Starting phenix.real_space_refine
on Tue Feb  3 18:50:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lry_63347/02_2026/9lry_63347.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lry_63347/02_2026/9lry_63347.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lry_63347/02_2026/9lry_63347.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lry_63347/02_2026/9lry_63347.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lry_63347/02_2026/9lry_63347.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lry_63347/02_2026/9lry_63347.cif"
  }
  resolution = 2.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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      26      5.16       5
     C    3901      2.51       5
     N    1097      2.21       5
     O    1184      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6208
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2166
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 279, 2166
          Classifications: {'peptide': 279}
          Link IDs: {'PTRANS': 2, 'TRANS': 276}
    Chain: "C"
      Number of atoms: 1846
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1846
          Classifications: {'peptide': 225}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 213}
    Chain: "B"
      Number of atoms: 2196
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 2196
          Classifications: {'peptide': 257}
          Link IDs: {'PTRANS': 9, 'TRANS': 247}
          Chain breaks: 1
  Time building chain proxies: 1.23, per 1000 atoms: 0.20
  Number of scatterers: 6208
  At special positions: 0
  Unit cell: (97.18, 118.65, 168.37, 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      26     16.00
     O    1184      8.00
     N    1097      7.00
     C    3901      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.33
  Conformation dependent library (CDL) restraints added in 235.9 milliseconds
  

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1462

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 3 sheets defined
      64.8% alpha, 8.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
    Processing helix  chain 'A' and resid 42 through 98
      removed outlier: 3.506A  pdb=" N   LEU A  80 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   GLU A  82 " --> pdb=" O   GLY A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 128
      removed outlier: 3.780A  pdb=" N   GLU A 113 " --> pdb=" O   GLN A 109 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLN A 116 " --> pdb=" O   VAL A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 243
      removed outlier: 3.842A  pdb=" N   GLY A 197 " --> pdb=" O   ASN A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 274
      removed outlier: 3.546A  pdb=" N   THR A 251 " --> pdb=" O   ALA A 247 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   SER A 274 " --> pdb=" O   ALA A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 279
      removed outlier: 3.747A  pdb=" N   ARG A 279 " --> pdb=" O   SER A 276 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 18 through 25
    Processing helix  chain 'C' and resid 26 through 31
      removed outlier: 3.558A  pdb=" N   LYS C  31 " --> pdb=" O   VAL C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 50 through 53
      removed outlier: 3.662A  pdb=" N   GLU C  53 " --> pdb=" O   ALA C  50 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 50 through 53'
    Processing helix  chain 'C' and resid 83 through 87
    Processing helix  chain 'C' and resid 150 through 152
      No H-bonds generated for 'chain 'C' and resid 150 through 152'
    Processing helix  chain 'C' and resid 183 through 185
      No H-bonds generated for 'chain 'C' and resid 183 through 185'
    Processing helix  chain 'C' and resid 192 through 201
    Processing helix  chain 'C' and resid 201 through 237
      removed outlier: 3.918A  pdb=" N   SER C 224 " --> pdb=" O   ASN C 220 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 238 through 241
      removed outlier: 3.767A  pdb=" N   TYR C 241 " --> pdb=" O   SER C 238 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 238 through 241'
    Processing helix  chain 'B' and resid 25 through 42
    Processing helix  chain 'B' and resid 51 through 57
      removed outlier: 4.622A  pdb=" N   GLN B  55 " --> pdb=" O   ASN B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 60
      No H-bonds generated for 'chain 'B' and resid 58 through 60'
    Processing helix  chain 'B' and resid 61 through 100
    Processing helix  chain 'B' and resid 107 through 146
      removed outlier: 3.848A  pdb=" N   GLU B 146 " --> pdb=" O   ASN B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 154
    Processing helix  chain 'B' and resid 155 through 176
    Processing helix  chain 'B' and resid 181 through 190
      removed outlier: 4.477A  pdb=" N   ILE B 185 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 197
    Processing helix  chain 'B' and resid 198 through 220
      removed outlier: 3.895A  pdb=" N   HIS B 202 " --> pdb=" O   GLU B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 246
    Processing helix  chain 'B' and resid 249 through 263
    Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 130
    Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 152
      removed outlier: 4.404A  pdb=" N   MET A 149 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 55 through 57

    428 hydrogen bonds defined for protein.
    1251 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: 0.96

  Time building geometry restraints manager: 0.45 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2081
        1.34 -     1.46: 1317
        1.46 -     1.58: 2872
        1.58 -     1.70: 0
        1.70 -     1.81: 49
  Bond restraints: 6319
  Sorted by residual:
  bond pdb=" CB  LYS C  21 "
       pdb=" CG  LYS C  21 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 1.01e+00
  bond pdb=" CB  GLU A 105 "
       pdb=" CG  GLU A 105 "
    ideal  model  delta    sigma   weight residual
    1.520  1.546 -0.026 3.00e-02 1.11e+03 7.74e-01
  bond pdb=" CA  PHE C 201 "
       pdb=" C   PHE C 201 "
    ideal  model  delta    sigma   weight residual
    1.527  1.516  0.010 1.21e-02 6.83e+03 7.36e-01
  bond pdb=" CB  GLU B 146 "
       pdb=" CG  GLU B 146 "
    ideal  model  delta    sigma   weight residual
    1.520  1.496  0.024 3.00e-02 1.11e+03 6.63e-01
  bond pdb=" N   PHE C 201 "
       pdb=" CA  PHE C 201 "
    ideal  model  delta    sigma   weight residual
    1.460  1.450  0.010 1.22e-02 6.72e+03 6.20e-01
  ... (remaining 6314 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.20: 8311
        1.20 -     2.41: 145
        2.41 -     3.61: 29
        3.61 -     4.81: 5
        4.81 -     6.02: 6
  Bond angle restraints: 8496
  Sorted by residual:
  angle pdb=" CA  LYS C  21 "
        pdb=" CB  LYS C  21 "
        pdb=" CG  LYS C  21 "
      ideal   model   delta    sigma   weight residual
     114.10  119.46   -5.36 2.00e+00 2.50e-01 7.17e+00
  angle pdb=" CB  LYS C  21 "
        pdb=" CG  LYS C  21 "
        pdb=" CD  LYS C  21 "
      ideal   model   delta    sigma   weight residual
     111.30  117.32   -6.02 2.30e+00 1.89e-01 6.85e+00
  angle pdb=" N   TYR B 199 "
        pdb=" CA  TYR B 199 "
        pdb=" C   TYR B 199 "
      ideal   model   delta    sigma   weight residual
     109.81  114.98   -5.17 2.21e+00 2.05e-01 5.47e+00
  angle pdb=" N   TYR C 202 "
        pdb=" CA  TYR C 202 "
        pdb=" C   TYR C 202 "
      ideal   model   delta    sigma   weight residual
     111.07  113.41   -2.34 1.07e+00 8.73e-01 4.79e+00
  angle pdb=" CA  PHE C 201 "
        pdb=" C   PHE C 201 "
        pdb=" N   TYR C 202 "
      ideal   model   delta    sigma   weight residual
     117.07  119.56   -2.49 1.21e+00 6.83e-01 4.23e+00
  ... (remaining 8491 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 3346
       17.96 -    35.91: 404
       35.91 -    53.87: 113
       53.87 -    71.82: 29
       71.82 -    89.78: 12
  Dihedral angle restraints: 3904
    sinusoidal: 1651
      harmonic: 2253
  Sorted by residual:
  dihedral pdb=" CA  ASN A 156 "
           pdb=" C   ASN A 156 "
           pdb=" N   MET A 157 "
           pdb=" CA  MET A 157 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.93  -20.07     0      5.00e+00 4.00e-02 1.61e+01
  dihedral pdb=" CA  PHE C 201 "
           pdb=" C   PHE C 201 "
           pdb=" N   TYR C 202 "
           pdb=" CA  TYR C 202 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.99  -18.01     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CG  ARG A  35 "
           pdb=" CD  ARG A  35 "
           pdb=" NE  ARG A  35 "
           pdb=" CZ  ARG A  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.11   48.89     2      1.50e+01 4.44e-03 1.21e+01
  ... (remaining 3901 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 542
       0.026 -    0.052: 243
       0.052 -    0.077: 71
       0.077 -    0.103: 32
       0.103 -    0.129: 22
  Chirality restraints: 910
  Sorted by residual:
  chirality pdb=" CA  ILE C 154 "
            pdb=" N   ILE C 154 "
            pdb=" C   ILE C 154 "
            pdb=" CB  ILE C 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.14e-01
  chirality pdb=" CA  ILE C 120 "
            pdb=" N   ILE C 120 "
            pdb=" C   ILE C 120 "
            pdb=" CB  ILE C 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.13e-01
  chirality pdb=" CA  LEU A 181 "
            pdb=" N   LEU A 181 "
            pdb=" C   LEU A 181 "
            pdb=" CB  LEU A 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.06e-01
  ... (remaining 907 not shown)

  Planarity restraints: 1108
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B  68 "   -0.007 2.00e-02 2.50e+03   1.42e-02 2.02e+00
        pdb=" CD  GLN B  68 "    0.025 2.00e-02 2.50e+03
        pdb=" OE1 GLN B  68 "   -0.009 2.00e-02 2.50e+03
        pdb=" NE2 GLN B  68 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 208 "   -0.006 2.00e-02 2.50e+03   9.22e-03 1.70e+00
        pdb=" CG  TYR C 208 "    0.022 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 208 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 208 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 208 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 208 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 208 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR C 208 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 199 "    0.021 5.00e-02 4.00e+02   3.20e-02 1.64e+00
        pdb=" N   PRO B 200 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO B 200 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 200 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1105 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 125
        2.72 -     3.27: 6026
        3.27 -     3.81: 10287
        3.81 -     4.36: 12064
        4.36 -     4.90: 20116
  Nonbonded interactions: 48618
  Sorted by model distance:
  nonbonded pdb=" N   GLU A 105 "
            pdb=" OE1 GLU A 105 "
     model   vdw
     2.176 3.120
  nonbonded pdb=" OG  SER A  49 "
            pdb=" OE2 GLU A 238 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OD1 ASP A  26 "
            pdb=" NE2 GLN A 249 "
     model   vdw
     2.240 3.120
  nonbonded pdb=" OD1 ASN C  87 "
            pdb=" ND2 ASN B  67 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" O   LEU C 182 "
            pdb=" NE  ARG C 194 "
     model   vdw
     2.370 3.120
  ... (remaining 48613 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:             3.780
  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:             0.020
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.340
  Find NCS groups from input model:        0.030
  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:6.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
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      :  0.002   0.030   6319  Z= 0.114
  Angle     :  0.446   6.018   8496  Z= 0.244
  Chirality :  0.037   0.129    910
  Planarity :  0.003   0.039   1108
  Dihedral  : 17.684  89.775   2442
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 17.78 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.69 (0.30), residues: 753
  helix:  3.07 (0.23), residues: 442
  sheet:  1.07 (0.69), residues: 59
  loop : -0.47 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  35 
 TYR   0.022   0.001   TYR C 208 
 PHE   0.014   0.002   PHE C 203 
 TRP   0.010   0.001   TRP B 109 
 HIS   0.005   0.001   HIS A 152 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 6319)
  covalent geometry    : angle       0.44604 ( 8496)
  hydrogen bonds       : bond        0.18374 (  428)
  hydrogen bonds       : angle       5.38554 ( 1251)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A   67 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8098 (mp0)
REVERT: C   53 GLU cc_start: 0.5476 (mt-10) cc_final: 0.4958 (tp30)
REVERT: C   60 LYS cc_start: 0.6879 (ttmt) cc_final: 0.6404 (mmtm)
REVERT: C  111 LYS cc_start: 0.4504 (OUTLIER) cc_final: 0.4113 (mtmp)
REVERT: C  130 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7713 (tt)
REVERT: C  195 ASN cc_start: 0.6734 (m-40) cc_final: 0.6411 (m110)
REVERT: C  226 LYS cc_start: 0.6442 (mttt) cc_final: 0.5898 (mtpp)
REVERT: C  230 LYS cc_start: 0.6898 (ttmm) cc_final: 0.6418 (ttpt)
REVERT: C  236 LYS cc_start: 0.7188 (mtmm) cc_final: 0.5993 (tptt)
REVERT: B   92 GLN cc_start: 0.8545 (tp40) cc_final: 0.8311 (tp-100)
REVERT: B  115 LYS cc_start: 0.8688 (ttmm) cc_final: 0.8398 (tttt)
REVERT: B  225 MET cc_start: 0.8810 (mmm) cc_final: 0.8535 (mmp)
  outliers start: 9
  outliers final: 4
  residues processed: 107
  average time/residue: 0.7596
  time to fit residues: 84.1004
Evaluate side-chains
  106 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain C residue   75 ASP
Chi-restraints excluded: chain C residue  111 LYS
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain C residue  185 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.1980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
C  20 ASN
C 160 HIS
B 257 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.167129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.132586 restraints weight = 6080.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 1.31
r_work: 0.3262 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.0725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6319  Z= 0.172
  Angle     :  0.525   5.902   8496  Z= 0.292
  Chirality :  0.041   0.145    910
  Planarity :  0.004   0.038   1108
  Dihedral  :  5.603  51.087    849
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 14.96 %
    Favored  : 82.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.93 (0.31), residues: 753
  helix:  3.28 (0.23), residues: 452
  sheet:  1.06 (0.67), residues: 61
  loop : -0.57 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  35 
 TYR   0.017   0.002   TYR C 123 
 PHE   0.017   0.002   PHE C  92 
 TRP   0.011   0.002   TRP B 109 
 HIS   0.007   0.002   HIS A 152 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 6319)
  covalent geometry    : angle       0.52499 ( 8496)
  hydrogen bonds       : bond        0.07899 (  428)
  hydrogen bonds       : angle       4.22994 ( 1251)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A   67 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8058 (mp0)
REVERT: C   53 GLU cc_start: 0.5437 (mt-10) cc_final: 0.4896 (tp30)
REVERT: C   60 LYS cc_start: 0.6997 (ttmt) cc_final: 0.6421 (mmtm)
REVERT: C  130 LEU cc_start: 0.7972 (tp) cc_final: 0.7600 (tt)
REVERT: C  195 ASN cc_start: 0.6600 (m-40) cc_final: 0.6334 (m-40)
REVERT: C  226 LYS cc_start: 0.6402 (mttt) cc_final: 0.5852 (mtpp)
REVERT: C  230 LYS cc_start: 0.6856 (ttmm) cc_final: 0.6350 (ttpt)
REVERT: C  236 LYS cc_start: 0.7133 (mtmm) cc_final: 0.5951 (mptt)
REVERT: B   14 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7748 (pt0)
REVERT: B   92 GLN cc_start: 0.8556 (tp40) cc_final: 0.8315 (tp-100)
REVERT: B  128 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8354 (ttmt)
REVERT: B  193 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7566 (m-30)
REVERT: B  225 MET cc_start: 0.8827 (mmm) cc_final: 0.8584 (mmp)
  outliers start: 20
  outliers final: 6
  residues processed: 110
  average time/residue: 0.7429
  time to fit residues: 84.7078
Evaluate side-chains
  106 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  188 THR
Chi-restraints excluded: chain C residue  221 ASP
Chi-restraints excluded: chain B residue   14 GLU
Chi-restraints excluded: chain B residue  128 LYS
Chi-restraints excluded: chain B residue  193 ASP
Chi-restraints excluded: chain B residue  207 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 54 optimal weight:    0.5980
   chunk 31 optimal weight:    0.1980
   chunk 27 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** C  26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 160 HIS
B 257 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.170708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.136149 restraints weight = 6102.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 1.16
r_work: 0.3232 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.0823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6319  Z= 0.148
  Angle     :  0.485   5.931   8496  Z= 0.268
  Chirality :  0.039   0.144    910
  Planarity :  0.004   0.033   1108
  Dihedral  :  4.944  49.283    840
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 15.85 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.07 (0.31), residues: 753
  helix:  3.46 (0.23), residues: 451
  sheet:  1.05 (0.74), residues: 51
  loop : -0.57 (0.37), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  35 
 TYR   0.014   0.001   TYR C 123 
 PHE   0.015   0.002   PHE C 201 
 TRP   0.012   0.002   TRP B 109 
 HIS   0.005   0.001   HIS A 152 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6319)
  covalent geometry    : angle       0.48475 ( 8496)
  hydrogen bonds       : bond        0.07158 (  428)
  hydrogen bonds       : angle       3.99521 ( 1251)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A   67 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8074 (mp0)
REVERT: C   53 GLU cc_start: 0.5424 (mt-10) cc_final: 0.4893 (tp30)
REVERT: C   60 LYS cc_start: 0.7020 (ttmt) cc_final: 0.6434 (mmtm)
REVERT: C  130 LEU cc_start: 0.7982 (tp) cc_final: 0.7593 (tt)
REVERT: C  194 ARG cc_start: 0.5790 (mmt90) cc_final: 0.5274 (mmt90)
REVERT: C  195 ASN cc_start: 0.6670 (m-40) cc_final: 0.6391 (m-40)
REVERT: C  226 LYS cc_start: 0.6385 (mttt) cc_final: 0.5827 (mtpp)
REVERT: C  230 LYS cc_start: 0.6813 (ttmm) cc_final: 0.6316 (ttpt)
REVERT: B   14 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7708 (pt0)
REVERT: B   37 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7869 (mm-30)
REVERT: B   92 GLN cc_start: 0.8572 (tp40) cc_final: 0.8334 (tp-100)
REVERT: B  115 LYS cc_start: 0.8574 (ttmm) cc_final: 0.8229 (tttt)
REVERT: B  128 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8337 (ttmt)
REVERT: B  193 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7553 (m-30)
REVERT: B  225 MET cc_start: 0.8788 (mmm) cc_final: 0.8558 (mmp)
  outliers start: 17
  outliers final: 6
  residues processed: 112
  average time/residue: 0.7251
  time to fit residues: 84.1517
Evaluate side-chains
  104 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  185 VAL
Chi-restraints excluded: chain C residue  221 ASP
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain B residue   14 GLU
Chi-restraints excluded: chain B residue  128 LYS
Chi-restraints excluded: chain B residue  193 ASP
Chi-restraints excluded: chain B residue  207 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 49 optimal weight:    0.0980
   chunk 24 optimal weight:    0.2980
   chunk 48 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0670
   overall best weight:    0.3718

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

Flipped N/Q/H residues before XYZ refinement:
** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 160 HIS
B 257 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.172284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.138359 restraints weight = 6101.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 1.10
r_work: 0.3260 rms_B_bonded: 1.68 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 2.75 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.1010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6319  Z= 0.127
  Angle     :  0.456   6.659   8496  Z= 0.249
  Chirality :  0.038   0.143    910
  Planarity :  0.003   0.037   1108
  Dihedral  :  4.697  49.784    839
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 16.00 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.32 (0.31), residues: 753
  helix:  3.69 (0.23), residues: 454
  sheet:  0.96 (0.73), residues: 51
  loop : -0.55 (0.37), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  35 
 TYR   0.011   0.001   TYR C  44 
 PHE   0.014   0.002   PHE C  92 
 TRP   0.011   0.001   TRP B 109 
 HIS   0.004   0.001   HIS B 236 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 6319)
  covalent geometry    : angle       0.45593 ( 8496)
  hydrogen bonds       : bond        0.06353 (  428)
  hydrogen bonds       : angle       3.80270 ( 1251)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A   67 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8059 (mp0)
REVERT: C   53 GLU cc_start: 0.5436 (mt-10) cc_final: 0.4920 (tp30)
REVERT: C   60 LYS cc_start: 0.7045 (ttmt) cc_final: 0.6457 (mmtm)
REVERT: C  130 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7591 (tt)
REVERT: C  194 ARG cc_start: 0.5754 (OUTLIER) cc_final: 0.5348 (mmt90)
REVERT: C  195 ASN cc_start: 0.6704 (m-40) cc_final: 0.6408 (m-40)
REVERT: C  226 LYS cc_start: 0.6408 (mttt) cc_final: 0.5841 (mtpp)
REVERT: C  230 LYS cc_start: 0.6763 (ttmm) cc_final: 0.6296 (ttpt)
REVERT: B   14 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7665 (pt0)
REVERT: B   92 GLN cc_start: 0.8560 (tp40) cc_final: 0.8318 (tp-100)
REVERT: B  128 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8325 (ttmt)
REVERT: B  193 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7548 (m-30)
REVERT: B  225 MET cc_start: 0.8771 (mmm) cc_final: 0.8537 (mmp)
  outliers start: 20
  outliers final: 8
  residues processed: 114
  average time/residue: 0.7038
  time to fit residues: 83.3228
Evaluate side-chains
  113 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  185 VAL
Chi-restraints excluded: chain C residue  188 THR
Chi-restraints excluded: chain C residue  194 ARG
Chi-restraints excluded: chain C residue  221 ASP
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain B residue   14 GLU
Chi-restraints excluded: chain B residue  100 LYS
Chi-restraints excluded: chain B residue  128 LYS
Chi-restraints excluded: chain B residue  193 ASP
Chi-restraints excluded: chain B residue  207 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 73 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0980
   chunk 66 optimal weight:    0.0170
   chunk 21 optimal weight:    0.0870
   chunk 44 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.3396

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

Flipped N/Q/H residues before XYZ refinement:
** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 160 HIS
B 257 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.172801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.138628 restraints weight = 6222.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 1.14
r_work: 0.3308 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 2.72 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.1074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6319  Z= 0.123
  Angle     :  0.452   6.974   8496  Z= 0.245
  Chirality :  0.037   0.143    910
  Planarity :  0.003   0.035   1108
  Dihedral  :  4.444  50.262    838
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 16.44 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.41 (0.31), residues: 753
  helix:  3.78 (0.23), residues: 454
  sheet:  0.96 (0.73), residues: 51
  loop : -0.54 (0.38), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  35 
 TYR   0.011   0.001   TYR C 123 
 PHE   0.014   0.002   PHE C  92 
 TRP   0.011   0.001   TRP B 109 
 HIS   0.004   0.001   HIS B 236 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 6319)
  covalent geometry    : angle       0.45168 ( 8496)
  hydrogen bonds       : bond        0.06167 (  428)
  hydrogen bonds       : angle       3.72816 ( 1251)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A   67 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7970 (mp0)
REVERT: C   53 GLU cc_start: 0.5238 (mt-10) cc_final: 0.4736 (tp30)
REVERT: C   60 LYS cc_start: 0.7047 (ttmt) cc_final: 0.6458 (mmtm)
REVERT: C   95 MET cc_start: 0.7456 (ptt) cc_final: 0.7131 (ppp)
REVERT: C  130 LEU cc_start: 0.7953 (tp) cc_final: 0.7559 (tt)
REVERT: C  170 GLU cc_start: 0.5115 (OUTLIER) cc_final: 0.4898 (tt0)
REVERT: C  194 ARG cc_start: 0.5805 (OUTLIER) cc_final: 0.5389 (mmt90)
REVERT: C  195 ASN cc_start: 0.6704 (m-40) cc_final: 0.6400 (m-40)
REVERT: C  226 LYS cc_start: 0.6223 (mttt) cc_final: 0.5849 (mtpp)
REVERT: C  230 LYS cc_start: 0.6751 (ttmm) cc_final: 0.6283 (ttpt)
REVERT: B   14 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7663 (pt0)
REVERT: B   92 GLN cc_start: 0.8541 (tp40) cc_final: 0.8289 (tp-100)
REVERT: B  115 LYS cc_start: 0.8616 (ttmm) cc_final: 0.8307 (tttt)
REVERT: B  128 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8312 (ttmt)
REVERT: B  193 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7535 (m-30)
REVERT: B  225 MET cc_start: 0.8753 (mmm) cc_final: 0.8521 (mmp)
  outliers start: 18
  outliers final: 8
  residues processed: 118
  average time/residue: 0.7415
  time to fit residues: 90.7002
Evaluate side-chains
  115 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  170 GLU
Chi-restraints excluded: chain C residue  185 VAL
Chi-restraints excluded: chain C residue  188 THR
Chi-restraints excluded: chain C residue  194 ARG
Chi-restraints excluded: chain C residue  221 ASP
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain B residue   14 GLU
Chi-restraints excluded: chain B residue  100 LYS
Chi-restraints excluded: chain B residue  128 LYS
Chi-restraints excluded: chain B residue  193 ASP
Chi-restraints excluded: chain B residue  207 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 54 optimal weight:    0.0970
   chunk 22 optimal weight:    0.6980
   chunk 63 optimal weight:    0.5980
   chunk 67 optimal weight:    0.0570
   chunk 29 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 15 optimal weight:    0.2980
   chunk 12 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 30 optimal weight:    8.9990
   overall best weight:    0.3296

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

Flipped N/Q/H residues before XYZ refinement:
** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 160 HIS
B 257 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.172623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.138693 restraints weight = 6108.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 1.11
r_work: 0.3269 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 2.79 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.1166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6319  Z= 0.122
  Angle     :  0.450   7.445   8496  Z= 0.244
  Chirality :  0.037   0.142    910
  Planarity :  0.003   0.036   1108
  Dihedral  :  4.401  50.605    838
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 17.19 %
    Favored  : 80.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.47 (0.31), residues: 753
  helix:  3.84 (0.23), residues: 454
  sheet:  0.98 (0.73), residues: 51
  loop : -0.51 (0.38), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  35 
 TYR   0.010   0.001   TYR C 123 
 PHE   0.014   0.002   PHE C  92 
 TRP   0.011   0.001   TRP B 109 
 HIS   0.004   0.001   HIS B 236 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 6319)
  covalent geometry    : angle       0.45002 ( 8496)
  hydrogen bonds       : bond        0.06035 (  428)
  hydrogen bonds       : angle       3.66947 ( 1251)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.278 
Fit side-chains
REVERT: C   53 GLU cc_start: 0.5285 (mt-10) cc_final: 0.4800 (tp30)
REVERT: C   60 LYS cc_start: 0.7054 (ttmt) cc_final: 0.6448 (mmtm)
REVERT: C   75 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8017 (t70)
REVERT: C   95 MET cc_start: 0.7475 (ptt) cc_final: 0.7107 (ppp)
REVERT: C  130 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7557 (tt)
REVERT: C  194 ARG cc_start: 0.5820 (OUTLIER) cc_final: 0.5356 (mmt90)
REVERT: C  226 LYS cc_start: 0.6227 (mttt) cc_final: 0.5850 (mtpp)
REVERT: C  230 LYS cc_start: 0.6749 (ttmm) cc_final: 0.6282 (ttpt)
REVERT: B   14 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7663 (pt0)
REVERT: B   37 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7941 (mm-30)
REVERT: B   92 GLN cc_start: 0.8526 (tp40) cc_final: 0.8270 (tp-100)
REVERT: B  115 LYS cc_start: 0.8686 (ttmm) cc_final: 0.8370 (tttt)
REVERT: B  128 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8321 (ttmt)
REVERT: B  225 MET cc_start: 0.8786 (mmm) cc_final: 0.8556 (mmp)
  outliers start: 18
  outliers final: 8
  residues processed: 115
  average time/residue: 0.6822
  time to fit residues: 81.5513
Evaluate side-chains
  115 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain C residue   75 ASP
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  185 VAL
Chi-restraints excluded: chain C residue  188 THR
Chi-restraints excluded: chain C residue  194 ARG
Chi-restraints excluded: chain C residue  221 ASP
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain B residue   14 GLU
Chi-restraints excluded: chain B residue  100 LYS
Chi-restraints excluded: chain B residue  128 LYS
Chi-restraints excluded: chain B residue  207 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 16 optimal weight:    0.2980
   chunk 49 optimal weight:    0.0670
   chunk 36 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.5920

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

Flipped N/Q/H residues before XYZ refinement:
** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 160 HIS
B 257 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.171102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.137702 restraints weight = 6115.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 1.66
r_work: 0.3246 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3155 rms_B_bonded: 2.63 restraints_weight: 0.2500
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.1090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6319  Z= 0.146
  Angle     :  0.492   7.901   8496  Z= 0.267
  Chirality :  0.039   0.143    910
  Planarity :  0.004   0.038   1108
  Dihedral  :  3.772  20.449    835
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 16.89 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.27 (0.31), residues: 753
  helix:  3.65 (0.23), residues: 454
  sheet:  0.90 (0.73), residues: 51
  loop : -0.54 (0.37), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  35 
 TYR   0.016   0.002   TYR C 123 
 PHE   0.015   0.002   PHE C  92 
 TRP   0.010   0.002   TRP B 109 
 HIS   0.005   0.001   HIS B 236 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6319)
  covalent geometry    : angle       0.49152 ( 8496)
  hydrogen bonds       : bond        0.06900 (  428)
  hydrogen bonds       : angle       3.81509 ( 1251)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.261 
Fit side-chains
REVERT: C   53 GLU cc_start: 0.5282 (mt-10) cc_final: 0.4771 (tp30)
REVERT: C   60 LYS cc_start: 0.6998 (ttmt) cc_final: 0.6386 (mmtm)
REVERT: C   95 MET cc_start: 0.7456 (ptt) cc_final: 0.7066 (ppp)
REVERT: C  130 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7508 (tt)
REVERT: C  194 ARG cc_start: 0.5805 (OUTLIER) cc_final: 0.5437 (mmt90)
REVERT: C  195 ASN cc_start: 0.6625 (m-40) cc_final: 0.6339 (m-40)
REVERT: C  226 LYS cc_start: 0.6181 (mttt) cc_final: 0.5800 (mtpp)
REVERT: C  230 LYS cc_start: 0.6715 (ttmm) cc_final: 0.6241 (ttpt)
REVERT: B   14 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7667 (pt0)
REVERT: B   37 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7855 (mm-30)
REVERT: B   92 GLN cc_start: 0.8507 (tp40) cc_final: 0.8246 (tp-100)
REVERT: B  115 LYS cc_start: 0.8612 (ttmm) cc_final: 0.8252 (tttt)
REVERT: B  128 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8320 (ttmt)
REVERT: B  193 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7516 (m-30)
REVERT: B  225 MET cc_start: 0.8743 (mmm) cc_final: 0.8512 (mmp)
  outliers start: 19
  outliers final: 9
  residues processed: 111
  average time/residue: 0.7277
  time to fit residues: 83.7829
Evaluate side-chains
  111 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  185 VAL
Chi-restraints excluded: chain C residue  188 THR
Chi-restraints excluded: chain C residue  194 ARG
Chi-restraints excluded: chain C residue  221 ASP
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain B residue   14 GLU
Chi-restraints excluded: chain B residue  100 LYS
Chi-restraints excluded: chain B residue  128 LYS
Chi-restraints excluded: chain B residue  193 ASP
Chi-restraints excluded: chain B residue  207 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 4 optimal weight:    0.1980
   chunk 48 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 58 optimal weight:    0.1980
   chunk 33 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 55 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 160 HIS
B 257 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.171443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.137506 restraints weight = 6097.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 1.09
r_work: 0.3248 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.1115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6319  Z= 0.140
  Angle     :  0.489   9.775   8496  Z= 0.264
  Chirality :  0.039   0.145    910
  Planarity :  0.003   0.041   1108
  Dihedral  :  3.750  19.954    835
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 17.63 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.31 (0.31), residues: 753
  helix:  3.68 (0.23), residues: 454
  sheet:  0.89 (0.72), residues: 51
  loop : -0.53 (0.37), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  35 
 TYR   0.014   0.001   TYR C 123 
 PHE   0.015   0.002   PHE C  92 
 TRP   0.010   0.001   TRP B 109 
 HIS   0.005   0.001   HIS B 236 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 6319)
  covalent geometry    : angle       0.48906 ( 8496)
  hydrogen bonds       : bond        0.06705 (  428)
  hydrogen bonds       : angle       3.79155 ( 1251)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.340 
Fit side-chains
REVERT: C   53 GLU cc_start: 0.5300 (mt-10) cc_final: 0.4794 (tp30)
REVERT: C   60 LYS cc_start: 0.7037 (ttmt) cc_final: 0.6434 (mmtm)
REVERT: C   95 MET cc_start: 0.7430 (ptt) cc_final: 0.7047 (ppp)
REVERT: C  130 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7459 (tt)
REVERT: C  194 ARG cc_start: 0.5818 (OUTLIER) cc_final: 0.5375 (mmt90)
REVERT: C  195 ASN cc_start: 0.6678 (m-40) cc_final: 0.6388 (m-40)
REVERT: C  226 LYS cc_start: 0.6235 (mttt) cc_final: 0.5861 (mtpp)
REVERT: C  230 LYS cc_start: 0.6772 (ttmm) cc_final: 0.6306 (ttpt)
REVERT: B   14 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7692 (pt0)
REVERT: B   37 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7922 (mm-30)
REVERT: B   92 GLN cc_start: 0.8541 (tp40) cc_final: 0.8292 (tp-100)
REVERT: B  128 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8323 (ttmt)
REVERT: B  193 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7545 (m-30)
REVERT: B  225 MET cc_start: 0.8764 (mmm) cc_final: 0.8537 (mmp)
  outliers start: 16
  outliers final: 9
  residues processed: 108
  average time/residue: 0.7469
  time to fit residues: 83.8002
Evaluate side-chains
  112 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  185 VAL
Chi-restraints excluded: chain C residue  188 THR
Chi-restraints excluded: chain C residue  194 ARG
Chi-restraints excluded: chain C residue  221 ASP
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain B residue   14 GLU
Chi-restraints excluded: chain B residue  100 LYS
Chi-restraints excluded: chain B residue  128 LYS
Chi-restraints excluded: chain B residue  193 ASP
Chi-restraints excluded: chain B residue  207 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 67 optimal weight:    0.3980
   chunk 59 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0970
   chunk 70 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 57 optimal weight:    0.4980
   chunk 47 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 160 HIS
B 257 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.171482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.137532 restraints weight = 6101.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 1.10
r_work: 0.3247 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 2.69 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.1096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6319  Z= 0.140
  Angle     :  0.503  10.070   8496  Z= 0.269
  Chirality :  0.039   0.143    910
  Planarity :  0.004   0.042   1108
  Dihedral  :  3.753  19.983    835
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 17.63 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.31 (0.31), residues: 753
  helix:  3.68 (0.23), residues: 454
  sheet:  0.93 (0.73), residues: 51
  loop : -0.52 (0.37), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  35 
 TYR   0.014   0.001   TYR C 123 
 PHE   0.015   0.002   PHE C  92 
 TRP   0.011   0.001   TRP B 109 
 HIS   0.005   0.001   HIS B 236 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6319)
  covalent geometry    : angle       0.50304 ( 8496)
  hydrogen bonds       : bond        0.06705 (  428)
  hydrogen bonds       : angle       3.78858 ( 1251)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.263 
Fit side-chains
REVERT: C   53 GLU cc_start: 0.5307 (mt-10) cc_final: 0.4815 (tp30)
REVERT: C   60 LYS cc_start: 0.7049 (ttmt) cc_final: 0.6461 (mmtm)
REVERT: C   95 MET cc_start: 0.7442 (ptt) cc_final: 0.7065 (ppp)
REVERT: C  130 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7445 (tt)
REVERT: C  194 ARG cc_start: 0.5848 (OUTLIER) cc_final: 0.5412 (mmt90)
REVERT: C  195 ASN cc_start: 0.6706 (m-40) cc_final: 0.6417 (m-40)
REVERT: C  226 LYS cc_start: 0.6243 (mttt) cc_final: 0.5869 (mtpp)
REVERT: C  230 LYS cc_start: 0.6780 (ttmm) cc_final: 0.6312 (ttpt)
REVERT: B   14 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7687 (pt0)
REVERT: B   37 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7903 (mm-30)
REVERT: B   92 GLN cc_start: 0.8540 (tp40) cc_final: 0.8293 (tp-100)
REVERT: B  115 LYS cc_start: 0.8633 (ttmm) cc_final: 0.8282 (tttt)
REVERT: B  128 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8320 (ttmt)
REVERT: B  193 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7547 (m-30)
REVERT: B  225 MET cc_start: 0.8764 (mmm) cc_final: 0.8537 (mmp)
  outliers start: 16
  outliers final: 10
  residues processed: 109
  average time/residue: 0.7022
  time to fit residues: 79.5897
Evaluate side-chains
  114 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  185 VAL
Chi-restraints excluded: chain C residue  188 THR
Chi-restraints excluded: chain C residue  194 ARG
Chi-restraints excluded: chain C residue  221 ASP
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain B residue   14 GLU
Chi-restraints excluded: chain B residue  100 LYS
Chi-restraints excluded: chain B residue  128 LYS
Chi-restraints excluded: chain B residue  193 ASP
Chi-restraints excluded: chain B residue  207 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 60 optimal weight:    0.5980
   chunk 72 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0670
   chunk 54 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 69 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0770
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.4276

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

Flipped N/Q/H residues before XYZ refinement:
** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 160 HIS
B 257 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.172147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.138199 restraints weight = 6154.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 1.10
r_work: 0.3258 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3168 rms_B_bonded: 2.72 restraints_weight: 0.2500
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.1162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6319  Z= 0.133
  Angle     :  0.491  10.193   8496  Z= 0.262
  Chirality :  0.038   0.144    910
  Planarity :  0.003   0.040   1108
  Dihedral  :  3.696  19.259    835
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 17.78 %
    Favored  : 79.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.40 (0.31), residues: 753
  helix:  3.75 (0.23), residues: 454
  sheet:  0.99 (0.73), residues: 51
  loop : -0.50 (0.38), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  35 
 TYR   0.011   0.001   TYR C 123 
 PHE   0.014   0.002   PHE C  92 
 TRP   0.011   0.001   TRP B 109 
 HIS   0.004   0.001   HIS B 236 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 6319)
  covalent geometry    : angle       0.49088 ( 8496)
  hydrogen bonds       : bond        0.06411 (  428)
  hydrogen bonds       : angle       3.73546 ( 1251)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.193 
Fit side-chains
REVERT: C   53 GLU cc_start: 0.5320 (mt-10) cc_final: 0.5067 (tp30)
REVERT: C   60 LYS cc_start: 0.7042 (ttmt) cc_final: 0.6466 (mptm)
REVERT: C   95 MET cc_start: 0.7476 (ptt) cc_final: 0.7077 (ppp)
REVERT: C  130 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7441 (tt)
REVERT: C  194 ARG cc_start: 0.5840 (OUTLIER) cc_final: 0.5414 (mmt90)
REVERT: C  195 ASN cc_start: 0.6698 (m-40) cc_final: 0.6407 (m-40)
REVERT: C  226 LYS cc_start: 0.6236 (mttt) cc_final: 0.5832 (mtpp)
REVERT: C  230 LYS cc_start: 0.6771 (ttmm) cc_final: 0.6300 (ttpt)
REVERT: B   14 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7680 (pt0)
REVERT: B   37 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7914 (mm-30)
REVERT: B   92 GLN cc_start: 0.8539 (tp40) cc_final: 0.8293 (tp-100)
REVERT: B  115 LYS cc_start: 0.8687 (ttmm) cc_final: 0.8352 (tttt)
REVERT: B  128 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8318 (ttmt)
REVERT: B  193 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7545 (m-30)
REVERT: B  225 MET cc_start: 0.8762 (mmm) cc_final: 0.8535 (mmp)
  outliers start: 16
  outliers final: 10
  residues processed: 109
  average time/residue: 0.6450
  time to fit residues: 73.2082
Evaluate side-chains
  112 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  185 VAL
Chi-restraints excluded: chain C residue  188 THR
Chi-restraints excluded: chain C residue  194 ARG
Chi-restraints excluded: chain C residue  221 ASP
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain B residue   14 GLU
Chi-restraints excluded: chain B residue  100 LYS
Chi-restraints excluded: chain B residue  128 LYS
Chi-restraints excluded: chain B residue  193 ASP
Chi-restraints excluded: chain B residue  207 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0010
   chunk 23 optimal weight:    0.0980
   chunk 57 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0670
   chunk 36 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.2524

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

Flipped N/Q/H residues before XYZ refinement:
** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 160 HIS
B 257 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.174372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.140693 restraints weight = 6173.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 1.69
r_work: 0.3399 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 2.72 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.1350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6319  Z= 0.117
  Angle     :  0.467   9.868   8496  Z= 0.247
  Chirality :  0.037   0.142    910
  Planarity :  0.003   0.039   1108
  Dihedral  :  3.527  16.902    835
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 18.22 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.61 (0.31), residues: 753
  helix:  3.92 (0.23), residues: 454
  sheet:  1.15 (0.73), residues: 51
  loop : -0.44 (0.38), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  35 
 TYR   0.010   0.001   TYR C  44 
 PHE   0.013   0.001   PHE C  92 
 TRP   0.012   0.001   TRP B 109 
 HIS   0.003   0.001   HIS B 236 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 6319)
  covalent geometry    : angle       0.46696 ( 8496)
  hydrogen bonds       : bond        0.05622 (  428)
  hydrogen bonds       : angle       3.57864 ( 1251)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4362.86 seconds
wall clock time: 74 minutes 41.62 seconds (4481.62 seconds total)