Starting phenix.real_space_refine
on Wed Jun  4 15:48:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w5e_37287/06_2025/8w5e_37287.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w5e_37287/06_2025/8w5e_37287.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w5e_37287/06_2025/8w5e_37287.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w5e_37287/06_2025/8w5e_37287.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w5e_37287/06_2025/8w5e_37287.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w5e_37287/06_2025/8w5e_37287.cif"
  }
  resolution = 3.8
  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=   0.007 sd=   0.119
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      11      5.16       5
     C    2128      2.51       5
     N     575      2.21       5
     O     680      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 3396
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "H"
      Number of atoms: 782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 782
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 944
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 944
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 8, 'TRANS': 118}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 726
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 7, 'TRANS': 86}
  Restraints were copied for chains:
    c
  Time building chain proxies: 2.87, per 1000 atoms: 0.85
  Number of scatterers: 3396
  At special positions: 0
  Unit cell: (91.8, 66.15, 85.05, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      11     16.00
     P       2     15.00
     O     680      8.00
     N     575      7.00
     C    2128      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=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.97
  Conformation dependent library (CDL) restraints added in 433.0 milliseconds
  

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  832

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 6 sheets defined
      10.3% alpha, 25.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'c' and resid 101 through 116
      removed outlier: 3.884A  pdb=" N   VAL c 108 " --> pdb=" O   GLU c 104 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ARG c 109 " --> pdb=" O   ARG c 105 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 120 through 126
      removed outlier: 3.533A  pdb=" N   ASP c 126 " --> pdb=" O   ILE c 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 116
      removed outlier: 3.885A  pdb=" N   VAL C 108 " --> pdb=" O   GLU C 104 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ARG C 109 " --> pdb=" O   ARG C 105 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 120 through 126
      removed outlier: 3.533A  pdb=" N   ASP C 126 " --> pdb=" O   ILE C 122 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 7 through 10
      removed outlier: 3.729A  pdb=" N   ASN H  80 " --> pdb=" O   ARG H  75 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 37 through 39
      removed outlier: 3.824A  pdb=" N   TYR H 112 " --> pdb=" O   ARG H 101 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'c' and resid 22 through 27
      removed outlier: 4.996A  pdb=" N   SER c  34 " --> pdb=" O   ARG c  24 " (cutoff:3.500A)
      removed outlier: 4.982A  pdb=" N   VAL c  26 " --> pdb=" O   VAL c  32 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   VAL c  32 " --> pdb=" O   VAL c  26 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ASN c  70 " --> pdb=" O   ALA c  88 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ARG c  86 " --> pdb=" O   THR c  72 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   CYS c  74 " --> pdb=" O   VAL c  84 " (cutoff:3.500A)
      removed outlier: 5.674A  pdb=" N   VAL c  84 " --> pdb=" O   CYS c  74 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 22 through 27
      removed outlier: 4.996A  pdb=" N   SER C  34 " --> pdb=" O   ARG C  24 " (cutoff:3.500A)
      removed outlier: 4.982A  pdb=" N   VAL C  26 " --> pdb=" O   VAL C  32 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   VAL C  32 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ASN C  70 " --> pdb=" O   ALA C  88 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ARG C  86 " --> pdb=" O   THR C  72 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   CYS C  74 " --> pdb=" O   VAL C  84 " (cutoff:3.500A)
      removed outlier: 5.673A  pdb=" N   VAL C  84 " --> pdb=" O   CYS C  74 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 8 through 9
    Processing sheet with id=AA6, first strand: chain 'L' and resid 48 through 49
      removed outlier: 3.799A  pdb=" N   ASP L  88 " --> pdb=" O   GLN L  41 " (cutoff:3.500A)

    99 hydrogen bonds defined for protein.
    264 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: 0.72

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 973
        1.33 -     1.45: 599
        1.45 -     1.57: 1863
        1.57 -     1.70: 8
        1.70 -     1.82: 14
  Bond restraints: 3457
  Sorted by residual:
  bond pdb=" C   VAL H   8 "
       pdb=" O   VAL H   8 "
    ideal  model  delta    sigma   weight residual
    1.237  1.212  0.024 1.07e-02 8.73e+03 5.08e+00
  bond pdb=" CA  VAL H   8 "
       pdb=" CB  VAL H   8 "
    ideal  model  delta    sigma   weight residual
    1.540  1.513  0.028 1.23e-02 6.61e+03 5.01e+00
  bond pdb=" CA  SER H  10 "
       pdb=" CB  SER H  10 "
    ideal  model  delta    sigma   weight residual
    1.534  1.500  0.033 1.78e-02 3.16e+03 3.50e+00
  bond pdb=" C   SER H  10 "
       pdb=" O   SER H  10 "
    ideal  model  delta    sigma   weight residual
    1.234  1.212  0.022 1.22e-02 6.72e+03 3.37e+00
  bond pdb=" N   THR L  81 "
       pdb=" CA  THR L  81 "
    ideal  model  delta    sigma   weight residual
    1.460  1.486 -0.027 1.54e-02 4.22e+03 3.02e+00
  ... (remaining 3452 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.81: 4560
        2.81 -     5.61: 117
        5.61 -     8.42: 23
        8.42 -    11.22: 5
       11.22 -    14.03: 4
  Bond angle restraints: 4709
  Sorted by residual:
  angle pdb=" N   VAL H   8 "
        pdb=" CA  VAL H   8 "
        pdb=" C   VAL H   8 "
      ideal   model   delta    sigma   weight residual
     108.11  122.14  -14.03 1.40e+00 5.10e-01 1.00e+02
  angle pdb=" N   VAL H   8 "
        pdb=" CA  VAL H   8 "
        pdb=" CB  VAL H   8 "
      ideal   model   delta    sigma   weight residual
     111.41  104.80    6.61 1.38e+00 5.25e-01 2.29e+01
  angle pdb=" N   ILE L  51 "
        pdb=" CA  ILE L  51 "
        pdb=" C   ILE L  51 "
      ideal   model   delta    sigma   weight residual
     109.34  119.25   -9.91 2.08e+00 2.31e-01 2.27e+01
  angle pdb=" C   LEU L  50 "
        pdb=" N   ILE L  51 "
        pdb=" CA  ILE L  51 "
      ideal   model   delta    sigma   weight residual
     121.97  130.29   -8.32 1.80e+00 3.09e-01 2.14e+01
  angle pdb=" C   VAL H   8 "
        pdb=" CA  VAL H   8 "
        pdb=" CB  VAL H   8 "
      ideal   model   delta    sigma   weight residual
     110.63  103.90    6.73 1.48e+00 4.57e-01 2.07e+01
  ... (remaining 4704 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.23: 1970
       15.23 -    30.46: 83
       30.46 -    45.69: 24
       45.69 -    60.92: 7
       60.92 -    76.14: 4
  Dihedral angle restraints: 2088
    sinusoidal: 799
      harmonic: 1289
  Sorted by residual:
  dihedral pdb=" CA  LEU L  50 "
           pdb=" C   LEU L  50 "
           pdb=" N   ILE L  51 "
           pdb=" CA  ILE L  51 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.45  -30.55     0      5.00e+00 4.00e-02 3.73e+01
  dihedral pdb=" CA  ASN L  96 "
           pdb=" C   ASN L  96 "
           pdb=" N   MET L  97 "
           pdb=" CA  MET L  97 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.34  -23.66     0      5.00e+00 4.00e-02 2.24e+01
  dihedral pdb=" CA  ILE L  78 "
           pdb=" C   ILE L  78 "
           pdb=" N   GLU L  79 "
           pdb=" CA  GLU L  79 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.63  -22.37     0      5.00e+00 4.00e-02 2.00e+01
  ... (remaining 2085 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 332
       0.048 -    0.096: 144
       0.096 -    0.145: 52
       0.145 -    0.193: 15
       0.193 -    0.241: 4
  Chirality restraints: 547
  Sorted by residual:
  chirality pdb=" CB  ILE c  68 "
            pdb=" CA  ILE c  68 "
            pdb=" CG1 ILE c  68 "
            pdb=" CG2 ILE c  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.45e+00
  chirality pdb=" CB  ILE C  68 "
            pdb=" CA  ILE C  68 "
            pdb=" CG1 ILE C  68 "
            pdb=" CG2 ILE C  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" CB  VAL L  61 "
            pdb=" CA  VAL L  61 "
            pdb=" CG1 VAL L  61 "
            pdb=" CG2 VAL L  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 544 not shown)

  Planarity restraints: 612
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE L  78 "    0.012 2.00e-02 2.50e+03   2.49e-02 6.18e+00
        pdb=" C   ILE L  78 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   ILE L  78 "    0.016 2.00e-02 2.50e+03
        pdb=" N   GLU L  79 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN c  70 "   -0.033 5.00e-02 4.00e+02   5.07e-02 4.12e+00
        pdb=" N   PRO c  71 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO c  71 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO c  71 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C  70 "   -0.033 5.00e-02 4.00e+02   5.04e-02 4.07e+00
        pdb=" N   PRO C  71 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO C  71 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO C  71 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 609 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 38
        2.61 -     3.19: 2878
        3.19 -     3.76: 4920
        3.76 -     4.33: 6298
        4.33 -     4.90: 10746
  Nonbonded interactions: 24880
  Sorted by model distance:
  nonbonded pdb=" SG  CYS L  26 "
            pdb=" SG  CYS L  91 "
     model   vdw
     2.042 3.760
  nonbonded pdb=" OE1 GLU H   9 "
            pdb=" C   ARG H 115 "
     model   vdw
     2.158 3.270
  nonbonded pdb=" OD1 ASP c  91 "
            pdb=" OG1 THR C  93 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OG1 THR c  93 "
            pdb=" OD1 ASP C  91 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" O   SER L  52 "
            pdb=" OG1 THR L  56 "
     model   vdw
     2.318 3.040
  ... (remaining 24875 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'
}

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:             0.650
  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:                     13.850
  Find NCS groups from input model:        0.060
  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:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
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      :  0.007   0.039   3458  Z= 0.317
  Angle     :  1.177  14.027   4711  Z= 0.621
  Chirality :  0.064   0.241    547
  Planarity :  0.008   0.051    612
  Dihedral  : 11.145  76.144   1253
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  :  9.86 %
    Favored  : 89.67 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  5.91 %
    Favored  : 93.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -4.58 (0.34), residues: 426
  helix: -3.63 (0.59), residues: 44
  sheet: -2.33 (0.39), residues: 158
  loop : -3.50 (0.32), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP H 113 
 PHE   0.021   0.003   PHE H 110 
 TYR   0.022   0.003   TYR c  62 
 ARG   0.005   0.001   ARG C 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14312 (   99)
  hydrogen bonds       : angle       7.14855 (  264)
  SS BOND              : bond        0.00205 (    1)
  SS BOND              : angle       0.79572 (    2)
  covalent geometry    : bond        0.00675 ( 3457)
  covalent geometry    : angle       1.17757 ( 4709)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 182
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
REVERT: H   41 ARG cc_start: 0.6838 (ptp-170) cc_final: 0.5625 (mmm160)
REVERT: H   55 SER cc_start: 0.9381 (t) cc_final: 0.9087 (t)
REVERT: H   80 ASN cc_start: 0.8341 (p0) cc_final: 0.8121 (p0)
REVERT: H  101 ARG cc_start: 0.8177 (ptm-80) cc_final: 0.7852 (ptt90)
REVERT: H  106 SER cc_start: 0.8089 (t) cc_final: 0.7331 (t)
REVERT: c   13 LYS cc_start: 0.8920 (tppp) cc_final: 0.7829 (tppp)
REVERT: c   27 ASN cc_start: 0.8595 (t0) cc_final: 0.8182 (t0)
REVERT: c   32 VAL cc_start: 0.9273 (t) cc_final: 0.9021 (m)
REVERT: c   34 SER cc_start: 0.9509 (m) cc_final: 0.9063 (t)
REVERT: c   87 GLN cc_start: 0.8429 (mp-120) cc_final: 0.8206 (mm-40)
REVERT: c  100 SER cc_start: 0.9434 (m) cc_final: 0.9150 (p)
REVERT: c  103 GLU cc_start: 0.8355 (tp30) cc_final: 0.8146 (mm-30)
REVERT: c  122 ILE cc_start: 0.9094 (pp) cc_final: 0.8707 (pp)
REVERT: c  123 ASP cc_start: 0.7901 (t70) cc_final: 0.7489 (t0)
REVERT: C   13 LYS cc_start: 0.8795 (tppp) cc_final: 0.8400 (tppp)
REVERT: C   34 SER cc_start: 0.9452 (m) cc_final: 0.9030 (p)
REVERT: C   36 SER cc_start: 0.8738 (p) cc_final: 0.8414 (p)
REVERT: C   91 ASP cc_start: 0.8553 (p0) cc_final: 0.8344 (p0)
REVERT: C  104 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8120 (tm-30)
REVERT: C  122 ILE cc_start: 0.8522 (pp) cc_final: 0.8299 (tt)
REVERT: C  123 ASP cc_start: 0.8563 (t70) cc_final: 0.7670 (t0)
REVERT: C  127 GLN cc_start: 0.9275 (mp10) cc_final: 0.8690 (mp-120)
REVERT: C  129 ASN cc_start: 0.8495 (m-40) cc_final: 0.8094 (m110)
REVERT: L    9 GLN cc_start: 0.8338 (tp-100) cc_final: 0.8105 (mp10)
REVERT: L   13 SER cc_start: 0.7775 (m) cc_final: 0.7295 (p)
REVERT: L   27 ILE cc_start: 0.8314 (tt) cc_final: 0.7936 (tt)
REVERT: L   35 ASP cc_start: 0.7146 (m-30) cc_final: 0.6701 (m-30)
REVERT: L   45 GLU cc_start: 0.8116 (pm20) cc_final: 0.7533 (pm20)
REVERT: L   93 GLN cc_start: 0.8762 (pm20) cc_final: 0.8381 (pm20)
  outliers start: 2
  outliers final: 1
  residues processed: 183
  average time/residue: 0.1846
  time to fit residues: 39.2687
Evaluate side-chains
  140 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   67 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:   20.0000
   chunk 31 optimal weight:    0.7980
   chunk 17 optimal weight:    9.9990
   chunk 10 optimal weight:    2.9990
   chunk 21 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   chunk 12 optimal weight:   10.0000
   chunk 20 optimal weight:    4.9990
   chunk 24 optimal weight:    9.9990
   chunk 38 optimal weight:   10.0000
   chunk 11 optimal weight:    7.9990
   overall best weight:    3.7588

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

Flipped N/Q/H residues before XYZ refinement:
C  10 ASN
C  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.103570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.083702 restraints weight = 7449.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.086181 restraints weight = 3423.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.087689 restraints weight = 2027.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.3415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3458  Z= 0.198
  Angle     :  0.825   9.767   4711  Z= 0.418
  Chirality :  0.049   0.175    547
  Planarity :  0.006   0.052    612
  Dihedral  :  5.709  25.818    483
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 10.09 %
    Favored  : 89.67 %
  Rotamer:
    Outliers :  6.99 %
    Allowed  : 13.98 %
    Favored  : 79.03 %
  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: -4.00 (0.36), residues: 426
  helix: -2.12 (0.69), residues: 46
  sheet: -2.26 (0.40), residues: 151
  loop : -3.10 (0.34), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP H 113 
 PHE   0.015   0.002   PHE L  74 
 TYR   0.017   0.002   TYR L  39 
 ARG   0.003   0.001   ARG H  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03728 (   99)
  hydrogen bonds       : angle       5.86557 (  264)
  SS BOND              : bond        0.00008 (    1)
  SS BOND              : angle       0.56174 (    2)
  covalent geometry    : bond        0.00439 ( 3457)
  covalent geometry    : angle       0.82558 ( 4709)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   41 ARG cc_start: 0.7603 (ptp-170) cc_final: 0.6009 (mmm160)
REVERT: H   45 ARG cc_start: 0.8290 (tpp-160) cc_final: 0.7940 (mmp-170)
REVERT: H   54 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8166 (tp)
REVERT: H   55 SER cc_start: 0.9163 (t) cc_final: 0.8911 (t)
REVERT: H   62 TYR cc_start: 0.7324 (OUTLIER) cc_final: 0.6413 (p90)
REVERT: H   79 LYS cc_start: 0.8774 (mttt) cc_final: 0.8504 (ptmt)
REVERT: H  105 ASP cc_start: 0.8746 (m-30) cc_final: 0.8508 (m-30)
REVERT: H  112 TYR cc_start: 0.8866 (m-80) cc_final: 0.8638 (m-10)
REVERT: c    4 GLU cc_start: 0.7907 (tp30) cc_final: 0.7653 (tp30)
REVERT: c    6 VAL cc_start: 0.9169 (t) cc_final: 0.8950 (p)
REVERT: c   13 LYS cc_start: 0.9256 (tppp) cc_final: 0.8979 (tppp)
REVERT: c   24 ARG cc_start: 0.8584 (ttm-80) cc_final: 0.8040 (mmt180)
REVERT: c   27 ASN cc_start: 0.8833 (t0) cc_final: 0.8277 (t0)
REVERT: c   87 GLN cc_start: 0.8319 (mp-120) cc_final: 0.8050 (mm-40)
REVERT: c  100 SER cc_start: 0.9629 (m) cc_final: 0.9318 (p)
REVERT: c  122 ILE cc_start: 0.9112 (pp) cc_final: 0.8815 (pp)
REVERT: c  123 ASP cc_start: 0.7935 (t70) cc_final: 0.7534 (t0)
REVERT: C   87 GLN cc_start: 0.8969 (mp10) cc_final: 0.8704 (mt0)
REVERT: C   91 ASP cc_start: 0.8802 (p0) cc_final: 0.8598 (p0)
REVERT: C  122 ILE cc_start: 0.8829 (pp) cc_final: 0.8605 (tt)
REVERT: C  123 ASP cc_start: 0.8648 (t70) cc_final: 0.7798 (t0)
REVERT: C  127 GLN cc_start: 0.9350 (mp10) cc_final: 0.8826 (mp-120)
REVERT: C  129 ASN cc_start: 0.8622 (m-40) cc_final: 0.8186 (m110)
REVERT: L    9 GLN cc_start: 0.8241 (tp-100) cc_final: 0.8015 (mp10)
REVERT: L   13 SER cc_start: 0.7450 (m) cc_final: 0.7022 (p)
REVERT: L   45 GLU cc_start: 0.8137 (pm20) cc_final: 0.7569 (pm20)
REVERT: L   70 TYR cc_start: 0.7703 (t80) cc_final: 0.7072 (t80)
REVERT: L   74 PHE cc_start: 0.8603 (m-80) cc_final: 0.8303 (m-10)
REVERT: L   93 GLN cc_start: 0.9007 (pm20) cc_final: 0.8710 (pm20)
  outliers start: 26
  outliers final: 19
  residues processed: 154
  average time/residue: 0.1764
  time to fit residues: 31.8326
Evaluate side-chains
  147 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   60 SER
Chi-restraints excluded: chain H residue   62 TYR
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue  110 PHE
Chi-restraints excluded: chain c residue   41 VAL
Chi-restraints excluded: chain c residue   49 THR
Chi-restraints excluded: chain c residue   53 SER
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain c residue  102 ASP
Chi-restraints excluded: chain c residue  118 SER
Chi-restraints excluded: chain c residue  120 LEU
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue   88 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 41 optimal weight:   10.0000
   chunk 30 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   chunk 25 optimal weight:   10.0000
   chunk 36 optimal weight:    7.9990
   chunk 18 optimal weight:    9.9990
   chunk 10 optimal weight:    8.9990
   overall best weight:    4.9788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.101602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.081102 restraints weight = 7315.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.083471 restraints weight = 3449.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.084928 restraints weight = 2096.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.3931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   3458  Z= 0.243
  Angle     :  0.842  14.099   4711  Z= 0.421
  Chirality :  0.049   0.179    547
  Planarity :  0.005   0.043    612
  Dihedral  :  5.498  23.239    483
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 11.74 %
    Favored  : 88.03 %
  Rotamer:
    Outliers :  6.99 %
    Allowed  : 18.82 %
    Favored  : 74.19 %
  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: -3.90 (0.36), residues: 426
  helix: -1.88 (0.68), residues: 46
  sheet: -2.17 (0.40), residues: 155
  loop : -3.10 (0.34), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP H 113 
 PHE   0.014   0.002   PHE H  53 
 TYR   0.014   0.002   TYR L  89 
 ARG   0.004   0.001   ARG L  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03795 (   99)
  hydrogen bonds       : angle       5.70008 (  264)
  SS BOND              : bond        0.00120 (    1)
  SS BOND              : angle       0.40753 (    2)
  covalent geometry    : bond        0.00552 ( 3457)
  covalent geometry    : angle       0.84207 ( 4709)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 125
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   22 LYS cc_start: 0.8694 (ttmt) cc_final: 0.8418 (ttmm)
REVERT: H   32 PHE cc_start: 0.8951 (t80) cc_final: 0.8714 (t80)
REVERT: H   40 VAL cc_start: 0.8233 (OUTLIER) cc_final: 0.7995 (p)
REVERT: H   41 ARG cc_start: 0.7734 (ptp-170) cc_final: 0.6032 (mmm160)
REVERT: H   53 PHE cc_start: 0.8866 (t80) cc_final: 0.8640 (t80)
REVERT: H   54 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8248 (tp)
REVERT: H   55 SER cc_start: 0.9217 (t) cc_final: 0.8888 (t)
REVERT: H   62 TYR cc_start: 0.7631 (OUTLIER) cc_final: 0.6513 (p90)
REVERT: H   79 LYS cc_start: 0.8765 (mttt) cc_final: 0.8351 (ptmt)
REVERT: H  112 TYR cc_start: 0.8843 (m-80) cc_final: 0.8638 (m-10)
REVERT: c    4 GLU cc_start: 0.8009 (tp30) cc_final: 0.7762 (tp30)
REVERT: c   27 ASN cc_start: 0.8885 (t0) cc_final: 0.8373 (t0)
REVERT: c   70 ASN cc_start: 0.8654 (m-40) cc_final: 0.8294 (m-40)
REVERT: c   87 GLN cc_start: 0.8304 (mp-120) cc_final: 0.7917 (mm-40)
REVERT: c  103 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8066 (mm-30)
REVERT: c  123 ASP cc_start: 0.8155 (t70) cc_final: 0.7720 (t0)
REVERT: C   30 ASN cc_start: 0.9290 (p0) cc_final: 0.9069 (p0)
REVERT: C  122 ILE cc_start: 0.8901 (pp) cc_final: 0.8610 (tt)
REVERT: C  123 ASP cc_start: 0.8727 (t70) cc_final: 0.7889 (t0)
REVERT: C  127 GLN cc_start: 0.9375 (mp10) cc_final: 0.8883 (mp-120)
REVERT: C  129 ASN cc_start: 0.8579 (m-40) cc_final: 0.8006 (m110)
REVERT: L    9 GLN cc_start: 0.8183 (tp-100) cc_final: 0.7973 (mp10)
REVERT: L   13 SER cc_start: 0.7482 (m) cc_final: 0.7007 (p)
REVERT: L   45 GLU cc_start: 0.8231 (pm20) cc_final: 0.7603 (pm20)
  outliers start: 26
  outliers final: 16
  residues processed: 141
  average time/residue: 0.1811
  time to fit residues: 30.1214
Evaluate side-chains
  135 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   62 TYR
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue  110 PHE
Chi-restraints excluded: chain c residue   34 SER
Chi-restraints excluded: chain c residue   41 VAL
Chi-restraints excluded: chain c residue   49 THR
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain c residue   80 CYS
Chi-restraints excluded: chain c residue  118 SER
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain L residue   35 ASP
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue   88 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 36 optimal weight:    8.9990
   chunk 20 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 4 optimal weight:   10.0000
   chunk 6 optimal weight:   20.0000
   chunk 11 optimal weight:    0.4980
   chunk 32 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0570
   overall best weight:    1.9104

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.104756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.083991 restraints weight = 7367.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.086483 restraints weight = 3445.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.088000 restraints weight = 2066.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.4270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3458  Z= 0.139
  Angle     :  0.776  12.920   4711  Z= 0.389
  Chirality :  0.048   0.168    547
  Planarity :  0.005   0.037    612
  Dihedral  :  5.177  23.385    483
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 10.09 %
    Favored  : 89.67 %
  Rotamer:
    Outliers :  7.53 %
    Allowed  : 19.62 %
    Favored  : 72.85 %
  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: -3.47 (0.37), residues: 426
  helix: -1.46 (0.76), residues: 44
  sheet: -1.89 (0.40), residues: 158
  loop : -2.82 (0.36), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H 113 
 PHE   0.007   0.001   PHE H  53 
 TYR   0.013   0.002   TYR L  90 
 ARG   0.003   0.000   ARG C  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03217 (   99)
  hydrogen bonds       : angle       5.44863 (  264)
  SS BOND              : bond        0.00139 (    1)
  SS BOND              : angle       0.35551 (    2)
  covalent geometry    : bond        0.00306 ( 3457)
  covalent geometry    : angle       0.77583 ( 4709)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 123
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   22 LYS cc_start: 0.8736 (ttmt) cc_final: 0.8447 (ttmm)
REVERT: H   40 VAL cc_start: 0.8150 (OUTLIER) cc_final: 0.7943 (p)
REVERT: H   41 ARG cc_start: 0.7749 (ptp-170) cc_final: 0.6070 (mmm160)
REVERT: H   45 ARG cc_start: 0.8461 (tpp-160) cc_final: 0.8104 (mmp-170)
REVERT: H   53 PHE cc_start: 0.8785 (t80) cc_final: 0.8547 (t80)
REVERT: H   55 SER cc_start: 0.9078 (t) cc_final: 0.8640 (t)
REVERT: H   62 TYR cc_start: 0.7580 (OUTLIER) cc_final: 0.5937 (p90)
REVERT: c    4 GLU cc_start: 0.7922 (tp30) cc_final: 0.7693 (tp30)
REVERT: c   27 ASN cc_start: 0.8806 (t0) cc_final: 0.8284 (t0)
REVERT: c   87 GLN cc_start: 0.8269 (mp-120) cc_final: 0.8027 (mm-40)
REVERT: c  123 ASP cc_start: 0.8104 (t70) cc_final: 0.7632 (t0)
REVERT: C  122 ILE cc_start: 0.8800 (pp) cc_final: 0.8565 (tt)
REVERT: C  123 ASP cc_start: 0.8684 (t70) cc_final: 0.7742 (t0)
REVERT: C  127 GLN cc_start: 0.9373 (mp10) cc_final: 0.8908 (mp-120)
REVERT: C  129 ASN cc_start: 0.8606 (m-40) cc_final: 0.8024 (m110)
REVERT: L   13 SER cc_start: 0.7350 (m) cc_final: 0.6924 (p)
REVERT: L   45 GLU cc_start: 0.8152 (pm20) cc_final: 0.7710 (pm20)
REVERT: L   50 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8702 (mm)
REVERT: L   97 MET cc_start: 0.7691 (mmm) cc_final: 0.5356 (mmm)
  outliers start: 28
  outliers final: 18
  residues processed: 140
  average time/residue: 0.1594
  time to fit residues: 26.6599
Evaluate side-chains
  140 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   59 TYR
Chi-restraints excluded: chain H residue   62 TYR
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue  110 PHE
Chi-restraints excluded: chain c residue   34 SER
Chi-restraints excluded: chain c residue   41 VAL
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain c residue  118 SER
Chi-restraints excluded: chain c residue  120 LEU
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain L residue   20 GLU
Chi-restraints excluded: chain L residue   35 ASP
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   57 LEU
Chi-restraints excluded: chain L residue   78 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 11 optimal weight:    7.9990
   chunk 15 optimal weight:    8.9990
   chunk 17 optimal weight:    5.9990
   chunk 26 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 12 optimal weight:    9.9990
   chunk 9 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   overall best weight:    2.9386

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

Flipped N/Q/H residues before XYZ refinement:
C  65 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.102990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.082215 restraints weight = 7448.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.084664 restraints weight = 3516.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.086211 restraints weight = 2131.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.4475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3458  Z= 0.169
  Angle     :  0.785  14.273   4711  Z= 0.392
  Chirality :  0.048   0.163    547
  Planarity :  0.005   0.037    612
  Dihedral  :  5.176  23.279    483
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 12.21 %
    Favored  : 87.56 %
  Rotamer:
    Outliers :  6.72 %
    Allowed  : 22.31 %
    Favored  : 70.97 %
  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: -3.34 (0.37), residues: 426
  helix: -1.32 (0.78), residues: 44
  sheet: -1.75 (0.40), residues: 156
  loop : -2.79 (0.36), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  39 
 PHE   0.017   0.002   PHE c  94 
 TYR   0.008   0.001   TYR L  90 
 ARG   0.002   0.000   ARG C  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03348 (   99)
  hydrogen bonds       : angle       5.38268 (  264)
  SS BOND              : bond        0.00132 (    1)
  SS BOND              : angle       0.34151 (    2)
  covalent geometry    : bond        0.00387 ( 3457)
  covalent geometry    : angle       0.78473 ( 4709)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 122
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   41 ARG cc_start: 0.7679 (ptp-170) cc_final: 0.5997 (mmm160)
REVERT: H   53 PHE cc_start: 0.8892 (t80) cc_final: 0.8605 (t80)
REVERT: H   55 SER cc_start: 0.9124 (t) cc_final: 0.8877 (t)
REVERT: H   62 TYR cc_start: 0.7750 (OUTLIER) cc_final: 0.6099 (p90)
REVERT: c   27 ASN cc_start: 0.8823 (t0) cc_final: 0.8304 (t0)
REVERT: c  123 ASP cc_start: 0.8152 (t70) cc_final: 0.7677 (t0)
REVERT: C  122 ILE cc_start: 0.8929 (pp) cc_final: 0.8610 (tt)
REVERT: C  123 ASP cc_start: 0.8713 (t70) cc_final: 0.7786 (t0)
REVERT: C  127 GLN cc_start: 0.9387 (mp10) cc_final: 0.8928 (mp-120)
REVERT: C  129 ASN cc_start: 0.8663 (m-40) cc_final: 0.8101 (m110)
REVERT: L   13 SER cc_start: 0.7377 (m) cc_final: 0.6936 (p)
REVERT: L   45 GLU cc_start: 0.8236 (pm20) cc_final: 0.7766 (pm20)
REVERT: L   50 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8602 (mm)
REVERT: L   97 MET cc_start: 0.7772 (mmm) cc_final: 0.5301 (mmm)
  outliers start: 25
  outliers final: 19
  residues processed: 135
  average time/residue: 0.1632
  time to fit residues: 26.4340
Evaluate side-chains
  141 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   59 TYR
Chi-restraints excluded: chain H residue   62 TYR
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue  110 PHE
Chi-restraints excluded: chain c residue   34 SER
Chi-restraints excluded: chain c residue   41 VAL
Chi-restraints excluded: chain c residue   49 THR
Chi-restraints excluded: chain c residue   50 VAL
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain c residue  118 SER
Chi-restraints excluded: chain c residue  120 LEU
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain L residue   35 ASP
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue   78 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 3 optimal weight:    7.9990
   chunk 2 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   chunk 39 optimal weight:    6.9990
   chunk 40 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   chunk 18 optimal weight:   10.0000
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
c 129 ASN
L  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.100773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.080242 restraints weight = 7554.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.082651 restraints weight = 3545.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.084187 restraints weight = 2134.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.4783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   3458  Z= 0.219
  Angle     :  0.828  14.211   4711  Z= 0.413
  Chirality :  0.049   0.172    547
  Planarity :  0.005   0.040    612
  Dihedral  :  5.313  22.802    483
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.68 %
    Favored  : 87.32 %
  Rotamer:
    Outliers :  7.26 %
    Allowed  : 22.31 %
    Favored  : 70.43 %
  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: -3.35 (0.37), residues: 426
  helix: -1.33 (0.80), residues: 44
  sheet: -1.92 (0.41), residues: 146
  loop : -2.65 (0.36), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H 113 
 PHE   0.013   0.002   PHE c  94 
 TYR   0.022   0.002   TYR H  35 
 ARG   0.003   0.001   ARG c  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03566 (   99)
  hydrogen bonds       : angle       5.47685 (  264)
  SS BOND              : bond        0.00162 (    1)
  SS BOND              : angle       0.41312 (    2)
  covalent geometry    : bond        0.00498 ( 3457)
  covalent geometry    : angle       0.82843 ( 4709)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 119
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   41 ARG cc_start: 0.7563 (ptp-170) cc_final: 0.5812 (mmm160)
REVERT: c   27 ASN cc_start: 0.8769 (t0) cc_final: 0.8276 (t0)
REVERT: c   87 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7457 (mm-40)
REVERT: c  103 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8366 (mm-30)
REVERT: c  123 ASP cc_start: 0.8156 (t70) cc_final: 0.7686 (t0)
REVERT: C   13 LYS cc_start: 0.8952 (ttmm) cc_final: 0.8561 (ttpt)
REVERT: C  122 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8865 (tt)
REVERT: C  123 ASP cc_start: 0.8770 (t70) cc_final: 0.7862 (t0)
REVERT: C  127 GLN cc_start: 0.9397 (mp10) cc_final: 0.8913 (mp-120)
REVERT: C  129 ASN cc_start: 0.8728 (m-40) cc_final: 0.8175 (m110)
REVERT: L   45 GLU cc_start: 0.8312 (pm20) cc_final: 0.7798 (pm20)
REVERT: L   50 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8572 (mm)
REVERT: L   93 GLN cc_start: 0.8930 (pm20) cc_final: 0.8609 (pm20)
REVERT: L   97 MET cc_start: 0.7655 (mmm) cc_final: 0.7387 (tpt)
  outliers start: 27
  outliers final: 19
  residues processed: 135
  average time/residue: 0.1665
  time to fit residues: 26.7056
Evaluate side-chains
  139 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   59 TYR
Chi-restraints excluded: chain H residue   62 TYR
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue  110 PHE
Chi-restraints excluded: chain c residue   34 SER
Chi-restraints excluded: chain c residue   41 VAL
Chi-restraints excluded: chain c residue   49 THR
Chi-restraints excluded: chain c residue   50 VAL
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain c residue  118 SER
Chi-restraints excluded: chain c residue  120 LEU
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain C residue  122 ILE
Chi-restraints excluded: chain L residue   35 ASP
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue   78 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 14 optimal weight:    8.9990
   chunk 21 optimal weight:   10.0000
   chunk 9 optimal weight:    6.9990
   chunk 28 optimal weight:    0.0770
   chunk 40 optimal weight:    9.9990
   chunk 18 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0030
   chunk 20 optimal weight:    0.9980
   overall best weight:    1.0152

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.103183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.082810 restraints weight = 7468.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.085285 restraints weight = 3463.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.086851 restraints weight = 2050.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.4900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3458  Z= 0.131
  Angle     :  0.791  13.089   4711  Z= 0.391
  Chirality :  0.047   0.156    547
  Planarity :  0.004   0.038    612
  Dihedral  :  5.083  23.133    483
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.86 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  7.26 %
    Allowed  : 23.39 %
    Favored  : 69.35 %
  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: -3.20 (0.38), residues: 426
  helix: -1.38 (0.77), residues: 48
  sheet: -1.70 (0.41), residues: 145
  loop : -2.62 (0.36), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  50 
 PHE   0.011   0.001   PHE c  94 
 TYR   0.021   0.001   TYR H  35 
 ARG   0.002   0.000   ARG C  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03078 (   99)
  hydrogen bonds       : angle       5.29914 (  264)
  SS BOND              : bond        0.00165 (    1)
  SS BOND              : angle       0.32631 (    2)
  covalent geometry    : bond        0.00288 ( 3457)
  covalent geometry    : angle       0.79087 ( 4709)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 131
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   41 ARG cc_start: 0.7448 (ptp-170) cc_final: 0.5778 (mmm160)
REVERT: c   27 ASN cc_start: 0.8695 (t0) cc_final: 0.8181 (t0)
REVERT: c   46 LYS cc_start: 0.9158 (mttp) cc_final: 0.8931 (mttm)
REVERT: c   65 GLN cc_start: 0.7751 (pt0) cc_final: 0.7383 (tt0)
REVERT: c   87 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7543 (mm-40)
REVERT: c  103 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8194 (mm-30)
REVERT: c  122 ILE cc_start: 0.8952 (pp) cc_final: 0.8623 (mm)
REVERT: c  123 ASP cc_start: 0.7920 (t70) cc_final: 0.7362 (t0)
REVERT: C   13 LYS cc_start: 0.8942 (ttmm) cc_final: 0.8455 (ttmt)
REVERT: C  123 ASP cc_start: 0.8729 (t70) cc_final: 0.7744 (t0)
REVERT: C  127 GLN cc_start: 0.9417 (mp10) cc_final: 0.8962 (mp-120)
REVERT: C  129 ASN cc_start: 0.8645 (m-40) cc_final: 0.8072 (m110)
REVERT: L   13 SER cc_start: 0.7250 (m) cc_final: 0.6870 (p)
REVERT: L   45 GLU cc_start: 0.8202 (pm20) cc_final: 0.7719 (pm20)
REVERT: L   50 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8450 (mm)
REVERT: L   97 MET cc_start: 0.7643 (mmm) cc_final: 0.7436 (tpt)
  outliers start: 27
  outliers final: 19
  residues processed: 142
  average time/residue: 0.1606
  time to fit residues: 27.2511
Evaluate side-chains
  144 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   59 TYR
Chi-restraints excluded: chain H residue   62 TYR
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   73 ILE
Chi-restraints excluded: chain H residue  110 PHE
Chi-restraints excluded: chain c residue   34 SER
Chi-restraints excluded: chain c residue   49 THR
Chi-restraints excluded: chain c residue   50 VAL
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain c residue  118 SER
Chi-restraints excluded: chain c residue  120 LEU
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain L residue   35 ASP
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue   78 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9980
   chunk 38 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   chunk 16 optimal weight:   20.0000
   chunk 36 optimal weight:    9.9990
   chunk 7 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   chunk 39 optimal weight:   10.0000
   chunk 34 optimal weight:    4.9990
   overall best weight:    5.1988

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

Flipped N/Q/H residues before XYZ refinement:
c  17 GLN
c  22 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.099687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.079079 restraints weight = 7528.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.081387 restraints weight = 3577.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.082917 restraints weight = 2175.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.5121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   3458  Z= 0.246
  Angle     :  0.841  14.574   4711  Z= 0.420
  Chirality :  0.050   0.167    547
  Planarity :  0.005   0.039    612
  Dihedral  :  5.363  22.699    483
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.62 %
    Favored  : 86.38 %
  Rotamer:
    Outliers :  6.72 %
    Allowed  : 23.12 %
    Favored  : 70.16 %
  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: -3.25 (0.38), residues: 426
  helix: -1.19 (0.80), residues: 44
  sheet: -1.88 (0.41), residues: 147
  loop : -2.58 (0.37), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H 113 
 PHE   0.011   0.002   PHE c  94 
 TYR   0.021   0.002   TYR H  35 
 ARG   0.005   0.001   ARG C  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03663 (   99)
  hydrogen bonds       : angle       5.42659 (  264)
  SS BOND              : bond        0.00231 (    1)
  SS BOND              : angle       0.33202 (    2)
  covalent geometry    : bond        0.00566 ( 3457)
  covalent geometry    : angle       0.84153 ( 4709)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 119
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   41 ARG cc_start: 0.7357 (ptp-170) cc_final: 0.5671 (mmm160)
REVERT: H   79 LYS cc_start: 0.8045 (ttpt) cc_final: 0.7828 (ttpt)
REVERT: c   27 ASN cc_start: 0.8789 (t0) cc_final: 0.8305 (t0)
REVERT: c   69 GLN cc_start: 0.8521 (pt0) cc_final: 0.8290 (pt0)
REVERT: c   87 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7464 (mm-40)
REVERT: c  103 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8312 (mm-30)
REVERT: c  123 ASP cc_start: 0.8077 (t70) cc_final: 0.7614 (t0)
REVERT: C   13 LYS cc_start: 0.8947 (ttmm) cc_final: 0.8279 (ttmt)
REVERT: C  123 ASP cc_start: 0.8798 (t70) cc_final: 0.7932 (t0)
REVERT: C  127 GLN cc_start: 0.9434 (mp10) cc_final: 0.8937 (mp-120)
REVERT: C  129 ASN cc_start: 0.8353 (m-40) cc_final: 0.7806 (m110)
REVERT: L   20 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8304 (pm20)
REVERT: L   45 GLU cc_start: 0.8279 (pm20) cc_final: 0.7618 (pm20)
REVERT: L   50 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8461 (mm)
REVERT: L   93 GLN cc_start: 0.8984 (pm20) cc_final: 0.8736 (pm20)
  outliers start: 25
  outliers final: 22
  residues processed: 134
  average time/residue: 0.1689
  time to fit residues: 27.0115
Evaluate side-chains
  142 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   59 TYR
Chi-restraints excluded: chain H residue   62 TYR
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   73 ILE
Chi-restraints excluded: chain H residue  110 PHE
Chi-restraints excluded: chain c residue    6 VAL
Chi-restraints excluded: chain c residue   34 SER
Chi-restraints excluded: chain c residue   48 VAL
Chi-restraints excluded: chain c residue   49 THR
Chi-restraints excluded: chain c residue   50 VAL
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain c residue  118 SER
Chi-restraints excluded: chain c residue  120 LEU
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain L residue   20 GLU
Chi-restraints excluded: chain L residue   35 ASP
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue   78 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 36 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   chunk 39 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   chunk 41 optimal weight:    9.9990
   chunk 8 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 13 optimal weight:    4.9990
   chunk 34 optimal weight:   10.0000
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
c  17 GLN
L  55 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.097567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.077379 restraints weight = 7596.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.079667 restraints weight = 3574.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.081149 restraints weight = 2158.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.5229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   3458  Z= 0.271
  Angle     :  0.867  14.854   4711  Z= 0.434
  Chirality :  0.051   0.164    547
  Planarity :  0.005   0.041    612
  Dihedral  :  5.505  22.026    483
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 12.68 %
    Favored  : 87.09 %
  Rotamer:
    Outliers :  7.80 %
    Allowed  : 21.77 %
    Favored  : 70.43 %
  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: -3.40 (0.37), residues: 426
  helix: -1.66 (0.73), residues: 48
  sheet: -1.98 (0.42), residues: 140
  loop : -2.61 (0.36), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H 113 
 PHE   0.012   0.002   PHE H  53 
 TYR   0.021   0.002   TYR H  35 
 ARG   0.005   0.001   ARG C  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03801 (   99)
  hydrogen bonds       : angle       5.67761 (  264)
  SS BOND              : bond        0.00291 (    1)
  SS BOND              : angle       0.21632 (    2)
  covalent geometry    : bond        0.00622 ( 3457)
  covalent geometry    : angle       0.86767 ( 4709)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 118
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   41 ARG cc_start: 0.7432 (ptp-170) cc_final: 0.5726 (mmm160)
REVERT: H   62 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.6420 (p90)
REVERT: H   80 ASN cc_start: 0.8038 (p0) cc_final: 0.7771 (p0)
REVERT: c   27 ASN cc_start: 0.8843 (t0) cc_final: 0.8380 (t0)
REVERT: c   87 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7440 (mm-40)
REVERT: c  103 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8246 (mm-30)
REVERT: c  104 GLU cc_start: 0.8673 (pt0) cc_final: 0.8445 (pt0)
REVERT: c  123 ASP cc_start: 0.8158 (t70) cc_final: 0.7670 (t0)
REVERT: C   13 LYS cc_start: 0.9020 (ttmm) cc_final: 0.8029 (ttpt)
REVERT: C   24 ARG cc_start: 0.5260 (OUTLIER) cc_final: 0.3723 (mmt180)
REVERT: C  123 ASP cc_start: 0.8852 (t70) cc_final: 0.7973 (t0)
REVERT: C  127 GLN cc_start: 0.9436 (mp10) cc_final: 0.8890 (mp-120)
REVERT: C  129 ASN cc_start: 0.8681 (m-40) cc_final: 0.8111 (m110)
REVERT: L   45 GLU cc_start: 0.8294 (pm20) cc_final: 0.7784 (pm20)
REVERT: L   50 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8453 (mm)
  outliers start: 29
  outliers final: 24
  residues processed: 135
  average time/residue: 0.1658
  time to fit residues: 26.5463
Evaluate side-chains
  145 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 118
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   59 TYR
Chi-restraints excluded: chain H residue   62 TYR
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   73 ILE
Chi-restraints excluded: chain H residue  110 PHE
Chi-restraints excluded: chain c residue    6 VAL
Chi-restraints excluded: chain c residue   34 SER
Chi-restraints excluded: chain c residue   48 VAL
Chi-restraints excluded: chain c residue   49 THR
Chi-restraints excluded: chain c residue   50 VAL
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain c residue  118 SER
Chi-restraints excluded: chain c residue  120 LEU
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   24 ARG
Chi-restraints excluded: chain C residue   98 GLN
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain L residue   20 GLU
Chi-restraints excluded: chain L residue   35 ASP
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue   88 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 39 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 6 optimal weight:    8.9990
   chunk 23 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 20 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
c  17 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.100773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.080490 restraints weight = 7490.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.082890 restraints weight = 3499.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.084349 restraints weight = 2092.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.5320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3458  Z= 0.161
  Angle     :  0.817  13.908   4711  Z= 0.407
  Chirality :  0.050   0.158    547
  Planarity :  0.005   0.039    612
  Dihedral  :  5.256  21.326    483
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 11.27 %
    Favored  : 88.50 %
  Rotamer:
    Outliers :  6.18 %
    Allowed  : 23.39 %
    Favored  : 70.43 %
  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: -3.25 (0.38), residues: 426
  helix: -1.43 (0.76), residues: 48
  sheet: -1.80 (0.42), residues: 140
  loop : -2.59 (0.36), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H 113 
 PHE   0.008   0.001   PHE c  94 
 TYR   0.016   0.001   TYR H 112 
 ARG   0.004   0.000   ARG C  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03419 (   99)
  hydrogen bonds       : angle       5.48733 (  264)
  SS BOND              : bond        0.00240 (    1)
  SS BOND              : angle       0.29599 (    2)
  covalent geometry    : bond        0.00368 ( 3457)
  covalent geometry    : angle       0.81685 ( 4709)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 125
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   41 ARG cc_start: 0.7584 (ptp-170) cc_final: 0.5788 (mmm160)
REVERT: H   62 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.6356 (p90)
REVERT: H   79 LYS cc_start: 0.8248 (ttpt) cc_final: 0.7995 (ttpt)
REVERT: H   80 ASN cc_start: 0.8001 (p0) cc_final: 0.7778 (p0)
REVERT: c    4 GLU cc_start: 0.7845 (tp30) cc_final: 0.7631 (tp30)
REVERT: c   27 ASN cc_start: 0.8765 (t0) cc_final: 0.8288 (t0)
REVERT: c   87 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7445 (mm-40)
REVERT: c  103 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8324 (mm-30)
REVERT: c  104 GLU cc_start: 0.8567 (pt0) cc_final: 0.8330 (pt0)
REVERT: c  123 ASP cc_start: 0.8117 (t70) cc_final: 0.7604 (t0)
REVERT: c  127 GLN cc_start: 0.9297 (mp10) cc_final: 0.9076 (mp10)
REVERT: C   13 LYS cc_start: 0.8975 (ttmm) cc_final: 0.8565 (ttmm)
REVERT: C  123 ASP cc_start: 0.8785 (t70) cc_final: 0.7842 (t0)
REVERT: C  127 GLN cc_start: 0.9436 (mp10) cc_final: 0.8880 (mp-120)
REVERT: C  129 ASN cc_start: 0.8527 (m-40) cc_final: 0.7972 (m110)
REVERT: L   45 GLU cc_start: 0.8274 (pm20) cc_final: 0.7767 (pm20)
REVERT: L   50 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8381 (mm)
REVERT: L   70 TYR cc_start: 0.7631 (t80) cc_final: 0.7320 (t80)
REVERT: L   74 PHE cc_start: 0.8506 (m-80) cc_final: 0.8226 (m-10)
REVERT: L   93 GLN cc_start: 0.8954 (pm20) cc_final: 0.8739 (pm20)
  outliers start: 23
  outliers final: 20
  residues processed: 138
  average time/residue: 0.1735
  time to fit residues: 28.1554
Evaluate side-chains
  144 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 122
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   59 TYR
Chi-restraints excluded: chain H residue   62 TYR
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue  110 PHE
Chi-restraints excluded: chain c residue   34 SER
Chi-restraints excluded: chain c residue   48 VAL
Chi-restraints excluded: chain c residue   49 THR
Chi-restraints excluded: chain c residue   50 VAL
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain c residue  118 SER
Chi-restraints excluded: chain c residue  120 LEU
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain L residue   35 ASP
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue   88 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 1 optimal weight:    0.0870
   chunk 29 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 24 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   chunk 3 optimal weight:    8.9990
   chunk 22 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 39 optimal weight:    9.9990
   overall best weight:    4.4166

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

Flipped N/Q/H residues before XYZ refinement:
c  17 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.099132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.078905 restraints weight = 7527.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.081236 restraints weight = 3543.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.082743 restraints weight = 2131.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.5348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   3458  Z= 0.222
  Angle     :  0.855  14.575   4711  Z= 0.423
  Chirality :  0.051   0.153    547
  Planarity :  0.005   0.040    612
  Dihedral  :  5.400  21.307    483
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.15 %
    Favored  : 86.85 %
  Rotamer:
    Outliers :  7.80 %
    Allowed  : 21.77 %
    Favored  : 70.43 %
  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: -3.26 (0.37), residues: 426
  helix: -1.48 (0.74), residues: 48
  sheet: -1.82 (0.41), residues: 140
  loop : -2.57 (0.36), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H 113 
 PHE   0.009   0.002   PHE c  94 
 TYR   0.029   0.002   TYR H 112 
 ARG   0.004   0.001   ARG C  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03689 (   99)
  hydrogen bonds       : angle       5.57971 (  264)
  SS BOND              : bond        0.00267 (    1)
  SS BOND              : angle       0.20886 (    2)
  covalent geometry    : bond        0.00514 ( 3457)
  covalent geometry    : angle       0.85564 ( 4709)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1425.97 seconds
wall clock time: 25 minutes 30.99 seconds (1530.99 seconds total)