.9121 (p)
REVERT: C  104 GLU cc_start: 0.9062 (pt0) cc_final: 0.8724 (pt0)
REVERT: C  123 ASP cc_start: 0.9191 (t0) cc_final: 0.8791 (t0)
REVERT: c    3 LEU cc_start: 0.9220 (mp) cc_final: 0.8701 (mt)
REVERT: c   37 GLN cc_start: 0.8638 (pp30) cc_final: 0.8316 (pp30)
REVERT: c  102 ASP cc_start: 0.9495 (p0) cc_final: 0.9157 (p0)
REVERT: c  111 GLU cc_start: 0.9555 (pt0) cc_final: 0.9155 (pt0)
REVERT: c  121 LEU cc_start: 0.9557 (mm) cc_final: 0.9278 (mm)
REVERT: c  122 ILE cc_start: 0.8785 (tt) cc_final: 0.8226 (tt)
REVERT: c  123 ASP cc_start: 0.9245 (t70) cc_final: 0.8889 (t0)
REVERT: c  126 ASP cc_start: 0.8449 (m-30) cc_final: 0.8147 (m-30)
REVERT: c  127 GLN cc_start: 0.9183 (mp10) cc_final: 0.8869 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.2021
  time to fit residues: 26.8823
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  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 17 optimal weight:   20.0000
   chunk 23 optimal weight:    8.9990
   chunk 19 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   chunk 30 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9980
   chunk 2 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   chunk 4 optimal weight:    7.9990
   chunk 35 optimal weight:    8.9990
   overall best weight:    5.3988

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

Flipped N/Q/H residues before XYZ refinement:
C  87 GLN
** c  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.058432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.048616 restraints weight = 20349.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.050075 restraints weight = 11481.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.051065 restraints weight = 7688.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.5869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   3635  Z= 0.218
  Angle     :  0.750  10.145   4939  Z= 0.385
  Chirality :  0.048   0.221    557
  Planarity :  0.006   0.102    639
  Dihedral  :  5.746  27.058    505
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 15.13
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 10.11 %
    Favored  : 89.01 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  3.13 %
    Favored  : 96.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.33 (0.38), residues: 455
  helix: -0.07 (0.75), residues: 50
  sheet: -0.53 (0.42), residues: 155
  loop : -2.65 (0.36), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP H  50 
 HIS   0.005   0.003   HIS L  93 
 PHE   0.018   0.002   PHE L  94 
 TYR   0.013   0.002   TYR H  38 
 ARG   0.003   0.000   ARG H  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03524 (  111)
  hydrogen bonds       : angle       5.44756 (  291)
  SS BOND              : bond        0.00492 (    1)
  SS BOND              : angle       0.95186 (    2)
  covalent geometry    : bond        0.00486 ( 3634)
  covalent geometry    : angle       0.74990 ( 4937)

*********************** 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
  112 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 111
  time to evaluate  : 0.346 
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   41 ARG cc_start: 0.9549 (tpt90) cc_final: 0.9138 (tpm170)
REVERT: H  116 TRP cc_start: 0.7349 (t-100) cc_final: 0.6751 (t-100)
REVERT: C   13 LYS cc_start: 0.8755 (ttmm) cc_final: 0.8520 (ttmt)
REVERT: C   14 ASP cc_start: 0.9434 (p0) cc_final: 0.9143 (p0)
REVERT: C   37 GLN cc_start: 0.9068 (tt0) cc_final: 0.8526 (tm-30)
REVERT: C   63 LYS cc_start: 0.9163 (tmtt) cc_final: 0.8606 (ttpp)
REVERT: C   65 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7744 (tm-30)
REVERT: C  100 SER cc_start: 0.9469 (p) cc_final: 0.9152 (p)
REVERT: C  104 GLU cc_start: 0.9004 (pt0) cc_final: 0.8670 (pt0)
REVERT: C  123 ASP cc_start: 0.9176 (t0) cc_final: 0.8819 (t0)
REVERT: c   37 GLN cc_start: 0.8611 (pp30) cc_final: 0.8216 (pp30)
REVERT: c  111 GLU cc_start: 0.9549 (pt0) cc_final: 0.9244 (pt0)
REVERT: c  121 LEU cc_start: 0.9570 (mm) cc_final: 0.9258 (mm)
REVERT: c  122 ILE cc_start: 0.8784 (tt) cc_final: 0.8151 (tt)
REVERT: c  123 ASP cc_start: 0.9204 (t70) cc_final: 0.8898 (t0)
REVERT: c  126 ASP cc_start: 0.8567 (m-30) cc_final: 0.8034 (m-30)
REVERT: c  127 GLN cc_start: 0.9162 (mp10) cc_final: 0.8950 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 112
  average time/residue: 0.2048
  time to fit residues: 26.6633
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  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 16 optimal weight:    0.5980
   chunk 28 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 40 optimal weight:    6.9990
   chunk 37 optimal weight:    9.9990
   chunk 11 optimal weight:    8.9990
   chunk 31 optimal weight:    0.7980
   chunk 20 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   overall best weight:    4.0786

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.059422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.049516 restraints weight = 19844.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.051015 restraints weight = 11229.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.052036 restraints weight = 7463.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.5999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3635  Z= 0.181
  Angle     :  0.778  14.735   4939  Z= 0.385
  Chirality :  0.048   0.260    557
  Planarity :  0.007   0.155    639
  Dihedral  :  5.688  31.697    505
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 15.13
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 10.77 %
    Favored  : 88.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.35 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.23 (0.38), residues: 455
  helix:  0.18 (0.75), residues: 50
  sheet: -0.45 (0.42), residues: 155
  loop : -2.63 (0.36), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP H  50 
 HIS   0.003   0.002   HIS L  93 
 PHE   0.015   0.001   PHE L  94 
 TYR   0.012   0.002   TYR H  38 
 ARG   0.002   0.000   ARG H  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03240 (  111)
  hydrogen bonds       : angle       5.35875 (  291)
  SS BOND              : bond        0.00539 (    1)
  SS BOND              : angle       0.97370 (    2)
  covalent geometry    : bond        0.00408 ( 3634)
  covalent geometry    : angle       0.77829 ( 4937)

*********************** 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
  110 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   41 ARG cc_start: 0.9536 (tpt90) cc_final: 0.9155 (tpm170)
REVERT: H  103 ARG cc_start: 0.8238 (mmp-170) cc_final: 0.7644 (mmm160)
REVERT: H  113 PHE cc_start: 0.6477 (p90) cc_final: 0.5257 (p90)
REVERT: H  116 TRP cc_start: 0.7409 (t-100) cc_final: 0.6768 (t-100)
REVERT: C    5 THR cc_start: 0.9347 (p) cc_final: 0.8437 (p)
REVERT: C   13 LYS cc_start: 0.8749 (ttmm) cc_final: 0.8525 (ttmt)
REVERT: C   14 ASP cc_start: 0.9448 (p0) cc_final: 0.9168 (p0)
REVERT: C   37 GLN cc_start: 0.9041 (tt0) cc_final: 0.8526 (tm-30)
REVERT: C   63 LYS cc_start: 0.9108 (tmtt) cc_final: 0.8584 (ttpp)
REVERT: C   65 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7784 (tm-30)
REVERT: C  100 SER cc_start: 0.9458 (p) cc_final: 0.9113 (p)
REVERT: C  104 GLU cc_start: 0.9009 (pt0) cc_final: 0.8680 (pt0)
REVERT: C  123 ASP cc_start: 0.9271 (t0) cc_final: 0.8876 (t0)
REVERT: c    3 LEU cc_start: 0.9050 (mp) cc_final: 0.8463 (mt)
REVERT: c   13 LYS cc_start: 0.9616 (tttt) cc_final: 0.9387 (tttp)
REVERT: c   37 GLN cc_start: 0.8892 (pp30) cc_final: 0.8512 (pp30)
REVERT: c   96 PHE cc_start: 0.9121 (m-80) cc_final: 0.8896 (m-80)
REVERT: c  111 GLU cc_start: 0.9493 (pt0) cc_final: 0.9201 (pt0)
REVERT: c  121 LEU cc_start: 0.9547 (mm) cc_final: 0.9239 (mm)
REVERT: c  122 ILE cc_start: 0.8800 (tt) cc_final: 0.8151 (tt)
REVERT: c  123 ASP cc_start: 0.9210 (t70) cc_final: 0.8902 (t0)
REVERT: c  126 ASP cc_start: 0.8420 (m-30) cc_final: 0.8071 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1936
  time to fit residues: 24.9062
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  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 7 optimal weight:   30.0000
   chunk 30 optimal weight:    7.9990
   chunk 6 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 35 optimal weight:    7.9990
   chunk 43 optimal weight:    6.9990
   chunk 12 optimal weight:    0.0770
   chunk 36 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:   10.0000
   chunk 40 optimal weight:    8.9990
   overall best weight:    3.9944

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.058941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.048810 restraints weight = 20016.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.050258 restraints weight = 11490.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.051258 restraints weight = 7816.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.6194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3635  Z= 0.179
  Angle     :  0.763  11.075   4939  Z= 0.385
  Chirality :  0.049   0.229    557
  Planarity :  0.007   0.131    639
  Dihedral  :  5.659  31.523    505
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 14.85
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  9.89 %
    Favored  : 89.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.35 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.22 (0.38), residues: 455
  helix:  0.17 (0.73), residues: 50
  sheet: -0.37 (0.41), residues: 160
  loop : -2.72 (0.36), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP H  50 
 HIS   0.004   0.003   HIS L  93 
 PHE   0.031   0.002   PHE L 101 
 TYR   0.012   0.002   TYR L  90 
 ARG   0.002   0.000   ARG H  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03306 (  111)
  hydrogen bonds       : angle       5.35254 (  291)
  SS BOND              : bond        0.00501 (    1)
  SS BOND              : angle       0.87560 (    2)
  covalent geometry    : bond        0.00403 ( 3634)
  covalent geometry    : angle       0.76267 ( 4937)

*********************** 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
  107 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   41 ARG cc_start: 0.9547 (tpt90) cc_final: 0.9149 (tpm170)
REVERT: L  101 PHE cc_start: 0.8949 (t80) cc_final: 0.8680 (t80)
REVERT: H   65 ASP cc_start: 0.8861 (t0) cc_final: 0.8651 (t0)
REVERT: H   86 MET cc_start: 0.9051 (mpp) cc_final: 0.8723 (mpp)
REVERT: H  116 TRP cc_start: 0.7479 (t-100) cc_final: 0.6816 (t-100)
REVERT: C    5 THR cc_start: 0.9352 (p) cc_final: 0.8519 (p)
REVERT: C   13 LYS cc_start: 0.8768 (ttmm) cc_final: 0.8435 (ttmt)
REVERT: C   14 ASP cc_start: 0.9487 (p0) cc_final: 0.9247 (p0)
REVERT: C   37 GLN cc_start: 0.9074 (tt0) cc_final: 0.8533 (tm-30)
REVERT: C   63 LYS cc_start: 0.9069 (tmtt) cc_final: 0.8535 (ttpp)
REVERT: C   65 GLN cc_start: 0.8101 (tm-30) cc_final: 0.7849 (tm-30)
REVERT: C   70 ASN cc_start: 0.9525 (t0) cc_final: 0.9250 (t0)
REVERT: C  100 SER cc_start: 0.9493 (p) cc_final: 0.9193 (p)
REVERT: C  104 GLU cc_start: 0.8986 (pt0) cc_final: 0.8655 (pt0)
REVERT: C  123 ASP cc_start: 0.9274 (t0) cc_final: 0.8923 (t0)
REVERT: c    3 LEU cc_start: 0.9082 (mp) cc_final: 0.8509 (mt)
REVERT: c   13 LYS cc_start: 0.9356 (tttt) cc_final: 0.9153 (tttp)
REVERT: c   14 ASP cc_start: 0.8848 (p0) cc_final: 0.8565 (p0)
REVERT: c   37 GLN cc_start: 0.8791 (pp30) cc_final: 0.8413 (pp30)
REVERT: c  111 GLU cc_start: 0.9492 (pt0) cc_final: 0.9215 (pt0)
REVERT: c  121 LEU cc_start: 0.9565 (mm) cc_final: 0.9198 (mm)
REVERT: c  122 ILE cc_start: 0.8782 (tt) cc_final: 0.8116 (tt)
REVERT: c  123 ASP cc_start: 0.9153 (t70) cc_final: 0.8725 (t0)
REVERT: c  126 ASP cc_start: 0.8620 (m-30) cc_final: 0.8048 (m-30)
REVERT: c  127 GLN cc_start: 0.9110 (mp10) cc_final: 0.8739 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1900
  time to fit residues: 23.9249
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  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 38 optimal weight:    8.9990
   chunk 0 optimal weight:   30.0000
   chunk 30 optimal weight:    5.9990
   chunk 19 optimal weight:    8.9990
   chunk 24 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 29 optimal weight:    0.4980
   chunk 37 optimal weight:    9.9990
   chunk 34 optimal weight:   10.0000
   chunk 17 optimal weight:    3.9990
   chunk 20 optimal weight:    7.9990
   overall best weight:    2.8988

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.060303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.050297 restraints weight = 19303.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.051699 restraints weight = 11260.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.052702 restraints weight = 7722.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.6183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3635  Z= 0.150
  Angle     :  0.741  11.295   4939  Z= 0.374
  Chirality :  0.049   0.255    557
  Planarity :  0.004   0.041    639
  Dihedral  :  5.629  44.549    505
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 13.86
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 10.99 %
    Favored  : 88.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.35 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.12 (0.38), residues: 455
  helix:  0.26 (0.73), residues: 50
  sheet: -0.29 (0.42), residues: 155
  loop : -2.63 (0.36), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  50 
 HIS   0.004   0.003   HIS L  93 
 PHE   0.025   0.002   PHE L 101 
 TYR   0.011   0.002   TYR H 105 
 ARG   0.002   0.000   ARG H  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03191 (  111)
  hydrogen bonds       : angle       5.25851 (  291)
  SS BOND              : bond        0.00514 (    1)
  SS BOND              : angle       0.88684 (    2)
  covalent geometry    : bond        0.00340 ( 3634)
  covalent geometry    : angle       0.74117 ( 4937)

*********************** 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
  110 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   41 ARG cc_start: 0.9517 (tpt90) cc_final: 0.9220 (tpm170)
REVERT: H   85 GLN cc_start: 0.9030 (tp40) cc_final: 0.8645 (tp-100)
REVERT: H   86 MET cc_start: 0.9058 (mpp) cc_final: 0.8563 (mpp)
REVERT: H  103 ARG cc_start: 0.8307 (mmp-170) cc_final: 0.7826 (mmm160)
REVERT: H  113 PHE cc_start: 0.6397 (p90) cc_final: 0.5279 (p90)
REVERT: H  116 TRP cc_start: 0.7464 (t-100) cc_final: 0.6888 (t-100)
REVERT: C    5 THR cc_start: 0.9330 (p) cc_final: 0.8426 (p)
REVERT: C   13 LYS cc_start: 0.8781 (ttmm) cc_final: 0.8454 (ttmt)
REVERT: C   14 ASP cc_start: 0.9465 (p0) cc_final: 0.9222 (p0)
REVERT: C   37 GLN cc_start: 0.9028 (tt0) cc_final: 0.8502 (tm-30)
REVERT: C   63 LYS cc_start: 0.9084 (tmtt) cc_final: 0.8555 (ttpp)
REVERT: C   65 GLN cc_start: 0.8171 (tm-30) cc_final: 0.7790 (tm-30)
REVERT: C   70 ASN cc_start: 0.9513 (t0) cc_final: 0.9252 (t0)
REVERT: C  100 SER cc_start: 0.9489 (p) cc_final: 0.9161 (p)
REVERT: C  104 GLU cc_start: 0.8982 (pt0) cc_final: 0.8716 (pt0)
REVERT: C  123 ASP cc_start: 0.9258 (t0) cc_final: 0.8890 (t0)
REVERT: c    3 LEU cc_start: 0.9103 (mp) cc_final: 0.8692 (mt)
REVERT: c   13 LYS cc_start: 0.9475 (tttt) cc_final: 0.9173 (tttp)
REVERT: c   14 ASP cc_start: 0.8858 (p0) cc_final: 0.8551 (p0)
REVERT: c   37 GLN cc_start: 0.8837 (pp30) cc_final: 0.8340 (pp30)
REVERT: c  104 GLU cc_start: 0.9335 (pt0) cc_final: 0.9078 (pm20)
REVERT: c  111 GLU cc_start: 0.9462 (pt0) cc_final: 0.9159 (pt0)
REVERT: c  121 LEU cc_start: 0.9547 (mm) cc_final: 0.9215 (mm)
REVERT: c  122 ILE cc_start: 0.8803 (tt) cc_final: 0.8136 (tt)
REVERT: c  123 ASP cc_start: 0.9131 (t70) cc_final: 0.8716 (t0)
REVERT: c  126 ASP cc_start: 0.8452 (m-30) cc_final: 0.8051 (m-30)
REVERT: c  127 GLN cc_start: 0.9068 (mp10) cc_final: 0.8735 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1778
  time to fit residues: 23.1118
Evaluate side-chains
  93 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 41 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   chunk 21 optimal weight:    7.9990
   chunk 4 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 14 optimal weight:    7.9990
   chunk 7 optimal weight:    8.9990
   chunk 2 optimal weight:   10.0000
   chunk 26 optimal weight:    8.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    4.9990

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.059136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.049077 restraints weight = 20266.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.050464 restraints weight = 11963.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.051437 restraints weight = 8271.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.6371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   3635  Z= 0.206
  Angle     :  0.785  11.465   4939  Z= 0.394
  Chirality :  0.050   0.238    557
  Planarity :  0.005   0.043    639
  Dihedral  :  5.809  39.410    505
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 16.26
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 11.21 %
    Favored  : 88.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.35 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.22 (0.38), residues: 455
  helix:  0.15 (0.73), residues: 50
  sheet: -0.43 (0.42), residues: 157
  loop : -2.64 (0.36), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H  50 
 HIS   0.006   0.004   HIS L  93 
 PHE   0.030   0.002   PHE L 101 
 TYR   0.014   0.002   TYR H  38 
 ARG   0.004   0.000   ARG c  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03315 (  111)
  hydrogen bonds       : angle       5.38991 (  291)
  SS BOND              : bond        0.00439 (    1)
  SS BOND              : angle       0.73700 (    2)
  covalent geometry    : bond        0.00460 ( 3634)
  covalent geometry    : angle       0.78490 ( 4937)

********************** 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
  96 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  101 PHE cc_start: 0.8959 (t80) cc_final: 0.8733 (t80)
REVERT: H   65 ASP cc_start: 0.8856 (t70) cc_final: 0.8594 (t0)
REVERT: H  103 ARG cc_start: 0.8507 (mmp-170) cc_final: 0.7784 (mmm160)
REVERT: H  113 PHE cc_start: 0.6357 (p90) cc_final: 0.5955 (p90)
REVERT: H  116 TRP cc_start: 0.7615 (t-100) cc_final: 0.6925 (t-100)
REVERT: C    5 THR cc_start: 0.9363 (p) cc_final: 0.8414 (p)
REVERT: C   13 LYS cc_start: 0.8793 (ttmm) cc_final: 0.8493 (ttmt)
REVERT: C   14 ASP cc_start: 0.9476 (p0) cc_final: 0.9260 (p0)
REVERT: C   37 GLN cc_start: 0.8954 (tt0) cc_final: 0.8289 (tm-30)
REVERT: C   63 LYS cc_start: 0.9142 (tmtt) cc_final: 0.8624 (ttpp)
REVERT: C   65 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7856 (tm-30)
REVERT: C  100 SER cc_start: 0.9500 (p) cc_final: 0.9168 (p)
REVERT: C  104 GLU cc_start: 0.8970 (pt0) cc_final: 0.8681 (pt0)
REVERT: C  123 ASP cc_start: 0.9254 (t0) cc_final: 0.8892 (t0)
REVERT: c    3 LEU cc_start: 0.9113 (mp) cc_final: 0.8598 (mp)
REVERT: c   14 ASP cc_start: 0.8845 (p0) cc_final: 0.8522 (p0)
REVERT: c   37 GLN cc_start: 0.8873 (pp30) cc_final: 0.8460 (pp30)
REVERT: c   47 ARG cc_start: 0.9087 (ptm160) cc_final: 0.8698 (mtp-110)
REVERT: c  111 GLU cc_start: 0.9541 (pt0) cc_final: 0.9146 (pt0)
REVERT: c  122 ILE cc_start: 0.8814 (tt) cc_final: 0.8141 (tt)
REVERT: c  123 ASP cc_start: 0.9137 (t70) cc_final: 0.8744 (t0)
REVERT: c  126 ASP cc_start: 0.8612 (m-30) cc_final: 0.8041 (m-30)
REVERT: c  127 GLN cc_start: 0.9109 (mp10) cc_final: 0.8780 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.1863
  time to fit residues: 21.0361
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  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 9 optimal weight:   20.0000
   chunk 2 optimal weight:   10.0000
   chunk 23 optimal weight:    9.9990
   chunk 33 optimal weight:   10.0000
   chunk 43 optimal weight:   10.0000
   chunk 34 optimal weight:    6.9990
   chunk 41 optimal weight:    7.9990
   chunk 42 optimal weight:    2.9990
   chunk 5 optimal weight:    8.9990
   chunk 25 optimal weight:    8.9990
   chunk 7 optimal weight:    0.0770
   overall best weight:    5.4146

-------------------------------------------------------------------------------
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 = 0.3154 r_free = 0.3154 target = 0.058358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.048148 restraints weight = 19970.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.049589 restraints weight = 11694.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.050567 restraints weight = 7986.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.6497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   3635  Z= 0.219
  Angle     :  0.786  11.496   4939  Z= 0.398
  Chirality :  0.050   0.239    557
  Planarity :  0.005   0.047    639
  Dihedral  :  5.856  36.826    505
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 16.26
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.38), residues: 455
  helix: -0.00 (0.73), residues: 50
  sheet: -0.39 (0.42), residues: 155
  loop : -2.67 (0.37), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H  50 
 HIS   0.006   0.004   HIS L  93 
 PHE   0.028   0.002   PHE L 101 
 TYR   0.012   0.002   TYR H 115 
 ARG   0.005   0.000   ARG c  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03391 (  111)
  hydrogen bonds       : angle       5.45228 (  291)
  SS BOND              : bond        0.00393 (    1)
  SS BOND              : angle       0.59649 (    2)
  covalent geometry    : bond        0.00489 ( 3634)
  covalent geometry    : angle       0.78600 ( 4937)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1360.99 seconds
wall clock time: 24 minutes 32.79 seconds (1472.79 seconds total)