Starting phenix.real_space_refine
on Wed Mar  5 20:41:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w5q_37301/03_2025/8w5q_37301.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w5q_37301/03_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_37301/03_2025/8w5q_37301.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w5q_37301/03_2025/8w5q_37301.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w5q_37301/03_2025/8w5q_37301.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w5q_37301/03_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-5624/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: 2.67, per 1000 atoms: 0.75
  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: 0.82
  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: 0.37
  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: 0.81

  Time building geometry restraints manager: 0.96 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:             0.420
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.730
  Find NCS groups from input model:        0.080
  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:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.490
-------------------------------------------------------------------------------
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   3634  Z= 0.209
  Angle     :  0.810  24.835   4937  Z= 0.390
  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 

*********************** 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  : 0.427 
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: 0.2045
  time to fit residues: 40.5674
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  : 0.436 
-------------------------------------------------------------------------------
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 = 43)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.053027 restraints weight = 19071.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.054541 restraints weight = 11268.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.055604 restraints weight = 7725.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
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   3634  Z= 0.331
  Angle     :  0.784  11.085   4937  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 

*********************** 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  : 0.420 
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: 0.8859 (tt0) cc_final: 0.8255 (tm-30)
REVERT: C   63 LYS cc_start: 0.9148 (tmtt) cc_final: 0.8707 (tmtt)
REVERT: C  100 SER cc_start: 0.9480 (p) cc_final: 0.8649 (p)
REVERT: C  104 GLU cc_start: 0.9319 (pt0) cc_final: 0.8949 (pp20)
REVERT: C  123 ASP cc_start: 0.9123 (t0) cc_final: 0.8735 (t0)
REVERT: c    3 LEU cc_start: 0.9241 (mp) cc_final: 0.8247 (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: 0.8674 (p0)
REVERT: c   21 LEU cc_start: 0.9197 (pp) cc_final: 0.8684 (pp)
REVERT: c   37 GLN cc_start: 0.8641 (pp30) cc_final: 0.8318 (pp30)
REVERT: c  127 GLN cc_start: 0.9182 (mp10) cc_final: 0.8940 (mp10)
  outliers start: 3
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1729
  time to fit residues: 25.6784
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  : 0.419 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 12 optimal weight:    1.9990
   chunk 37 optimal weight:    8.9990
   chunk 32 optimal weight:    7.9990
   chunk 21 optimal weight:   10.0000
   chunk 41 optimal weight:    7.9990
   chunk 23 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
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 = 0.3187 r_free = 0.3187 target = 0.060061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.050243 restraints weight = 19103.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.051753 restraints weight = 11032.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.052818 restraints weight = 7363.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.4799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   3634  Z= 0.300
  Angle     :  0.727   8.291   4937  Z= 0.376
  Chirality :  0.046   0.206    557
  Planarity :  0.006   0.088    639
  Dihedral  :  5.627  28.907    505
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  9.67 %
    Favored  : 89.67 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  7.31 %
    Favored  : 92.43 %
  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: -2.40 (0.37), residues: 455
  helix:  0.41 (0.73), residues: 48
  sheet: -0.81 (0.39), residues: 162
  loop : -2.67 (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   0.017   0.002   TYR L  74 
 ARG   0.002   0.000   ARG c 109 

*********************** 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
  128 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.391 
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: 0.9367 (tpt90) cc_final: 0.9061 (tpt170)
REVERT: L   52 PHE cc_start: 0.8716 (m-80) cc_final: 0.8339 (m-10)
REVERT: H   35 TYR cc_start: 0.9042 (m-80) cc_final: 0.8553 (m-80)
REVERT: H   37 MET cc_start: 0.9158 (mmp) cc_final: 0.8936 (mmm)
REVERT: H   62 TYR cc_start: 0.8895 (m-80) cc_final: 0.8548 (m-80)
REVERT: H  116 TRP cc_start: 0.7411 (t-100) cc_final: 0.7143 (t-100)
REVERT: C   13 LYS cc_start: 0.8771 (ttmm) cc_final: 0.8414 (ptpt)
REVERT: C   37 GLN cc_start: 0.8984 (tt0) cc_final: 0.8230 (tm-30)
REVERT: C   63 LYS cc_start: 0.9082 (tmtt) cc_final: 0.8767 (tmtt)
REVERT: C   79 SER cc_start: 0.7592 (t) cc_final: 0.7255 (t)
REVERT: C  100 SER cc_start: 0.9456 (p) cc_final: 0.9125 (p)
REVERT: C  104 GLU cc_start: 0.8988 (pt0) cc_final: 0.8656 (pt0)
REVERT: C  123 ASP cc_start: 0.9161 (t0) cc_final: 0.8796 (t0)
REVERT: c    3 LEU cc_start: 0.9056 (mp) cc_final: 0.8402 (mt)
REVERT: c   13 LYS cc_start: 0.9657 (tttt) cc_final: 0.9437 (tttp)
REVERT: c   14 ASP cc_start: 0.9097 (p0) cc_final: 0.8747 (p0)
REVERT: c   37 GLN cc_start: 0.8524 (pp30) cc_final: 0.8208 (pp30)
REVERT: c  111 GLU cc_start: 0.9514 (pt0) cc_final: 0.9233 (pt0)
REVERT: c  121 LEU cc_start: 0.9569 (mm) cc_final: 0.9261 (mm)
REVERT: c  123 ASP cc_start: 0.9367 (t0) cc_final: 0.9146 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1884
  time to fit residues: 28.1860
Evaluate side-chains
  98 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 20 optimal weight:    9.9990
   chunk 35 optimal weight:    9.9990
   chunk 28 optimal weight:    9.9990
   chunk 14 optimal weight:    4.9990
   chunk 0 optimal weight:   30.0000
   chunk 6 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   chunk 38 optimal weight:   10.0000
   chunk 18 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    4.3788

-------------------------------------------------------------------------------
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 = 0.3170 r_free = 0.3170 target = 0.059582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.049674 restraints weight = 19797.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.051113 restraints weight = 11266.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.052140 restraints weight = 7597.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.5299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3634  Z= 0.259
  Angle     :  0.721   8.783   4937  Z= 0.368
  Chirality :  0.048   0.230    557
  Planarity :  0.006   0.118    639
  Dihedral  :  5.557  29.149    505
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  1.10 %
    Allowed  :  9.67 %
    Favored  : 89.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  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: -2.36 (0.37), residues: 455
  helix:  0.18 (0.73), residues: 49
  sheet: -0.64 (0.40), residues: 160
  loop : -2.69 (0.35), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H 116 
 HIS   0.002   0.002   HIS L  93 
 PHE   0.015   0.002   PHE L 101 
 TYR   0.011   0.002   TYR H  35 
 ARG   0.002   0.000   ARG c 109 

*********************** 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
  117 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.377 
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: 0.9380 (tpt90) cc_final: 0.9164 (tpt170)
REVERT: H   37 MET cc_start: 0.9155 (mmp) cc_final: 0.8937 (mmp)
REVERT: H   62 TYR cc_start: 0.8939 (m-80) cc_final: 0.8573 (m-80)
REVERT: H  116 TRP cc_start: 0.7601 (t-100) cc_final: 0.7129 (t-100)
REVERT: C   13 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8151 (mttp)
REVERT: C   14 ASP cc_start: 0.9428 (p0) cc_final: 0.9138 (p0)
REVERT: C   37 GLN cc_start: 0.9081 (tt0) cc_final: 0.8333 (tm-30)
REVERT: C   63 LYS cc_start: 0.9123 (tmtt) cc_final: 0.8794 (tmtt)
REVERT: C  100 SER cc_start: 0.9449 (p) cc_final: 0.9125 (p)
REVERT: C  104 GLU cc_start: 0.9056 (pt0) cc_final: 0.8652 (pt0)
REVERT: C  123 ASP cc_start: 0.9182 (t0) cc_final: 0.8788 (t0)
REVERT: c    3 LEU cc_start: 0.9104 (mp) cc_final: 0.8669 (mt)
REVERT: c    4 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8326 (mm-30)
REVERT: c   14 ASP cc_start: 0.9015 (p0) cc_final: 0.8705 (p0)
REVERT: c   37 GLN cc_start: 0.8590 (pp30) cc_final: 0.8314 (pp30)
REVERT: c  111 GLU cc_start: 0.9515 (pt0) cc_final: 0.9211 (pt0)
REVERT: c  121 LEU cc_start: 0.9584 (mm) cc_final: 0.9286 (mm)
REVERT: c  123 ASP cc_start: 0.9385 (t0) cc_final: 0.9102 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1863
  time to fit residues: 25.5552
Evaluate side-chains
  89 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
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:   30.0000
   chunk 27 optimal weight:   20.0000
   chunk 21 optimal weight:    0.6980
   chunk 28 optimal weight:    5.9990
   chunk 24 optimal weight:    8.9990
   chunk 36 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 11 optimal weight:   50.0000
   overall best weight:    3.5388

-------------------------------------------------------------------------------
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 = 0.3187 r_free = 0.3187 target = 0.060080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.050219 restraints weight = 19231.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.051783 restraints weight = 10894.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.052841 restraints weight = 7146.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.5464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3634  Z= 0.230
  Angle     :  0.716   9.706   4937  Z= 0.364
  Chirality :  0.047   0.227    557
  Planarity :  0.006   0.123    639
  Dihedral  :  5.404  26.762    505
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  1.10 %
    Allowed  :  9.89 %
    Favored  : 89.01 %
  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: -2.24 (0.38), residues: 455
  helix:  0.25 (0.75), residues: 49
  sheet: -0.49 (0.41), residues: 160
  loop : -2.67 (0.36), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  50 
 HIS   0.003   0.002   HIS L  93 
 PHE   0.019   0.002   PHE L 101 
 TYR   0.014   0.002   TYR L  39 
 ARG   0.002   0.000   ARG H 103 

*********************** 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
  115 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   41 ARG cc_start: 0.9419 (tpt90) cc_final: 0.9186 (tpt170)
REVERT: H   62 TYR cc_start: 0.9030 (m-80) cc_final: 0.8587 (m-80)
REVERT: H   86 MET cc_start: 0.9127 (mpp) cc_final: 0.8883 (mpp)
REVERT: H  116 TRP cc_start: 0.7530 (t-100) cc_final: 0.6979 (t-100)
REVERT: C   13 LYS cc_start: 0.8792 (ttmm) cc_final: 0.8485 (ptpt)
REVERT: C   14 ASP cc_start: 0.9449 (p0) cc_final: 0.9236 (p0)
REVERT: C   37 GLN cc_start: 0.8989 (tt0) cc_final: 0.8502 (tm-30)
REVERT: C   63 LYS cc_start: 0.9099 (tmtt) cc_final: 0.8505 (ttpp)
REVERT: C   65 GLN cc_start: 0.8042 (tm-30) cc_final: 0.7690 (tm-30)
REVERT: C  100 SER cc_start: 0.9450 (p) cc_final: 0.9122 (p)
REVERT: C  104 GLU cc_start: 0.9031 (pt0) cc_final: 0.8624 (pt0)
REVERT: C  123 ASP cc_start: 0.9212 (t0) cc_final: 0.8852 (t0)
REVERT: c    3 LEU cc_start: 0.9151 (mp) cc_final: 0.8760 (mt)
REVERT: c    4 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8301 (mm-30)
REVERT: c   37 GLN cc_start: 0.8762 (pp30) cc_final: 0.8350 (pp30)
REVERT: c  111 GLU cc_start: 0.9533 (pt0) cc_final: 0.9231 (pt0)
REVERT: c  121 LEU cc_start: 0.9537 (mm) cc_final: 0.9253 (mm)
REVERT: c  122 ILE cc_start: 0.9061 (tt) cc_final: 0.8169 (tt)
REVERT: c  123 ASP cc_start: 0.9379 (t0) cc_final: 0.9136 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.2030
  time to fit residues: 27.2175
Evaluate side-chains
  91 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 19 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   chunk 30 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 2 optimal weight:    5.9990
   chunk 10 optimal weight:   20.0000
   chunk 4 optimal weight:    8.9990
   chunk 35 optimal weight:    8.9990
   overall best weight:    7.5990

-------------------------------------------------------------------------------
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 = 0.3119 r_free = 0.3119 target = 0.057159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.047437 restraints weight = 19912.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.048919 restraints weight = 11128.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.049920 restraints weight = 7350.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.6025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062   3634  Z= 0.408
  Angle     :  0.801  10.553   4937  Z= 0.417
  Chirality :  0.048   0.226    557
  Planarity :  0.006   0.103    639
  Dihedral  :  6.012  27.513    505
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 18.10
  Ramachandran Plot:
    Outliers :  1.32 %
    Allowed  : 11.65 %
    Favored  : 87.03 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  4.44 %
    Favored  : 95.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.48 (0.37), residues: 455
  helix: -0.10 (0.71), residues: 50
  sheet: -0.60 (0.41), residues: 157
  loop : -2.81 (0.35), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP H  50 
 HIS   0.004   0.003   HIS L  93 
 PHE   0.019   0.002   PHE L  94 
 TYR   0.015   0.002   TYR H  38 
 ARG   0.002   0.000   ARG H  75 

*********************** 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
  104 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   24 ILE cc_start: 0.8726 (pt) cc_final: 0.8503 (mp)
REVERT: L   41 ARG cc_start: 0.9467 (tpt90) cc_final: 0.9034 (tpt170)
REVERT: H   37 MET cc_start: 0.9155 (mmp) cc_final: 0.8942 (mmp)
REVERT: H   86 MET cc_start: 0.9049 (mpp) cc_final: 0.8815 (mpp)
REVERT: H  116 TRP cc_start: 0.7549 (t-100) cc_final: 0.6802 (t-100)
REVERT: C    5 THR cc_start: 0.9356 (p) cc_final: 0.8512 (p)
REVERT: C   14 ASP cc_start: 0.9408 (p0) cc_final: 0.9101 (p0)
REVERT: C   37 GLN cc_start: 0.9123 (tt0) cc_final: 0.8608 (tm-30)
REVERT: C   63 LYS cc_start: 0.9146 (tmtt) cc_final: 0.8636 (ttpp)
REVERT: C  100 SER cc_start: 0.9455 (p) cc_final: 0.9159 (p)
REVERT: C  104 GLU cc_start: 0.9044 (pt0) cc_final: 0.8676 (pt0)
REVERT: C  123 ASP cc_start: 0.9193 (t0) cc_final: 0.8824 (t0)
REVERT: c    4 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8099 (mm-30)
REVERT: c   37 GLN cc_start: 0.9055 (pp30) cc_final: 0.8651 (pp30)
REVERT: c  102 ASP cc_start: 0.9464 (p0) cc_final: 0.9162 (p0)
REVERT: c  111 GLU cc_start: 0.9577 (pt0) cc_final: 0.9317 (pt0)
  outliers start: 1
  outliers final: 0
  residues processed: 104
  average time/residue: 0.2121
  time to fit residues: 25.5237
Evaluate side-chains
  77 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 16 optimal weight:   20.0000
   chunk 28 optimal weight:    8.9990
   chunk 26 optimal weight:    8.9990
   chunk 4 optimal weight:    0.0470
   chunk 40 optimal weight:    9.9990
   chunk 37 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 31 optimal weight:    0.8980
   chunk 20 optimal weight:    9.9990
   chunk 5 optimal weight:    8.9990
   overall best weight:    3.7884

-------------------------------------------------------------------------------
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 = 0.3174 r_free = 0.3174 target = 0.059003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.049250 restraints weight = 19203.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.050744 restraints weight = 10670.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.051786 restraints weight = 7091.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.6126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3634  Z= 0.246
  Angle     :  0.783  15.035   4937  Z= 0.390
  Chirality :  0.048   0.256    557
  Planarity :  0.007   0.157    639
  Dihedral  :  5.733  31.167    505
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 14.99
  Ramachandran Plot:
    Outliers :  1.32 %
    Allowed  : 10.33 %
    Favored  : 88.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.35 %
    Twisted General : 0.00 %

Rama-Z (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:  0.15 (0.73), residues: 50
  sheet: -0.47 (0.41), residues: 155
  loop : -2.79 (0.35), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP H  50 
 HIS   0.002   0.002   HIS L  93 
 PHE   0.015   0.001   PHE L  94 
 TYR   0.013   0.001   TYR H 105 
 ARG   0.003   0.000   ARG c  47 

*********************** 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
  113 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.401 
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: H  116 TRP cc_start: 0.7537 (t-100) cc_final: 0.6799 (t-100)
REVERT: C    5 THR cc_start: 0.9379 (p) cc_final: 0.8486 (p)
REVERT: C   13 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8430 (ttmt)
REVERT: C   14 ASP cc_start: 0.9474 (p0) cc_final: 0.9210 (p0)
REVERT: C   37 GLN cc_start: 0.9051 (tt0) cc_final: 0.8479 (tm-30)
REVERT: C   63 LYS cc_start: 0.9071 (tmtt) cc_final: 0.8533 (ttpp)
REVERT: C   65 GLN cc_start: 0.8080 (tm-30) cc_final: 0.7665 (tm-30)
REVERT: C  100 SER cc_start: 0.9435 (p) cc_final: 0.9121 (p)
REVERT: C  104 GLU cc_start: 0.9020 (pt0) cc_final: 0.8672 (pt0)
REVERT: C  123 ASP cc_start: 0.9241 (t0) cc_final: 0.8944 (t0)
REVERT: c    3 LEU cc_start: 0.8963 (mp) cc_final: 0.8656 (mm)
REVERT: c    4 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8167 (mm-30)
REVERT: c   13 LYS cc_start: 0.9412 (tttt) cc_final: 0.9086 (tttp)
REVERT: c   14 ASP cc_start: 0.8772 (p0) cc_final: 0.8471 (p0)
REVERT: c   37 GLN cc_start: 0.8860 (pp30) cc_final: 0.8549 (pp30)
REVERT: c  111 GLU cc_start: 0.9536 (pt0) cc_final: 0.9232 (pt0)
REVERT: c  121 LEU cc_start: 0.9512 (mm) cc_final: 0.9227 (mm)
REVERT: c  123 ASP cc_start: 0.9246 (t70) cc_final: 0.8908 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1869
  time to fit residues: 24.8318
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  : 0.413 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 30 optimal weight:    6.9990
   chunk 6 optimal weight:   30.0000
   chunk 24 optimal weight:    6.9990
   chunk 35 optimal weight:    9.9990
   chunk 43 optimal weight:    5.9990
   chunk 12 optimal weight:   10.0000
   chunk 36 optimal weight:   20.0000
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 40 optimal weight:    9.9990
   overall best weight:    4.3588

-------------------------------------------------------------------------------
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 = 0.058825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.048678 restraints weight = 19691.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.050163 restraints weight = 11249.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.051185 restraints weight = 7603.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.6288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3634  Z= 0.269
  Angle     :  0.768  11.272   4937  Z= 0.389
  Chirality :  0.049   0.229    557
  Planarity :  0.007   0.132    639
  Dihedral  :  5.768  31.679    505
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  1.32 %
    Allowed  :  9.67 %
    Favored  : 89.01 %
  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: -2.32 (0.37), residues: 455
  helix: -0.03 (0.72), residues: 51
  sheet: -0.39 (0.41), residues: 155
  loop : -2.78 (0.35), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP H  50 
 HIS   0.004   0.002   HIS L  93 
 PHE   0.030   0.002   PHE L 101 
 TYR   0.013   0.002   TYR H 105 
 ARG   0.002   0.000   ARG H  75 

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

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

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

  910 Ramachandran restraints generated.
    455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   86 MET cc_start: 0.9103 (mpp) cc_final: 0.8773 (mpp)
REVERT: H  103 ARG cc_start: 0.8474 (mmp-170) cc_final: 0.7669 (mmm160)
REVERT: H  113 PHE cc_start: 0.6270 (p90) cc_final: 0.5403 (p90)
REVERT: H  116 TRP cc_start: 0.7624 (t-100) cc_final: 0.6886 (t-100)
REVERT: C   13 LYS cc_start: 0.8788 (ttmm) cc_final: 0.8443 (ttmt)
REVERT: C   14 ASP cc_start: 0.9514 (p0) cc_final: 0.9245 (p0)
REVERT: C   37 GLN cc_start: 0.8935 (tt0) cc_final: 0.8271 (tm-30)
REVERT: C   63 LYS cc_start: 0.9072 (tmtt) cc_final: 0.8544 (ttpp)
REVERT: C   65 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7783 (tm-30)
REVERT: C   68 ILE cc_start: 0.9435 (mt) cc_final: 0.9208 (mp)
REVERT: C  100 SER cc_start: 0.9495 (p) cc_final: 0.9202 (p)
REVERT: C  104 GLU cc_start: 0.8999 (pt0) cc_final: 0.8671 (pt0)
REVERT: C  123 ASP cc_start: 0.9263 (t0) cc_final: 0.8938 (t0)
REVERT: c    3 LEU cc_start: 0.9002 (mp) cc_final: 0.8555 (mp)
REVERT: c    4 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8097 (mm-30)
REVERT: c   14 ASP cc_start: 0.8841 (p0) cc_final: 0.8544 (p0)
REVERT: c   37 GLN cc_start: 0.8929 (pp30) cc_final: 0.8540 (pp30)
REVERT: c  111 GLU cc_start: 0.9492 (pt0) cc_final: 0.9181 (pt0)
REVERT: c  122 ILE cc_start: 0.9042 (tt) cc_final: 0.8102 (tt)
REVERT: c  123 ASP cc_start: 0.9244 (t70) cc_final: 0.8950 (t0)
REVERT: c  126 ASP cc_start: 0.8910 (m-30) cc_final: 0.8523 (m-30)
REVERT: c  127 GLN cc_start: 0.9094 (mp10) cc_final: 0.8850 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.2070
  time to fit residues: 25.1266
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  : 0.420 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 0 optimal weight:   30.0000
   chunk 30 optimal weight:    3.9990
   chunk 19 optimal weight:   10.0000
   chunk 24 optimal weight:    6.9990
   chunk 36 optimal weight:    8.9990
   chunk 29 optimal weight:    3.9990
   chunk 37 optimal weight:    9.9990
   chunk 34 optimal weight:    0.1980
   chunk 17 optimal weight:   10.0000
   chunk 20 optimal weight:    0.8980
   overall best weight:    3.2186

-------------------------------------------------------------------------------
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 = 0.3188 r_free = 0.3188 target = 0.059715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.049774 restraints weight = 18746.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.051257 restraints weight = 10652.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.052300 restraints weight = 7181.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.6267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3634  Z= 0.226
  Angle     :  0.758  11.531   4937  Z= 0.381
  Chirality :  0.049   0.248    557
  Planarity :  0.004   0.042    639
  Dihedral  :  5.713  44.306    505
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 15.55
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 10.33 %
    Favored  : 89.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.35 %
    Twisted General : 0.00 %

Rama-Z (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: -2.31 (0.38), residues: 455
  helix:  0.17 (0.72), residues: 51
  sheet: -0.41 (0.42), residues: 155
  loop : -2.79 (0.35), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H  50 
 HIS   0.004   0.003   HIS L  93 
 PHE   0.040   0.002   PHE L 101 
 TYR   0.014   0.002   TYR H 105 
 ARG   0.002   0.000   ARG H  90 

*********************** 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
  106 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  101 PHE cc_start: 0.8986 (t80) cc_final: 0.8778 (t80)
REVERT: H  103 ARG cc_start: 0.8472 (mmp-170) cc_final: 0.7716 (mmm160)
REVERT: H  113 PHE cc_start: 0.6218 (p90) cc_final: 0.5448 (p90)
REVERT: H  116 TRP cc_start: 0.7640 (t-100) cc_final: 0.6912 (t-100)
REVERT: C    5 THR cc_start: 0.9357 (p) cc_final: 0.8445 (p)
REVERT: C   13 LYS cc_start: 0.8795 (ttmm) cc_final: 0.8449 (ttmt)
REVERT: C   14 ASP cc_start: 0.9501 (p0) cc_final: 0.9248 (p0)
REVERT: C   37 GLN cc_start: 0.9027 (tt0) cc_final: 0.8494 (tm-30)
REVERT: C   63 LYS cc_start: 0.9051 (tmtt) cc_final: 0.8551 (ttpp)
REVERT: C   65 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7694 (tm-30)
REVERT: C  100 SER cc_start: 0.9490 (p) cc_final: 0.9175 (p)
REVERT: C  104 GLU cc_start: 0.8994 (pt0) cc_final: 0.8734 (pt0)
REVERT: C  123 ASP cc_start: 0.9249 (t0) cc_final: 0.8932 (t0)
REVERT: c    3 LEU cc_start: 0.9043 (mp) cc_final: 0.8765 (mp)
REVERT: c    4 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8054 (mm-30)
REVERT: c    8 LEU cc_start: 0.9478 (mm) cc_final: 0.9277 (mm)
REVERT: c   13 LYS cc_start: 0.9509 (tttt) cc_final: 0.9223 (tttp)
REVERT: c   14 ASP cc_start: 0.8860 (p0) cc_final: 0.8555 (p0)
REVERT: c   37 GLN cc_start: 0.8979 (pp30) cc_final: 0.8608 (pp30)
REVERT: c  104 GLU cc_start: 0.9351 (pt0) cc_final: 0.9073 (pm20)
REVERT: c  111 GLU cc_start: 0.9519 (pt0) cc_final: 0.9227 (pt0)
REVERT: c  122 ILE cc_start: 0.9035 (tt) cc_final: 0.8072 (tt)
REVERT: c  123 ASP cc_start: 0.9203 (t70) cc_final: 0.8883 (t0)
REVERT: c  127 GLN cc_start: 0.9084 (mp10) cc_final: 0.8825 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1797
  time to fit residues: 22.6652
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  : 0.397 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 21 optimal weight:    8.9990
   chunk 4 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 22 optimal weight:    5.9990
   chunk 14 optimal weight:    7.9990
   chunk 7 optimal weight:   30.0000
   chunk 2 optimal weight:    6.9990
   chunk 26 optimal weight:   10.0000
   chunk 8 optimal weight:    7.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** c  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 = 0.3144 r_free = 0.3144 target = 0.057982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.047994 restraints weight = 19866.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.049373 restraints weight = 11502.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.050342 restraints weight = 7876.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.6540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   3634  Z= 0.330
  Angle     :  0.803  11.795   4937  Z= 0.409
  Chirality :  0.051   0.232    557
  Planarity :  0.005   0.043    639
  Dihedral  :  5.962  39.668    505
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 17.96
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 10.99 %
    Favored  : 88.35 %
  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: -2.40 (0.37), residues: 455
  helix:  0.23 (0.71), residues: 50
  sheet: -0.57 (0.41), residues: 159
  loop : -2.82 (0.35), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H  50 
 HIS   0.007   0.004   HIS L  93 
 PHE   0.037   0.002   PHE L 101 
 TYR   0.015   0.002   TYR L  90 
 ARG   0.002   0.000   ARG C  47 

********************** 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
  93 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  101 PHE cc_start: 0.8964 (t80) cc_final: 0.8701 (t80)
REVERT: H   82 LEU cc_start: 0.9351 (mt) cc_final: 0.9139 (mp)
REVERT: H   86 MET cc_start: 0.9061 (mpp) cc_final: 0.8755 (mpp)
REVERT: H  116 TRP cc_start: 0.7737 (t-100) cc_final: 0.6929 (t-100)
REVERT: C   13 LYS cc_start: 0.8840 (ttmm) cc_final: 0.8626 (ttmt)
REVERT: C   14 ASP cc_start: 0.9501 (p0) cc_final: 0.9245 (p0)
REVERT: C   37 GLN cc_start: 0.9003 (tt0) cc_final: 0.8318 (tm-30)
REVERT: C   63 LYS cc_start: 0.9130 (tmtt) cc_final: 0.8613 (ttpp)
REVERT: C   65 GLN cc_start: 0.8334 (tm-30) cc_final: 0.7822 (tm-30)
REVERT: C  100 SER cc_start: 0.9511 (p) cc_final: 0.9190 (p)
REVERT: C  104 GLU cc_start: 0.8994 (pt0) cc_final: 0.8711 (pt0)
REVERT: C  123 ASP cc_start: 0.9257 (t0) cc_final: 0.8870 (t0)
REVERT: c    3 LEU cc_start: 0.9065 (mp) cc_final: 0.8628 (mp)
REVERT: c    4 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8145 (mm-30)
REVERT: c   14 ASP cc_start: 0.8840 (p0) cc_final: 0.8545 (p0)
REVERT: c   37 GLN cc_start: 0.8990 (pp30) cc_final: 0.8526 (pp30)
REVERT: c  111 GLU cc_start: 0.9509 (pt0) cc_final: 0.9193 (pt0)
REVERT: c  122 ILE cc_start: 0.8956 (tt) cc_final: 0.8090 (tt)
REVERT: c  123 ASP cc_start: 0.9176 (t70) cc_final: 0.8825 (t0)
REVERT: c  126 ASP cc_start: 0.8736 (m-30) cc_final: 0.8357 (m-30)
REVERT: c  127 GLN cc_start: 0.9106 (mp10) cc_final: 0.8865 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.1930
  time to fit residues: 21.2799
Evaluate side-chains
  80 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 23 optimal weight:    9.9990
   chunk 33 optimal weight:    8.9990
   chunk 43 optimal weight:    0.0870
   chunk 34 optimal weight:    5.9990
   chunk 41 optimal weight:    7.9990
   chunk 42 optimal weight:    0.8980
   chunk 5 optimal weight:   20.0000
   chunk 25 optimal weight:   10.0000
   chunk 7 optimal weight:    4.9990
   overall best weight:    3.7964

-------------------------------------------------------------------------------
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 = 0.3161 r_free = 0.3161 target = 0.058759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.048584 restraints weight = 19375.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.050071 restraints weight = 10986.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.051098 restraints weight = 7396.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.6481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3634  Z= 0.252
  Angle     :  0.774  11.887   4937  Z= 0.392
  Chirality :  0.050   0.226    557
  Planarity :  0.004   0.046    639
  Dihedral  :  5.738  36.264    505
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 10.99 %
    Favored  : 88.35 %
  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: -2.24 (0.38), residues: 455
  helix:  0.31 (0.72), residues: 51
  sheet: -0.33 (0.43), residues: 154
  loop : -2.78 (0.36), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H  50 
 HIS   0.005   0.003   HIS L  93 
 PHE   0.039   0.002   PHE L 101 
 TYR   0.018   0.002   TYR L  33 
 ARG   0.002   0.000   ARG H  90 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1382.11 seconds
wall clock time: 24 minutes 46.25 seconds (1486.25 seconds total)