Starting phenix.real_space_refine
on Tue Feb  3 14:04:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w5q_37301/02_2026/8w5q_37301.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w5q_37301/02_2026/8w5q_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w5q_37301/02_2026/8w5q_37301.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w5q_37301/02_2026/8w5q_37301.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w5q_37301/02_2026/8w5q_37301.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w5q_37301/02_2026/8w5q_37301.map"
  }
  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-2.0-5952/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: 1.20, per 1000 atoms: 0.34
  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: 0.33
  Conformation dependent library (CDL) restraints added in 166.6 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: 0.12
  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: 0.42

  Time building geometry restraints manager: 0.46 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:             0.480
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.100
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.000
  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:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.130
-------------------------------------------------------------------------------
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 are 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  : 0.149 
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: L   36 LEU cc_start: 0.8148 (pt) cc_final: 0.7795 (pt)
REVERT: C   35 LEU cc_start: 0.8771 (mm) cc_final: 0.8228 (mt)
REVERT: C   37 GLN cc_start: 0.8271 (tt0) cc_final: 0.7352 (tm-30)
REVERT: C  111 GLU cc_start: 0.7456 (tt0) cc_final: 0.7256 (tt0)
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: 0.8796 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.0839
  time to fit residues: 16.7555
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  : 0.142 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    0.0770
   chunk 37 optimal weight:    3.9990
   overall best weight:    3.2144

-------------------------------------------------------------------------------
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 = 0.3357 r_free = 0.3357 target = 0.066770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.056181 restraints weight = 18888.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.057750 restraints weight = 11186.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.058857 restraints weight = 7652.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.059625 restraints weight = 5767.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.060193 restraints weight = 4686.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.3768

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= 0.164
  Angle     :  0.746   9.533   4939  Z= 0.374
  Chirality :  0.047   0.221    557
  Planarity :  0.006   0.107    639
  Dihedral  :  5.479  28.121    505
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 15.13
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  9.67 %
    Favored  : 89.67 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  6.53 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.21 (0.37), residues: 455
  helix:  0.75 (0.72), residues: 49
  sheet: -0.56 (0.41), residues: 155
  loop : -2.66 (0.34), residues: 251

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   0.009   0.001   TRP H 116 
 HIS   0.001   0.000   HIS L  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 3634)
  covalent geometry    : angle       0.74613 ( 4937)
  SS BOND              : bond        0.00413 (    1)
  SS BOND              : angle       1.34282 (    2)
  hydrogen bonds       : bond        0.03757 (  111)
  hydrogen bonds       : angle       6.01328 (  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
  131 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 129
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   52 PHE cc_start: 0.8113 (m-80) cc_final: 0.7389 (m-80)
REVERT: H   53 TYR cc_start: 0.8694 (t80) cc_final: 0.8487 (t80)
REVERT: C    5 THR cc_start: 0.8683 (p) cc_final: 0.8341 (p)
REVERT: C   13 LYS cc_start: 0.8694 (ttmm) cc_final: 0.7648 (ttmm)
REVERT: C   37 GLN cc_start: 0.8743 (tt0) cc_final: 0.8202 (tm-30)
REVERT: C   63 LYS cc_start: 0.9058 (tmtt) cc_final: 0.8676 (tmtt)
REVERT: C   74 CYS cc_start: 0.8840 (p) cc_final: 0.8568 (t)
REVERT: C  100 SER cc_start: 0.9456 (p) cc_final: 0.8991 (p)
REVERT: C  104 GLU cc_start: 0.9217 (pt0) cc_final: 0.8866 (pp20)
REVERT: C  111 GLU cc_start: 0.9499 (tt0) cc_final: 0.9238 (tt0)
REVERT: C  123 ASP cc_start: 0.9095 (t0) cc_final: 0.8692 (t0)
REVERT: c   14 ASP cc_start: 0.9132 (p0) cc_final: 0.8538 (p0)
REVERT: c   21 LEU cc_start: 0.9035 (pp) cc_final: 0.8498 (pp)
REVERT: c   37 GLN cc_start: 0.8633 (pp30) cc_final: 0.8269 (pp30)
REVERT: c  102 ASP cc_start: 0.9434 (p0) cc_final: 0.9220 (p0)
REVERT: c  127 GLN cc_start: 0.9186 (mp10) cc_final: 0.8880 (mp10)
  outliers start: 2
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0784
  time to fit residues: 12.2149
Evaluate side-chains
  101 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 35 optimal weight:    3.9990
   chunk 36 optimal weight:    7.9990
   chunk 33 optimal weight:    8.9990
   chunk 40 optimal weight:    8.9990
   chunk 39 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 38 optimal weight:    4.9990
   chunk 25 optimal weight:    9.9990
   chunk 41 optimal weight:    0.8980
   chunk 16 optimal weight:    6.9990
   overall best weight:    4.9788

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3233 r_free = 0.3233 target = 0.062663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.052358 restraints weight = 19245.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.053882 restraints weight = 11219.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.054969 restraints weight = 7684.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.055740 restraints weight = 5803.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.056245 restraints weight = 4693.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.4750

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= 0.209
  Angle     :  0.732   8.325   4939  Z= 0.382
  Chirality :  0.046   0.208    557
  Planarity :  0.006   0.087    639
  Dihedral  :  5.561  27.534    505
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 10.33 %
    Favored  : 89.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.31 (0.37), residues: 455
  helix:  0.56 (0.74), residues: 48
  sheet: -0.75 (0.40), residues: 160
  loop : -2.62 (0.35), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG c 109 
 TYR   0.020   0.002   TYR H 111 
 PHE   0.012   0.002   PHE L  94 
 TRP   0.015   0.002   TRP H 116 
 HIS   0.002   0.002   HIS L  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 3634)
  covalent geometry    : angle       0.73181 ( 4937)
  SS BOND              : bond        0.00701 (    1)
  SS BOND              : angle       1.67666 (    2)
  hydrogen bonds       : bond        0.03670 (  111)
  hydrogen bonds       : angle       5.74026 (  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
  122 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   41 ARG cc_start: 0.9351 (tpt90) cc_final: 0.9022 (tpt170)
REVERT: L   52 PHE cc_start: 0.8780 (m-80) cc_final: 0.8458 (m-10)
REVERT: L   97 THR cc_start: 0.9711 (m) cc_final: 0.9439 (m)
REVERT: H   35 TYR cc_start: 0.9055 (m-80) cc_final: 0.8554 (m-80)
REVERT: H   62 TYR cc_start: 0.8964 (m-80) cc_final: 0.8661 (m-80)
REVERT: C    5 THR cc_start: 0.8938 (p) cc_final: 0.8468 (p)
REVERT: C   13 LYS cc_start: 0.8750 (ttmm) cc_final: 0.7712 (ttmm)
REVERT: C   14 ASP cc_start: 0.9474 (p0) cc_final: 0.9269 (p0)
REVERT: C   37 GLN cc_start: 0.9050 (tt0) cc_final: 0.8300 (tm-30)
REVERT: C   63 LYS cc_start: 0.9029 (tmtt) cc_final: 0.8716 (tmtt)
REVERT: C  100 SER cc_start: 0.9458 (p) cc_final: 0.8663 (p)
REVERT: C  123 ASP cc_start: 0.9117 (t0) cc_final: 0.8642 (t0)
REVERT: c   13 LYS cc_start: 0.9644 (tttt) cc_final: 0.9407 (tttp)
REVERT: c   14 ASP cc_start: 0.9069 (p0) cc_final: 0.8691 (p0)
REVERT: c   37 GLN cc_start: 0.8524 (pp30) cc_final: 0.8160 (pp30)
REVERT: c  102 ASP cc_start: 0.9536 (p0) cc_final: 0.9305 (p0)
REVERT: c  111 GLU cc_start: 0.9486 (pt0) cc_final: 0.9180 (pt0)
REVERT: c  121 LEU cc_start: 0.9546 (mm) cc_final: 0.9191 (mm)
REVERT: c  123 ASP cc_start: 0.9353 (t0) cc_final: 0.9149 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.0567
  time to fit residues: 8.2648
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  : 0.086 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 22 optimal weight:    0.0770
   chunk 23 optimal weight:    0.8980
   chunk 0 optimal weight:   40.0000
   chunk 19 optimal weight:    0.0470
   chunk 17 optimal weight:    9.9990
   chunk 43 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 39 optimal weight:    8.9990
   chunk 3 optimal weight:    2.9990
   chunk 10 optimal weight:   20.0000
   overall best weight:    1.4040

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.064060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.053965 restraints weight = 19067.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.055414 restraints weight = 11420.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.056421 restraints weight = 7907.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.057142 restraints weight = 6030.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.057729 restraints weight = 4912.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.4988

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= 0.123
  Angle     :  0.713   8.619   4939  Z= 0.358
  Chirality :  0.047   0.224    557
  Planarity :  0.006   0.114    639
  Dihedral  :  5.198  26.618    505
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  9.45 %
    Favored  : 89.89 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  4.18 %
    Favored  : 95.56 %
  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 are not related in a simple way.
  whole: -2.29 (0.37), residues: 455
  helix:  0.46 (0.72), residues: 49
  sheet: -0.61 (0.41), residues: 170
  loop : -2.76 (0.35), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  90 
 TYR   0.013   0.001   TYR L  39 
 PHE   0.013   0.001   PHE L 101 
 TRP   0.008   0.001   TRP H  50 
 HIS   0.002   0.001   HIS L  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 3634)
  covalent geometry    : angle       0.71235 ( 4937)
  SS BOND              : bond        0.00600 (    1)
  SS BOND              : angle       1.18638 (    2)
  hydrogen bonds       : bond        0.03238 (  111)
  hydrogen bonds       : angle       5.35388 (  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
  130 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 0.139 
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: 0.7905 (pt) cc_final: 0.7696 (tp)
REVERT: H   35 TYR cc_start: 0.8760 (m-80) cc_final: 0.8361 (m-80)
REVERT: H   62 TYR cc_start: 0.8517 (m-80) cc_final: 0.8211 (m-80)
REVERT: H  103 ARG cc_start: 0.8330 (mmm160) cc_final: 0.7616 (ptt180)
REVERT: C   16 LYS cc_start: 0.8971 (mmpt) cc_final: 0.8690 (mmmt)
REVERT: C   37 GLN cc_start: 0.8898 (tt0) cc_final: 0.8199 (tm-30)
REVERT: C   63 LYS cc_start: 0.9082 (tmtt) cc_final: 0.8619 (ttpp)
REVERT: C   65 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7962 (tm-30)
REVERT: C   79 SER cc_start: 0.7635 (t) cc_final: 0.7301 (t)
REVERT: C  123 ASP cc_start: 0.9154 (t0) cc_final: 0.8623 (t0)
REVERT: c   14 ASP cc_start: 0.9146 (p0) cc_final: 0.8043 (p0)
REVERT: c   37 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8104 (pp30)
REVERT: c  100 SER cc_start: 0.9159 (p) cc_final: 0.7265 (p)
REVERT: c  105 ARG cc_start: 0.9414 (mtm-85) cc_final: 0.8895 (ptp-110)
REVERT: c  111 GLU cc_start: 0.9447 (pt0) cc_final: 0.9195 (pt0)
REVERT: c  121 LEU cc_start: 0.9601 (mm) cc_final: 0.9223 (mm)
REVERT: c  123 ASP cc_start: 0.9187 (t0) cc_final: 0.8935 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0861
  time to fit residues: 13.0532
Evaluate side-chains
  95 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 14 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 4 optimal weight:    8.9990
   chunk 2 optimal weight:    8.9990
   chunk 34 optimal weight:    7.9990
   chunk 1 optimal weight:    9.9990
   chunk 0 optimal weight:    5.9990
   chunk 20 optimal weight:   10.0000
   chunk 42 optimal weight:    1.9990
   chunk 23 optimal weight:   20.0000
   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  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3170 r_free = 0.3170 target = 0.059017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.049372 restraints weight = 19901.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.050865 restraints weight = 11221.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.051843 restraints weight = 7504.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.052555 restraints weight = 5624.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.053049 restraints weight = 4524.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.5562

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= 0.234
  Angle     :  0.765   9.577   4939  Z= 0.397
  Chirality :  0.047   0.218    557
  Planarity :  0.006   0.098    639
  Dihedral  :  5.615  28.495    505
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 14.70
  Ramachandran Plot:
    Outliers :  1.32 %
    Allowed  : 10.11 %
    Favored  : 88.57 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  4.96 %
    Favored  : 94.78 %
  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 are not related in a simple way.
  whole: -2.36 (0.37), residues: 455
  helix: -0.25 (0.70), residues: 49
  sheet: -0.49 (0.41), residues: 159
  loop : -2.71 (0.34), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG c 105 
 TYR   0.030   0.003   TYR L  74 
 PHE   0.018   0.002   PHE L 101 
 TRP   0.018   0.003   TRP H 116 
 HIS   0.002   0.002   HIS L  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 ( 3634)
  covalent geometry    : angle       0.76481 ( 4937)
  SS BOND              : bond        0.00288 (    1)
  SS BOND              : angle       0.84941 (    2)
  hydrogen bonds       : bond        0.03546 (  111)
  hydrogen bonds       : angle       5.48465 (  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
  103 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L    7 MET cc_start: 0.7821 (pmm) cc_final: 0.7294 (pmm)
REVERT: L   41 ARG cc_start: 0.9478 (tpt90) cc_final: 0.9184 (tpm170)
REVERT: H   37 MET cc_start: 0.9072 (mmp) cc_final: 0.8835 (mmp)
REVERT: H   68 LYS cc_start: 0.9147 (mmpt) cc_final: 0.8925 (mmtt)
REVERT: H   86 MET cc_start: 0.9005 (mpp) cc_final: 0.8784 (mpp)
REVERT: H  103 ARG cc_start: 0.8547 (mmm160) cc_final: 0.7831 (mmm160)
REVERT: H  116 TRP cc_start: 0.7389 (t-100) cc_final: 0.7059 (t-100)
REVERT: C    5 THR cc_start: 0.9349 (p) cc_final: 0.8455 (p)
REVERT: C   13 LYS cc_start: 0.9010 (ptpt) cc_final: 0.8714 (ptpt)
REVERT: C   37 GLN cc_start: 0.8978 (tt0) cc_final: 0.8631 (tm-30)
REVERT: C   63 LYS cc_start: 0.9135 (tmtt) cc_final: 0.8610 (ttpp)
REVERT: C   65 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7780 (tm-30)
REVERT: C  123 ASP cc_start: 0.9201 (t0) cc_final: 0.8746 (t0)
REVERT: c   13 LYS cc_start: 0.9681 (tttt) cc_final: 0.9471 (tttp)
REVERT: c   14 ASP cc_start: 0.9003 (p0) cc_final: 0.8667 (p0)
REVERT: c   37 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8646 (pp30)
REVERT: c  123 ASP cc_start: 0.9326 (t0) cc_final: 0.9001 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 103
  average time/residue: 0.0722
  time to fit residues: 8.7120
Evaluate side-chains
  79 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 26 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 30 optimal weight:    0.7980
   chunk 11 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 32 optimal weight:    0.7980
   chunk 43 optimal weight:   10.0000
   chunk 16 optimal weight:    7.9990
   chunk 28 optimal weight:    3.9990
   chunk 33 optimal weight:    7.9990
   overall best weight:    3.5186

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

Flipped N/Q/H residues before XYZ refinement:
** H  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.060244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.050403 restraints weight = 19956.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.051902 restraints weight = 11369.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.052894 restraints weight = 7664.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.053618 restraints weight = 5741.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.054078 restraints weight = 4619.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.5656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3635  Z= 0.163
  Angle     :  0.756  14.414   4939  Z= 0.377
  Chirality :  0.048   0.241    557
  Planarity :  0.007   0.154    639
  Dihedral  :  5.477  29.073    505
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  1.10 %
    Allowed  :  9.67 %
    Favored  : 89.23 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.34 (0.37), residues: 455
  helix: -0.36 (0.71), residues: 50
  sheet: -0.41 (0.43), residues: 154
  loop : -2.68 (0.34), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  47 
 TYR   0.023   0.002   TYR L  74 
 PHE   0.017   0.002   PHE L 101 
 TRP   0.013   0.002   TRP H 116 
 HIS   0.003   0.002   HIS L  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 3634)
  covalent geometry    : angle       0.75601 ( 4937)
  SS BOND              : bond        0.00403 (    1)
  SS BOND              : angle       0.97164 (    2)
  hydrogen bonds       : bond        0.03364 (  111)
  hydrogen bonds       : angle       5.29306 (  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
  108 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.158 
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   24 ILE cc_start: 0.8373 (pt) cc_final: 0.8118 (mp)
REVERT: L   41 ARG cc_start: 0.9489 (tpt90) cc_final: 0.9135 (tpm170)
REVERT: H   37 MET cc_start: 0.8995 (mmp) cc_final: 0.8698 (mmp)
REVERT: H  116 TRP cc_start: 0.7446 (t-100) cc_final: 0.7023 (t-100)
REVERT: C    5 THR cc_start: 0.9308 (p) cc_final: 0.8428 (p)
REVERT: C   13 LYS cc_start: 0.8928 (ptpt) cc_final: 0.7360 (mttp)
REVERT: C   14 ASP cc_start: 0.9438 (p0) cc_final: 0.9044 (p0)
REVERT: C   37 GLN cc_start: 0.8873 (tt0) cc_final: 0.8417 (tm-30)
REVERT: C   63 LYS cc_start: 0.9116 (tmtt) cc_final: 0.8597 (ttpp)
REVERT: C   65 GLN cc_start: 0.8103 (tm-30) cc_final: 0.7787 (tm-30)
REVERT: C   70 ASN cc_start: 0.9585 (t0) cc_final: 0.9370 (t0)
REVERT: C  123 ASP cc_start: 0.9213 (t0) cc_final: 0.8807 (t0)
REVERT: c   14 ASP cc_start: 0.9025 (p0) cc_final: 0.8695 (p0)
REVERT: c   37 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8621 (pp30)
REVERT: c  111 GLU cc_start: 0.9392 (pt0) cc_final: 0.8985 (pt0)
REVERT: c  122 ILE cc_start: 0.9161 (tt) cc_final: 0.8591 (tt)
REVERT: c  123 ASP cc_start: 0.9301 (t0) cc_final: 0.9000 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1007
  time to fit residues: 12.6481
Evaluate side-chains
  84 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 40 optimal weight:   20.0000
   chunk 29 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 1 optimal weight:    0.3980
   chunk 32 optimal weight:    0.0170
   chunk 7 optimal weight:   30.0000
   chunk 26 optimal weight:    7.9990
   chunk 37 optimal weight:    9.9990
   overall best weight:    2.2824

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

Flipped N/Q/H residues before XYZ refinement:
** H  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  87 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.060659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.051073 restraints weight = 19518.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.052609 restraints weight = 10814.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.053663 restraints weight = 7120.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.054397 restraints weight = 5217.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.054877 restraints weight = 4137.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.5758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3635  Z= 0.140
  Angle     :  0.751  10.411   4939  Z= 0.378
  Chirality :  0.047   0.225    557
  Planarity :  0.006   0.123    639
  Dihedral  :  5.179  28.243    505
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 10.11 %
    Favored  : 89.01 %
  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 : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.04 (0.38), residues: 455
  helix:  0.30 (0.73), residues: 48
  sheet: -0.20 (0.43), residues: 154
  loop : -2.57 (0.35), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG c  47 
 TYR   0.019   0.002   TYR L  74 
 PHE   0.021   0.002   PHE L  94 
 TRP   0.011   0.002   TRP H 116 
 HIS   0.003   0.002   HIS L  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 3634)
  covalent geometry    : angle       0.75127 ( 4937)
  SS BOND              : bond        0.00409 (    1)
  SS BOND              : angle       0.94601 (    2)
  hydrogen bonds       : bond        0.03344 (  111)
  hydrogen bonds       : angle       5.18166 (  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
  108 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   24 ILE cc_start: 0.8218 (pt) cc_final: 0.7937 (mp)
REVERT: H   37 MET cc_start: 0.9024 (mmp) cc_final: 0.8790 (mmp)
REVERT: H   65 ASP cc_start: 0.8783 (t0) cc_final: 0.8561 (t0)
REVERT: H   66 THR cc_start: 0.8823 (p) cc_final: 0.8611 (t)
REVERT: H  103 ARG cc_start: 0.8638 (mmm160) cc_final: 0.7783 (mmm160)
REVERT: H  116 TRP cc_start: 0.7373 (t-100) cc_final: 0.6932 (t-100)
REVERT: C    5 THR cc_start: 0.9283 (p) cc_final: 0.8425 (p)
REVERT: C   13 LYS cc_start: 0.8377 (ptpt) cc_final: 0.7266 (mttt)
REVERT: C   14 ASP cc_start: 0.9342 (p0) cc_final: 0.8845 (p0)
REVERT: C   37 GLN cc_start: 0.8810 (tt0) cc_final: 0.8345 (tm-30)
REVERT: C   63 LYS cc_start: 0.9055 (tmtt) cc_final: 0.8557 (ttpp)
REVERT: C   70 ASN cc_start: 0.9546 (t0) cc_final: 0.9330 (t0)
REVERT: C  123 ASP cc_start: 0.9300 (t0) cc_final: 0.8843 (t0)
REVERT: c   13 LYS cc_start: 0.9646 (tttt) cc_final: 0.9436 (tttp)
REVERT: c   14 ASP cc_start: 0.9062 (p0) cc_final: 0.7977 (p0)
REVERT: c   37 GLN cc_start: 0.9042 (tm-30) cc_final: 0.8607 (pp30)
REVERT: c  111 GLU cc_start: 0.9373 (pt0) cc_final: 0.8879 (pt0)
REVERT: c  122 ILE cc_start: 0.8836 (tt) cc_final: 0.8172 (tt)
REVERT: c  123 ASP cc_start: 0.9307 (t0) cc_final: 0.9037 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.0926
  time to fit residues: 11.7310
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  : 0.144 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 36 optimal weight:    9.9990
   chunk 32 optimal weight:   20.0000
   chunk 13 optimal weight:    0.9990
   chunk 41 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 20 optimal weight:    7.9990
   chunk 1 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   chunk 6 optimal weight:   20.0000
   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  85 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 = 0.3185 r_free = 0.3185 target = 0.059644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.049793 restraints weight = 20506.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.051256 restraints weight = 11801.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.052244 restraints weight = 8024.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.052955 restraints weight = 6066.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.053498 restraints weight = 4906.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.6024

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= 0.197
  Angle     :  0.798  10.818   4939  Z= 0.405
  Chirality :  0.048   0.214    557
  Planarity :  0.006   0.111    639
  Dihedral  :  5.397  28.273    505
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 16.82
  Ramachandran Plot:
    Outliers :  1.10 %
    Allowed  : 10.55 %
    Favored  : 88.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.23 (0.38), residues: 455
  helix: -0.35 (0.72), residues: 49
  sheet: -0.32 (0.42), residues: 156
  loop : -2.61 (0.35), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG c  47 
 TYR   0.024   0.002   TYR L  74 
 PHE   0.018   0.002   PHE L  94 
 TRP   0.015   0.002   TRP H 116 
 HIS   0.002   0.002   HIS L  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 3634)
  covalent geometry    : angle       0.79829 ( 4937)
  SS BOND              : bond        0.00381 (    1)
  SS BOND              : angle       0.81758 (    2)
  hydrogen bonds       : bond        0.03595 (  111)
  hydrogen bonds       : angle       5.29381 (  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
  99 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   24 ILE cc_start: 0.8412 (pt) cc_final: 0.8167 (mp)
REVERT: L   41 ARG cc_start: 0.9534 (tpt90) cc_final: 0.9147 (tpt170)
REVERT: H   37 MET cc_start: 0.9136 (mmp) cc_final: 0.8719 (mmp)
REVERT: H   65 ASP cc_start: 0.8834 (t0) cc_final: 0.8476 (t0)
REVERT: H   66 THR cc_start: 0.8859 (p) cc_final: 0.8529 (p)
REVERT: H  116 TRP cc_start: 0.7527 (t-100) cc_final: 0.6922 (t-100)
REVERT: C    5 THR cc_start: 0.9310 (p) cc_final: 0.8396 (p)
REVERT: C   13 LYS cc_start: 0.8076 (ptpt) cc_final: 0.7037 (mttt)
REVERT: C   14 ASP cc_start: 0.9292 (p0) cc_final: 0.8783 (p0)
REVERT: C   37 GLN cc_start: 0.8968 (tt0) cc_final: 0.8392 (tm-30)
REVERT: C   63 LYS cc_start: 0.9043 (tmtt) cc_final: 0.8606 (ttpp)
REVERT: C  123 ASP cc_start: 0.9281 (t0) cc_final: 0.8827 (t0)
REVERT: c   37 GLN cc_start: 0.9159 (tm-30) cc_final: 0.8726 (tm-30)
REVERT: c  111 GLU cc_start: 0.9419 (pt0) cc_final: 0.8901 (pt0)
REVERT: c  122 ILE cc_start: 0.8996 (tt) cc_final: 0.8179 (tt)
REVERT: c  123 ASP cc_start: 0.9280 (t0) cc_final: 0.9004 (t0)
REVERT: c  126 ASP cc_start: 0.8755 (m-30) cc_final: 0.8350 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.0737
  time to fit residues: 8.6369
Evaluate side-chains
  79 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 3 optimal weight:    0.9980
   chunk 5 optimal weight:   10.0000
   chunk 22 optimal weight:    0.0030
   chunk 10 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 6 optimal weight:    8.9990
   chunk 33 optimal weight:    9.9990
   chunk 9 optimal weight:    7.9990
   chunk 24 optimal weight:    8.9990
   chunk 26 optimal weight:    7.9990
   overall best weight:    3.1996

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

Flipped N/Q/H residues before XYZ refinement:
** H  85 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 = 0.3216 r_free = 0.3216 target = 0.061021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.050949 restraints weight = 20048.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.052403 restraints weight = 11528.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.053425 restraints weight = 7832.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.054111 restraints weight = 5932.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.054591 restraints weight = 4837.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.6078

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= 0.159
  Angle     :  0.778  11.072   4939  Z= 0.393
  Chirality :  0.050   0.252    557
  Planarity :  0.004   0.037    639
  Dihedral  :  5.537  43.195    505
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 15.55
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 10.33 %
    Favored  : 89.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  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 are not related in a simple way.
  whole: -2.17 (0.38), residues: 455
  helix: -0.27 (0.71), residues: 50
  sheet: -0.26 (0.42), residues: 156
  loop : -2.61 (0.36), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG c  47 
 TYR   0.020   0.002   TYR L  74 
 PHE   0.016   0.002   PHE L  94 
 TRP   0.010   0.002   TRP H 116 
 HIS   0.003   0.002   HIS L  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 3634)
  covalent geometry    : angle       0.77749 ( 4937)
  SS BOND              : bond        0.00394 (    1)
  SS BOND              : angle       0.88173 (    2)
  hydrogen bonds       : bond        0.03459 (  111)
  hydrogen bonds       : angle       5.19610 (  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
  104 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.139 
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: 0.8404 (pt) cc_final: 0.8174 (mp)
REVERT: L   41 ARG cc_start: 0.9450 (tpt90) cc_final: 0.9200 (tpt170)
REVERT: H   37 MET cc_start: 0.9147 (mmp) cc_final: 0.8775 (mmp)
REVERT: H   65 ASP cc_start: 0.8764 (t0) cc_final: 0.8506 (t0)
REVERT: H   66 THR cc_start: 0.8776 (p) cc_final: 0.8533 (t)
REVERT: H  116 TRP cc_start: 0.7560 (t-100) cc_final: 0.6942 (t-100)
REVERT: C    5 THR cc_start: 0.9308 (p) cc_final: 0.8365 (p)
REVERT: C   13 LYS cc_start: 0.8081 (ptpt) cc_final: 0.7351 (ptpt)
REVERT: C   14 ASP cc_start: 0.9231 (p0) cc_final: 0.8843 (p0)
REVERT: C   37 GLN cc_start: 0.8906 (tt0) cc_final: 0.8395 (tm-30)
REVERT: C   63 LYS cc_start: 0.9022 (tmtt) cc_final: 0.8573 (ttpp)
REVERT: C   65 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7790 (tm-30)
REVERT: C  118 SER cc_start: 0.9595 (t) cc_final: 0.8965 (t)
REVERT: C  123 ASP cc_start: 0.9290 (t0) cc_final: 0.8826 (t0)
REVERT: c   13 LYS cc_start: 0.9575 (tttt) cc_final: 0.9234 (tttp)
REVERT: c   14 ASP cc_start: 0.8932 (p0) cc_final: 0.8520 (p0)
REVERT: c   37 GLN cc_start: 0.9153 (tm-30) cc_final: 0.8710 (tm-30)
REVERT: c   47 ARG cc_start: 0.9026 (ptm160) cc_final: 0.8750 (mtp-110)
REVERT: c  111 GLU cc_start: 0.9422 (pt0) cc_final: 0.8920 (pt0)
REVERT: c  122 ILE cc_start: 0.9031 (tt) cc_final: 0.8139 (tt)
REVERT: c  123 ASP cc_start: 0.9241 (t0) cc_final: 0.8973 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.0659
  time to fit residues: 8.1109
Evaluate side-chains
  85 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 39 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   chunk 17 optimal weight:   10.0000
   chunk 29 optimal weight:    3.9990
   chunk 6 optimal weight:   20.0000
   chunk 15 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** H  85 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 = 0.3171 r_free = 0.3171 target = 0.059054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.049113 restraints weight = 19855.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.050560 restraints weight = 11327.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.051584 restraints weight = 7584.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.052304 restraints weight = 5661.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.052844 restraints weight = 4559.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.6293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   3635  Z= 0.203
  Angle     :  0.794  11.195   4939  Z= 0.402
  Chirality :  0.050   0.234    557
  Planarity :  0.004   0.038    639
  Dihedral  :  5.618  36.675    505
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 17.11
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 10.77 %
    Favored  : 88.57 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.24 (0.38), residues: 455
  helix: -0.37 (0.72), residues: 50
  sheet: -0.42 (0.41), residues: 158
  loop : -2.57 (0.37), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG c  47 
 TYR   0.023   0.002   TYR L  74 
 PHE   0.014   0.002   PHE L  94 
 TRP   0.009   0.002   TRP H 116 
 HIS   0.004   0.002   HIS L  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 3634)
  covalent geometry    : angle       0.79371 ( 4937)
  SS BOND              : bond        0.00368 (    1)
  SS BOND              : angle       0.79461 (    2)
  hydrogen bonds       : bond        0.03487 (  111)
  hydrogen bonds       : angle       5.36779 (  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
  92 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.144 
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: 0.8471 (pt) cc_final: 0.8270 (mp)
REVERT: L   41 ARG cc_start: 0.9517 (tpt90) cc_final: 0.9127 (tpt170)
REVERT: H   37 MET cc_start: 0.9151 (mmp) cc_final: 0.8769 (mmp)
REVERT: H   65 ASP cc_start: 0.8806 (t0) cc_final: 0.8413 (t0)
REVERT: H   66 THR cc_start: 0.8849 (p) cc_final: 0.8450 (p)
REVERT: C   13 LYS cc_start: 0.8036 (ptpt) cc_final: 0.7257 (ptpt)
REVERT: C   14 ASP cc_start: 0.9260 (p0) cc_final: 0.8858 (p0)
REVERT: C   37 GLN cc_start: 0.9016 (tt0) cc_final: 0.8497 (tm-30)
REVERT: C   63 LYS cc_start: 0.9038 (tmtt) cc_final: 0.8609 (ttpp)
REVERT: C   70 ASN cc_start: 0.9563 (t0) cc_final: 0.9332 (t0)
REVERT: C  115 LEU cc_start: 0.9750 (tp) cc_final: 0.9538 (tp)
REVERT: C  118 SER cc_start: 0.9492 (t) cc_final: 0.9231 (m)
REVERT: C  123 ASP cc_start: 0.9283 (t0) cc_final: 0.8830 (t0)
REVERT: c   16 LYS cc_start: 0.9207 (mptt) cc_final: 0.8959 (mmtm)
REVERT: c   37 GLN cc_start: 0.9206 (tm-30) cc_final: 0.8715 (tm-30)
REVERT: c   47 ARG cc_start: 0.9090 (ptm160) cc_final: 0.8789 (mtp-110)
REVERT: c  111 GLU cc_start: 0.9457 (pt0) cc_final: 0.9108 (pt0)
REVERT: c  122 ILE cc_start: 0.8956 (tt) cc_final: 0.8084 (tt)
REVERT: c  123 ASP cc_start: 0.9267 (t0) cc_final: 0.8998 (t0)
REVERT: c  126 ASP cc_start: 0.8774 (m-30) cc_final: 0.8337 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.0928
  time to fit residues: 9.9513
Evaluate side-chains
  79 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 28 optimal weight:    7.9990
   chunk 32 optimal weight:   20.0000
   chunk 39 optimal weight:    5.9990
   chunk 10 optimal weight:    0.5980
   chunk 4 optimal weight:    0.0670
   chunk 9 optimal weight:   20.0000
   chunk 35 optimal weight:    7.9990
   chunk 19 optimal weight:    4.9990
   chunk 17 optimal weight:    7.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    2.7324

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

Flipped N/Q/H residues before XYZ refinement:
** H  85 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 = 0.3204 r_free = 0.3204 target = 0.060395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.050369 restraints weight = 19289.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.051839 restraints weight = 10947.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.052893 restraints weight = 7360.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.053532 restraints weight = 5492.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.054117 restraints weight = 4462.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.6331

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= 0.153
  Angle     :  0.776  11.082   4939  Z= 0.392
  Chirality :  0.049   0.233    557
  Planarity :  0.004   0.037    639
  Dihedral  :  5.363  32.400    505
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 14.14
  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 are not related in a simple way.
  whole: -2.17 (0.39), residues: 455
  helix: -0.19 (0.76), residues: 50
  sheet: -0.24 (0.42), residues: 154
  loop : -2.62 (0.37), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG c  47 
 TYR   0.019   0.002   TYR L  74 
 PHE   0.019   0.002   PHE L 101 
 TRP   0.007   0.001   TRP H 116 
 HIS   0.003   0.002   HIS L  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 3634)
  covalent geometry    : angle       0.77570 ( 4937)
  SS BOND              : bond        0.00409 (    1)
  SS BOND              : angle       0.89807 (    2)
  hydrogen bonds       : bond        0.03482 (  111)
  hydrogen bonds       : angle       5.23630 (  291)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 720.02 seconds
wall clock time: 13 minutes 10.31 seconds (790.31 seconds total)