Starting phenix.real_space_refine
on Wed Jul 23 19:06:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yry_39553/07_2025/8yry_39553.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yry_39553/07_2025/8yry_39553.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yry_39553/07_2025/8yry_39553.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yry_39553/07_2025/8yry_39553.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yry_39553/07_2025/8yry_39553.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yry_39553/07_2025/8yry_39553.cif"
  }
  resolution = 2.93
  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=   0.000 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      18      5.16       5
     C    2551      2.51       5
     N     688      2.21       5
     O     811      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 4068
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 760
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 760
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 5, 'TRANS': 90}
          Chain breaks: 3
    Chain: "H"
      Number of atoms: 1665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1665
          Classifications: {'peptide': 220}
          Link IDs: {'PTRANS': 13, 'TRANS': 206}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "L"
      Number of atoms: 1643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1643
          Classifications: {'peptide': 214}
          Link IDs: {'PTRANS': 12, 'TRANS': 201}
  Time building chain proxies: 3.49, per 1000 atoms: 0.86
  Number of scatterers: 4068
  At special positions: 0
  Unit cell: (111.188, 62.092, 69.312, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      18     16.00
     O     811      8.00
     N     688      7.00
     C    2551      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 156 " - pdb=" SG  CYS A 183 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 186 " - pdb=" SG  CYS A 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 190 " - pdb=" SG  CYS A 202 " distance=2.24
    Simple disulfide: pdb=" SG  CYS H  41 " - pdb=" SG  CYS H 115 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 164 " - pdb=" SG  CYS H 220 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  42 " - pdb=" SG  CYS L 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 153 " - pdb=" SG  CYS L 213 " distance=2.01

  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: 0.84
  Conformation dependent library (CDL) restraints added in 475.4 milliseconds
  

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  982

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 10 sheets defined
      6.4% alpha, 34.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 187 through 191
    Processing helix  chain 'A' and resid 198 through 202
      removed outlier: 4.001A  pdb=" N   CYS A 202 " --> pdb=" O   SER A 199 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 180 through 182
      No H-bonds generated for 'chain 'H' and resid 180 through 182'
    Processing helix  chain 'H' and resid 211 through 213
      No H-bonds generated for 'chain 'H' and resid 211 through 213'
    Processing helix  chain 'L' and resid 98 through 102
      removed outlier: 4.257A  pdb=" N   ILE L 102 " --> pdb=" O   PRO L  99 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 140 through 147
      removed outlier: 3.659A  pdb=" N   LEU L 144 " --> pdb=" O   SER L 140 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   LYS L 145 " --> pdb=" O   ASP L 141 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   SER L 146 " --> pdb=" O   GLU L 142 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 202 through 206
      removed outlier: 3.758A  pdb=" N   GLU L 206 " --> pdb=" O   LYS L 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 202 through 206'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 98
    Processing sheet with id=AA2, first strand: chain 'H' and resid 23 through 26
    Processing sheet with id=AA3, first strand: chain 'H' and resid 30 through 31
      removed outlier: 3.665A  pdb=" N   VAL H  31 " --> pdb=" O   THR H 134 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   TRP H  54 " --> pdb=" O   TYR H  70 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   TYR H  70 " --> pdb=" O   TRP H  54 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   TRP H  56 " --> pdb=" O   MET H  68 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 144 through 148
      removed outlier: 6.191A  pdb=" N   TYR H 200 " --> pdb=" O   ASP H 168 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 144 through 148
      removed outlier: 6.191A  pdb=" N   TYR H 200 " --> pdb=" O   ASP H 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 174 through 178
      removed outlier: 4.678A  pdb=" N   TYR H 218 " --> pdb=" O   VAL H 235 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   THR H 229 " --> pdb=" O   HIS H 224 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 30 through 32
      removed outlier: 5.782A  pdb=" N   LEU L  30 " --> pdb=" O   GLU L 124 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   TRP L  54 " --> pdb=" O   LEU L  66 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 38 through 42
    Processing sheet with id=AA9, first strand: chain 'L' and resid 133 through 137
      removed outlier: 5.796A  pdb=" N   TYR L 192 " --> pdb=" O   ASN L 157 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 163 through 169

    128 hydrogen bonds defined for protein.
    336 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: 0.98

  Time building geometry restraints manager: 1.03 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 711
        1.32 -     1.45: 1124
        1.45 -     1.57: 2304
        1.57 -     1.69: 0
        1.69 -     1.82: 21
  Bond restraints: 4160
  Sorted by residual:
  bond pdb=" N   PRO L 160 "
       pdb=" CD  PRO L 160 "
    ideal  model  delta    sigma   weight residual
    1.473  1.518 -0.045 1.40e-02 5.10e+03 1.02e+01
  bond pdb=" CA  LEU A  77 "
       pdb=" C   LEU A  77 "
    ideal  model  delta    sigma   weight residual
    1.525  1.560 -0.035 1.11e-02 8.12e+03 1.01e+01
  bond pdb=" C   PRO H 143 "
       pdb=" O   PRO H 143 "
    ideal  model  delta    sigma   weight residual
    1.234  1.202  0.032 1.08e-02 8.57e+03 8.60e+00
  bond pdb=" N   VAL L  34 "
       pdb=" CA  VAL L  34 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.19e-02 7.06e+03 7.85e+00
  bond pdb=" N   VAL H 208 "
       pdb=" CA  VAL H 208 "
    ideal  model  delta    sigma   weight residual
    1.462  1.486 -0.024 8.70e-03 1.32e+04 7.56e+00
  ... (remaining 4155 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.51: 5403
        2.51 -     5.01: 199
        5.01 -     7.52: 44
        7.52 -    10.03: 9
       10.03 -    12.53: 1
  Bond angle restraints: 5656
  Sorted by residual:
  angle pdb=" N   GLN A  78 "
        pdb=" CA  GLN A  78 "
        pdb=" C   GLN A  78 "
      ideal   model   delta    sigma   weight residual
     112.89  103.65    9.24 1.24e+00 6.50e-01 5.56e+01
  angle pdb=" N   LEU L 144 "
        pdb=" CA  LEU L 144 "
        pdb=" C   LEU L 144 "
      ideal   model   delta    sigma   weight residual
     111.36  103.43    7.93 1.09e+00 8.42e-01 5.30e+01
  angle pdb=" N   SER H  50 "
        pdb=" CA  SER H  50 "
        pdb=" C   SER H  50 "
      ideal   model   delta    sigma   weight residual
     111.55  102.72    8.83 1.37e+00 5.33e-01 4.15e+01
  angle pdb=" N   SER L  71 "
        pdb=" CA  SER L  71 "
        pdb=" C   SER L  71 "
      ideal   model   delta    sigma   weight residual
     110.80  123.33  -12.53 2.13e+00 2.20e-01 3.46e+01
  angle pdb=" C   PRO L 160 "
        pdb=" CA  PRO L 160 "
        pdb=" CB  PRO L 160 "
      ideal   model   delta    sigma   weight residual
     111.71  119.21   -7.50 1.30e+00 5.92e-01 3.33e+01
  ... (remaining 5651 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.36: 2167
       17.36 -    34.72: 247
       34.72 -    52.08: 67
       52.08 -    69.44: 12
       69.44 -    86.80: 9
  Dihedral angle restraints: 2502
    sinusoidal: 973
      harmonic: 1529
  Sorted by residual:
  dihedral pdb=" CB  CYS L  42 "
           pdb=" SG  CYS L  42 "
           pdb=" SG  CYS L 107 "
           pdb=" CB  CYS L 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.03  -73.03     1      1.00e+01 1.00e-02 6.80e+01
  dihedral pdb=" CB  CYS A 190 "
           pdb=" SG  CYS A 190 "
           pdb=" SG  CYS A 202 "
           pdb=" CB  CYS A 202 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -158.59   72.59     1      1.00e+01 1.00e-02 6.73e+01
  dihedral pdb=" CB  CYS L 153 "
           pdb=" SG  CYS L 153 "
           pdb=" SG  CYS L 213 "
           pdb=" CB  CYS L 213 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -133.83   47.83     1      1.00e+01 1.00e-02 3.16e+01
  ... (remaining 2499 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 505
       0.072 -    0.144: 105
       0.144 -    0.216: 15
       0.216 -    0.288: 9
       0.288 -    0.360: 3
  Chirality restraints: 637
  Sorted by residual:
  chirality pdb=" CA  SER L  71 "
            pdb=" N   SER L  71 "
            pdb=" C   SER L  71 "
            pdb=" CB  SER L  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.24e+00
  chirality pdb=" CA  TYR L 159 "
            pdb=" N   TYR L 159 "
            pdb=" C   TYR L 159 "
            pdb=" CB  TYR L 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.67e+00
  chirality pdb=" CA  SER L  26 "
            pdb=" N   SER L  26 "
            pdb=" C   SER L  26 "
            pdb=" CB  SER L  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.47e+00
  ... (remaining 634 not shown)

  Planarity restraints: 724
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO L  27 "   -0.013 2.00e-02 2.50e+03   2.64e-02 6.95e+00
        pdb=" C   PRO L  27 "    0.046 2.00e-02 2.50e+03
        pdb=" O   PRO L  27 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   SER L  28 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU L 113 "    0.038 5.00e-02 4.00e+02   5.73e-02 5.26e+00
        pdb=" N   PRO L 114 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO L 114 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO L 114 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR L 159 "   -0.027 2.00e-02 2.50e+03   1.43e-02 4.09e+00
        pdb=" CG  TYR L 159 "    0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR L 159 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR L 159 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR L 159 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR L 159 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR L 159 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR L 159 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 721 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 549
        2.75 -     3.29: 3862
        3.29 -     3.83: 6646
        3.83 -     4.36: 7991
        4.36 -     4.90: 13722
  Nonbonded interactions: 32770
  Sorted by model distance:
  nonbonded pdb=" O   ALA L  44 "
            pdb=" OG  SER L  45 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   ASP H 122 "
            pdb=" OD1 ASP H 122 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   ILE L 125 "
            pdb=" OH  TYR L 159 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   ARG A 132 "
            pdb=" OH  TYR H 121 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   TYR H  73 "
            pdb=" NH1 ARG H  91 "
     model   vdw
     2.253 3.120
  ... (remaining 32765 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 individual isotropic
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:             3.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     13.920
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:14.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6708
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      :  0.006   0.212   4167  Z= 0.341
  Angle     :  1.109  12.533   5670  Z= 0.692
  Chirality :  0.068   0.360    637
  Planarity :  0.005   0.057    724
  Dihedral  : 16.466  86.803   1499
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 21.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.11 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 24.68 %
    Favored  : 73.18 %
  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: -1.92 (0.36), residues: 518
  helix: -5.62 (0.35), residues: 7
  sheet:  0.14 (0.37), residues: 184
  loop : -2.17 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP H 127 
 HIS   0.004   0.001   HIS H 188 
 PHE   0.020   0.002   PHE L 158 
 TYR   0.027   0.002   TYR L 159 
 ARG   0.004   0.000   ARG H  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15911 (  113)
  hydrogen bonds       : angle       8.71559 (  336)
  SS BOND              : bond        0.08073 (    7)
  SS BOND              : angle       1.41779 (   14)
  covalent geometry    : bond        0.00460 ( 4160)
  covalent geometry    : angle       1.10807 ( 5656)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
REVERT: H  131 THR cc_start: 0.5655 (p) cc_final: 0.5165 (t)
REVERT: H  238 LYS cc_start: 0.4852 (mttm) cc_final: 0.4222 (ptpp)
  outliers start: 10
  outliers final: 5
  residues processed: 58
  average time/residue: 1.0098
  time to fit residues: 61.0753
Evaluate side-chains
  51 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  174 VAL
Chi-restraints excluded: chain H residue  205 VAL
Chi-restraints excluded: chain H residue  219 ILE
Chi-restraints excluded: chain L residue  180 GLU
Chi-restraints excluded: chain L residue  190 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 133 GLN
** H 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  46 GLN
L 109 GLN
** L 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.211839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.186744 restraints weight = 4560.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.4243 rms_B_bonded: 1.95
r_work: 0.4168 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.4055 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.4055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6770
moved from start:          0.1433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4167  Z= 0.154
  Angle     :  0.668   6.622   5670  Z= 0.341
  Chirality :  0.046   0.186    637
  Planarity :  0.005   0.039    724
  Dihedral  :  6.484  50.608    573
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.30 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 24.03 %
    Favored  : 71.24 %
  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: -1.64 (0.37), residues: 518
  helix: -5.67 (0.31), residues: 7
  sheet:  0.20 (0.37), residues: 196
  loop : -1.94 (0.35), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H 178 
 HIS   0.004   0.001   HIS H 188 
 PHE   0.012   0.002   PHE H 124 
 TYR   0.015   0.002   TYR L  90 
 ARG   0.005   0.001   ARG H  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03174 (  113)
  hydrogen bonds       : angle       6.44836 (  336)
  SS BOND              : bond        0.00251 (    7)
  SS BOND              : angle       0.79587 (   14)
  covalent geometry    : bond        0.00347 ( 4160)
  covalent geometry    : angle       0.66765 ( 5656)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 48
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
REVERT: A  195 TRP cc_start: 0.7043 (m100) cc_final: 0.6728 (m100)
REVERT: H   24 GLN cc_start: 0.6322 (tp-100) cc_final: 0.6065 (tp-100)
REVERT: H  131 THR cc_start: 0.5743 (p) cc_final: 0.5279 (t)
REVERT: H  219 ILE cc_start: 0.7078 (OUTLIER) cc_final: 0.6426 (pp)
REVERT: H  238 LYS cc_start: 0.5048 (mttm) cc_final: 0.3911 (mtmm)
REVERT: L  109 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7148 (pt0)
  outliers start: 22
  outliers final: 7
  residues processed: 66
  average time/residue: 1.0848
  time to fit residues: 75.1343
Evaluate side-chains
  54 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain H residue  174 VAL
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain H residue  217 THR
Chi-restraints excluded: chain H residue  219 ILE
Chi-restraints excluded: chain L residue   24 THR
Chi-restraints excluded: chain L residue   50 ASN
Chi-restraints excluded: chain L residue   98 GLN
Chi-restraints excluded: chain L residue  109 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 22 optimal weight:    0.0970
   chunk 25 optimal weight:    5.9990
   chunk 16 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 28 optimal weight:    0.3980
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 143 GLN
** L 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.213116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.187545 restraints weight = 4590.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.4248 rms_B_bonded: 1.99
r_work: 0.4169 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.4051 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.4051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6766
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4167  Z= 0.136
  Angle     :  0.639   6.597   5670  Z= 0.325
  Chirality :  0.045   0.189    637
  Planarity :  0.004   0.036    724
  Dihedral  :  5.938  48.439    568
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.69 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 24.46 %
    Favored  : 70.60 %
  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: -1.53 (0.37), residues: 518
  helix: -5.66 (0.31), residues: 7
  sheet:  0.42 (0.38), residues: 191
  loop : -1.94 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP H 127 
 HIS   0.004   0.001   HIS H 188 
 PHE   0.009   0.001   PHE A  76 
 TYR   0.013   0.002   TYR L  90 
 ARG   0.003   0.000   ARG H  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03003 (  113)
  hydrogen bonds       : angle       6.09580 (  336)
  SS BOND              : bond        0.00229 (    7)
  SS BOND              : angle       0.64912 (   14)
  covalent geometry    : bond        0.00304 ( 4160)
  covalent geometry    : angle       0.63875 ( 5656)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 48
  time to evaluate  : 0.426 
Fit side-chains
REVERT: H   24 GLN cc_start: 0.6421 (tp-100) cc_final: 0.6216 (tp40)
REVERT: H  131 THR cc_start: 0.5770 (p) cc_final: 0.5401 (t)
REVERT: H  219 ILE cc_start: 0.7046 (OUTLIER) cc_final: 0.6783 (pp)
REVERT: H  238 LYS cc_start: 0.5158 (mttm) cc_final: 0.3952 (mtmm)
REVERT: L  109 GLN cc_start: 0.8139 (pp30) cc_final: 0.7257 (pt0)
REVERT: L  145 LYS cc_start: 0.7298 (mmtp) cc_final: 0.7064 (mptt)
  outliers start: 23
  outliers final: 12
  residues processed: 66
  average time/residue: 0.8430
  time to fit residues: 58.7267
Evaluate side-chains
  57 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 44
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain H residue   55 ASN
Chi-restraints excluded: chain H residue  162 LEU
Chi-restraints excluded: chain H residue  174 VAL
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain H residue  217 THR
Chi-restraints excluded: chain H residue  219 ILE
Chi-restraints excluded: chain L residue   24 THR
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   50 ASN
Chi-restraints excluded: chain L residue   84 SER
Chi-restraints excluded: chain L residue   98 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 23 optimal weight:    8.9990
   chunk 28 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 129 GLN
** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 221 ASN
L  46 GLN
** L 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.199649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.173703 restraints weight = 4744.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.4067 rms_B_bonded: 1.97
r_work: 0.3992 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3877 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7005
moved from start:          0.2721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.063   4167  Z= 0.311
  Angle     :  0.837   9.580   5670  Z= 0.436
  Chirality :  0.052   0.168    637
  Planarity :  0.006   0.047    724
  Dihedral  :  7.182  50.879    568
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 16.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.04 %
    Favored  : 89.96 %
  Rotamer:
    Outliers :  6.22 %
    Allowed  : 25.11 %
    Favored  : 68.67 %
  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: -1.84 (0.36), residues: 518
  helix: -5.65 (0.31), residues: 7
  sheet:  0.18 (0.38), residues: 191
  loop : -2.14 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.004   TRP H 127 
 HIS   0.009   0.002   HIS A 129 
 PHE   0.025   0.003   PHE L 158 
 TYR   0.019   0.003   TYR L 159 
 ARG   0.005   0.001   ARG H  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04164 (  113)
  hydrogen bonds       : angle       7.24339 (  336)
  SS BOND              : bond        0.00600 (    7)
  SS BOND              : angle       1.04061 (   14)
  covalent geometry    : bond        0.00713 ( 4160)
  covalent geometry    : angle       0.83660 ( 5656)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 50
  time to evaluate  : 0.433 
Fit side-chains
REVERT: H  100 LEU cc_start: 0.5497 (OUTLIER) cc_final: 0.4721 (tp)
REVERT: H  219 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7045 (mm)
REVERT: H  238 LYS cc_start: 0.5143 (mttm) cc_final: 0.3636 (mtmm)
  outliers start: 29
  outliers final: 13
  residues processed: 72
  average time/residue: 1.1632
  time to fit residues: 87.9348
Evaluate side-chains
  60 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 45
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain H residue  100 LEU
Chi-restraints excluded: chain H residue  174 VAL
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain H residue  217 THR
Chi-restraints excluded: chain H residue  219 ILE
Chi-restraints excluded: chain L residue   24 THR
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   50 ASN
Chi-restraints excluded: chain L residue   84 SER
Chi-restraints excluded: chain L residue   93 THR
Chi-restraints excluded: chain L residue   98 GLN
Chi-restraints excluded: chain L residue  197 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9990
   chunk 8 optimal weight:    0.4980
   chunk 29 optimal weight:    0.9990
   chunk 22 optimal weight:    8.9990
   chunk 18 optimal weight:    0.7980
   chunk 49 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  53 ASN
** L 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.206762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.180795 restraints weight = 4748.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.4137 rms_B_bonded: 2.06
r_work: 0.4063 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3943 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6852
moved from start:          0.2622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4167  Z= 0.152
  Angle     :  0.662   7.047   5670  Z= 0.340
  Chirality :  0.046   0.172    637
  Planarity :  0.005   0.048    724
  Dihedral  :  5.876  33.009    568
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.30 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 28.11 %
    Favored  : 66.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.58 (0.37), residues: 518
  helix: -5.65 (0.31), residues: 7
  sheet:  0.30 (0.39), residues: 189
  loop : -1.91 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP H 127 
 HIS   0.003   0.001   HIS A 129 
 PHE   0.012   0.002   PHE H 124 
 TYR   0.013   0.002   TYR L  90 
 ARG   0.003   0.000   ARG H  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03196 (  113)
  hydrogen bonds       : angle       6.22229 (  336)
  SS BOND              : bond        0.00237 (    7)
  SS BOND              : angle       0.80547 (   14)
  covalent geometry    : bond        0.00343 ( 4160)
  covalent geometry    : angle       0.66210 ( 5656)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 45
  time to evaluate  : 0.458 
Fit side-chains
REVERT: H   57 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.7245 (mt)
REVERT: H  238 LYS cc_start: 0.5120 (mttm) cc_final: 0.3728 (mtmm)
REVERT: L  109 GLN cc_start: 0.8436 (pp30) cc_final: 0.8159 (pm20)
REVERT: L  180 GLU cc_start: 0.6041 (mp0) cc_final: 0.5838 (mp0)
  outliers start: 25
  outliers final: 12
  residues processed: 65
  average time/residue: 0.7539
  time to fit residues: 51.7958
Evaluate side-chains
  56 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain H residue   55 ASN
Chi-restraints excluded: chain H residue   57 ILE
Chi-restraints excluded: chain H residue  174 VAL
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain H residue  217 THR
Chi-restraints excluded: chain L residue   24 THR
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   50 ASN
Chi-restraints excluded: chain L residue   84 SER
Chi-restraints excluded: chain L residue   88 THR
Chi-restraints excluded: chain L residue   93 THR
Chi-restraints excluded: chain L residue   98 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0270
   chunk 43 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0770
   chunk 51 optimal weight:    2.9990
   chunk 26 optimal weight:    0.4980
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  53 ASN
** L 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.213619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.188676 restraints weight = 4578.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.4222 rms_B_bonded: 1.98
r_work: 0.4146 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.4027 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.4027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6792
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4167  Z= 0.126
  Angle     :  0.616   6.710   5670  Z= 0.314
  Chirality :  0.044   0.132    637
  Planarity :  0.004   0.047    724
  Dihedral  :  5.329  30.172    566
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 29.18 %
    Favored  : 66.74 %
  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: -1.37 (0.38), residues: 518
  helix: -5.65 (0.31), residues: 7
  sheet:  0.37 (0.39), residues: 190
  loop : -1.70 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP H 127 
 HIS   0.002   0.001   HIS A 157 
 PHE   0.011   0.001   PHE H 124 
 TYR   0.011   0.002   TYR L 159 
 ARG   0.002   0.000   ARG H  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02878 (  113)
  hydrogen bonds       : angle       5.73028 (  336)
  SS BOND              : bond        0.00173 (    7)
  SS BOND              : angle       0.67078 (   14)
  covalent geometry    : bond        0.00287 ( 4160)
  covalent geometry    : angle       0.61560 ( 5656)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 48
  time to evaluate  : 0.407 
Fit side-chains
REVERT: H   57 ILE cc_start: 0.7377 (OUTLIER) cc_final: 0.7157 (mt)
REVERT: H   63 LYS cc_start: 0.6781 (tppp) cc_final: 0.6506 (ttmt)
REVERT: H  238 LYS cc_start: 0.5189 (mttm) cc_final: 0.3879 (mtmm)
  outliers start: 19
  outliers final: 11
  residues processed: 60
  average time/residue: 0.8543
  time to fit residues: 54.2100
Evaluate side-chains
  54 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain H residue   57 ILE
Chi-restraints excluded: chain H residue  174 VAL
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain H residue  217 THR
Chi-restraints excluded: chain L residue   24 THR
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   50 ASN
Chi-restraints excluded: chain L residue   84 SER
Chi-restraints excluded: chain L residue   98 GLN
Chi-restraints excluded: chain L residue  202 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    5.9990
   chunk 4 optimal weight:    6.9990
   chunk 23 optimal weight:    8.9990
   chunk 35 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 27 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 221 ASN
L  53 ASN
L 174 GLN
** L 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.202342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.175741 restraints weight = 4724.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.4087 rms_B_bonded: 2.04
r_work: 0.4011 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3896 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6954
moved from start:          0.3060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   4167  Z= 0.231
  Angle     :  0.736   8.307   5670  Z= 0.378
  Chirality :  0.048   0.146    637
  Planarity :  0.005   0.047    724
  Dihedral  :  6.069  34.973    566
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.88 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 28.97 %
    Favored  : 65.45 %
  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: -1.58 (0.37), residues: 518
  helix: -5.64 (0.32), residues: 7
  sheet:  0.19 (0.38), residues: 189
  loop : -1.82 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H 127 
 HIS   0.006   0.001   HIS A 129 
 PHE   0.018   0.002   PHE H 124 
 TYR   0.016   0.003   TYR L 159 
 ARG   0.004   0.001   ARG H  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03546 (  113)
  hydrogen bonds       : angle       6.44154 (  336)
  SS BOND              : bond        0.00335 (    7)
  SS BOND              : angle       0.78664 (   14)
  covalent geometry    : bond        0.00528 ( 4160)
  covalent geometry    : angle       0.73599 ( 5656)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 46
  time to evaluate  : 0.403 
Fit side-chains
REVERT: H   57 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.7217 (mt)
REVERT: H  100 LEU cc_start: 0.5366 (OUTLIER) cc_final: 0.5034 (tp)
REVERT: H  238 LYS cc_start: 0.5203 (mttm) cc_final: 0.3815 (mtmm)
  outliers start: 26
  outliers final: 18
  residues processed: 64
  average time/residue: 0.9420
  time to fit residues: 64.1982
Evaluate side-chains
  64 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 44
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain H residue   55 ASN
Chi-restraints excluded: chain H residue   57 ILE
Chi-restraints excluded: chain H residue  100 LEU
Chi-restraints excluded: chain H residue  174 VAL
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain H residue  196 SER
Chi-restraints excluded: chain H residue  207 THR
Chi-restraints excluded: chain H residue  217 THR
Chi-restraints excluded: chain L residue   24 THR
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   50 ASN
Chi-restraints excluded: chain L residue   84 SER
Chi-restraints excluded: chain L residue   88 THR
Chi-restraints excluded: chain L residue   93 THR
Chi-restraints excluded: chain L residue   98 GLN
Chi-restraints excluded: chain L residue  174 GLN
Chi-restraints excluded: chain L residue  202 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 29 optimal weight:    0.0870
   chunk 37 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 18 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 31 optimal weight:    0.3980
   chunk 9 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.5560

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  53 ASN
L 174 GLN
** L 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.211406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.185999 restraints weight = 4554.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.4193 rms_B_bonded: 2.00
r_work: 0.4116 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.4003 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.4003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6825
moved from start:          0.3004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4167  Z= 0.133
  Angle     :  0.639   6.955   5670  Z= 0.325
  Chirality :  0.045   0.129    637
  Planarity :  0.005   0.048    724
  Dihedral  :  5.469  31.845    566
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.14 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 29.40 %
    Favored  : 65.45 %
  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: -1.43 (0.37), residues: 518
  helix: -5.64 (0.32), residues: 7
  sheet:  0.20 (0.38), residues: 189
  loop : -1.63 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP H 127 
 HIS   0.003   0.001   HIS A 129 
 PHE   0.010   0.001   PHE H 124 
 TYR   0.013   0.002   TYR H 200 
 ARG   0.003   0.000   ARG H  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02977 (  113)
  hydrogen bonds       : angle       5.84296 (  336)
  SS BOND              : bond        0.00178 (    7)
  SS BOND              : angle       0.59840 (   14)
  covalent geometry    : bond        0.00303 ( 4160)
  covalent geometry    : angle       0.63904 ( 5656)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 45
  time to evaluate  : 0.458 
Fit side-chains
REVERT: H   57 ILE cc_start: 0.7387 (OUTLIER) cc_final: 0.7144 (mt)
REVERT: H  238 LYS cc_start: 0.5162 (mttm) cc_final: 0.3853 (mtmm)
  outliers start: 24
  outliers final: 15
  residues processed: 62
  average time/residue: 0.7929
  time to fit residues: 51.9432
Evaluate side-chains
  59 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 43
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain H residue   55 ASN
Chi-restraints excluded: chain H residue   57 ILE
Chi-restraints excluded: chain H residue  174 VAL
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain H residue  196 SER
Chi-restraints excluded: chain H residue  217 THR
Chi-restraints excluded: chain L residue   24 THR
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   50 ASN
Chi-restraints excluded: chain L residue   84 SER
Chi-restraints excluded: chain L residue   88 THR
Chi-restraints excluded: chain L residue   98 GLN
Chi-restraints excluded: chain L residue  174 GLN
Chi-restraints excluded: chain L residue  202 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 39 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0670
   chunk 42 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0870
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.5096

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  22 GLN
** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  53 ASN
L 174 GLN
** L 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.209305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.184307 restraints weight = 4605.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.4172 rms_B_bonded: 1.94
r_work: 0.4098 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3983 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6819
moved from start:          0.3048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4167  Z= 0.129
  Angle     :  0.629   6.997   5670  Z= 0.319
  Chirality :  0.045   0.134    637
  Planarity :  0.004   0.048    724
  Dihedral  :  5.346  30.852    566
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.72 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 30.69 %
    Favored  : 65.24 %
  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: -1.35 (0.38), residues: 518
  helix: -5.63 (0.32), residues: 7
  sheet:  0.15 (0.38), residues: 190
  loop : -1.51 (0.36), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP H 127 
 HIS   0.002   0.001   HIS A 129 
 PHE   0.012   0.001   PHE H 124 
 TYR   0.013   0.002   TYR L 159 
 ARG   0.003   0.000   ARG H  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02886 (  113)
  hydrogen bonds       : angle       5.70484 (  336)
  SS BOND              : bond        0.00180 (    7)
  SS BOND              : angle       0.59396 (   14)
  covalent geometry    : bond        0.00293 ( 4160)
  covalent geometry    : angle       0.62902 ( 5656)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 46
  time to evaluate  : 0.373 
Fit side-chains
REVERT: H   57 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.7193 (mt)
REVERT: H  238 LYS cc_start: 0.5180 (mttm) cc_final: 0.3938 (mtmm)
  outliers start: 19
  outliers final: 14
  residues processed: 59
  average time/residue: 1.1965
  time to fit residues: 74.1664
Evaluate side-chains
  58 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 43
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain H residue   55 ASN
Chi-restraints excluded: chain H residue   57 ILE
Chi-restraints excluded: chain H residue  174 VAL
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain H residue  196 SER
Chi-restraints excluded: chain H residue  217 THR
Chi-restraints excluded: chain L residue   24 THR
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   50 ASN
Chi-restraints excluded: chain L residue   84 SER
Chi-restraints excluded: chain L residue   88 THR
Chi-restraints excluded: chain L residue   98 GLN
Chi-restraints excluded: chain L residue  174 GLN
Chi-restraints excluded: chain L residue  202 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 25 optimal weight:    6.9990
   chunk 30 optimal weight:    0.3980
   chunk 46 optimal weight:    0.0050
   chunk 2 optimal weight:    9.9990
   chunk 18 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 221 ASN
L  53 ASN
L 174 GLN
** L 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.209813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.184601 restraints weight = 4579.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.4186 rms_B_bonded: 1.95
r_work: 0.4107 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3993 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6821
moved from start:          0.3076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4167  Z= 0.130
  Angle     :  0.650  11.473   5670  Z= 0.323
  Chirality :  0.045   0.133    637
  Planarity :  0.004   0.048    724
  Dihedral  :  5.298  31.237    566
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.72 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 31.33 %
    Favored  : 64.38 %
  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: -1.32 (0.38), residues: 518
  helix: -5.63 (0.33), residues: 7
  sheet:  0.12 (0.38), residues: 190
  loop : -1.45 (0.36), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP H 127 
 HIS   0.002   0.001   HIS A 129 
 PHE   0.012   0.001   PHE H 124 
 TYR   0.012   0.002   TYR L 159 
 ARG   0.003   0.000   ARG H  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02839 (  113)
  hydrogen bonds       : angle       5.66434 (  336)
  SS BOND              : bond        0.00200 (    7)
  SS BOND              : angle       0.56325 (   14)
  covalent geometry    : bond        0.00296 ( 4160)
  covalent geometry    : angle       0.65032 ( 5656)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 46
  time to evaluate  : 0.823 
Fit side-chains
REVERT: H   57 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.7185 (mt)
REVERT: H  238 LYS cc_start: 0.5176 (mttm) cc_final: 0.3954 (mtmm)
  outliers start: 20
  outliers final: 14
  residues processed: 60
  average time/residue: 1.4784
  time to fit residues: 93.0410
Evaluate side-chains
  61 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 46
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain H residue   55 ASN
Chi-restraints excluded: chain H residue   57 ILE
Chi-restraints excluded: chain H residue  174 VAL
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain H residue  217 THR
Chi-restraints excluded: chain L residue   24 THR
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   50 ASN
Chi-restraints excluded: chain L residue   84 SER
Chi-restraints excluded: chain L residue   88 THR
Chi-restraints excluded: chain L residue   98 GLN
Chi-restraints excluded: chain L residue  174 GLN
Chi-restraints excluded: chain L residue  202 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0040
   chunk 42 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0170
   chunk 34 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 21 optimal weight:    0.2980
   chunk 51 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.4432

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  53 ASN
L 174 GLN
** L 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.211176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.186245 restraints weight = 4614.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.4233 rms_B_bonded: 1.95
r_work: 0.4154 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.4038 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.4038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6788
moved from start:          0.3123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4167  Z= 0.122
  Angle     :  0.642  11.282   5670  Z= 0.319
  Chirality :  0.045   0.136    637
  Planarity :  0.004   0.048    724
  Dihedral  :  5.191  30.062    566
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.34 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 32.40 %
    Favored  : 63.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.38), residues: 518
  helix: -5.62 (0.33), residues: 7
  sheet:  0.16 (0.38), residues: 190
  loop : -1.42 (0.36), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP H 127 
 HIS   0.002   0.001   HIS A 129 
 PHE   0.012   0.001   PHE H 124 
 TYR   0.012   0.002   TYR L 159 
 ARG   0.003   0.000   ARG H  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02761 (  113)
  hydrogen bonds       : angle       5.57276 (  336)
  SS BOND              : bond        0.00157 (    7)
  SS BOND              : angle       0.57945 (   14)
  covalent geometry    : bond        0.00278 ( 4160)
  covalent geometry    : angle       0.64196 ( 5656)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3968.53 seconds
wall clock time: 72 minutes 6.89 seconds (4326.89 seconds total)