Starting phenix.real_space_refine
on Thu Jun  5 04:34:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p73_17516/06_2025/8p73_17516.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p73_17516/06_2025/8p73_17516.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8p73_17516/06_2025/8p73_17516.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p73_17516/06_2025/8p73_17516.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p73_17516/06_2025/8p73_17516.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p73_17516/06_2025/8p73_17516.cif"
  }
  resolution = 2.0
  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=   0.001
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      31      5.16       5
     C    3292      2.51       5
     N     870      2.21       5
     O     976      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5169
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "H"
      Number of atoms: 512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 512
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 5, 'TRANS': 59}
    Chain: "I"
      Number of atoms: 2247
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2247
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 275, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 260}
          Chain breaks: 2
    Chain: "J"
      Number of atoms: 2283
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2283
          Classifications: {'peptide': 286}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267}
          Chain breaks: 2
    Chain: "J"
      Number of atoms: 60
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1, 30
          Unusual residues: {'X50': 1}
          Classifications: {'undetermined': 1}
      Conformer: "B"
        Number of residues, atoms: 1, 30
          Unusual residues: {'X58': 1}
          Classifications: {'undetermined': 1}
    Chain: "H"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
    Chain: "I"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 28
          Classifications: {'water': 28}
          Link IDs: {None: 27}
    Chain: "J"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 33
          Classifications: {'water': 33}
          Link IDs: {None: 32}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" C01AX50 J 401 " occ=0.29
      ... (28 atoms not shown)
      pdb=" O28AX50 J 401 " occ=0.29
    residue:
      pdb=" C01BX58 J 402 " occ=0.71
      ... (28 atoms not shown)
      pdb=" O28BX58 J 402 " occ=0.71
  Time building chain proxies: 4.93, per 1000 atoms: 0.95
  Number of scatterers: 5169
  At special positions: 0
  Unit cell: (84.075, 93.3375, 67.6875, 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      31     16.00
     O     976      8.00
     N     870      7.00
     C    3292      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: 1.43
  Conformation dependent library (CDL) restraints added in 577.0 milliseconds
  

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1188

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 3 sheets defined
      63.1% alpha, 4.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'H' and resid 262 through 275
      removed outlier: 4.151A  pdb=" N   GLY H 267 " --> pdb=" O   GLU H 264 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   GLY H 270 " --> pdb=" O   GLY H 267 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   TYR H 271 " --> pdb=" O   ARG H 268 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   LEU H 272 " --> pdb=" O   LEU H 269 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   VAL H 275 " --> pdb=" O   LEU H 272 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 279 through 286
    Processing helix  chain 'H' and resid 288 through 302
      removed outlier: 3.853A  pdb=" N   ALA H 292 " --> pdb=" O   THR H 288 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 1 through 4
    Processing helix  chain 'I' and resid 5 through 11
    Processing helix  chain 'I' and resid 15 through 37
    Processing helix  chain 'I' and resid 49 through 71
    Processing helix  chain 'I' and resid 76 through 93
      removed outlier: 3.890A  pdb=" N   ASN I  93 " --> pdb=" O   ARG I  89 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 100 through 117
      removed outlier: 3.511A  pdb=" N   LYS I 114 " --> pdb=" O   PHE I 110 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 121 through 127
    Processing helix  chain 'I' and resid 132 through 154
      removed outlier: 4.660A  pdb=" N   LEU I 148 " --> pdb=" O   LEU I 144 " (cutoff:3.500A)
      removed outlier: 4.676A  pdb=" N   LEU I 149 " --> pdb=" O   GLU I 145 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 163 through 178
    Processing helix  chain 'I' and resid 183 through 186
    Processing helix  chain 'I' and resid 187 through 201
      removed outlier: 3.604A  pdb=" N   THR I 201 " --> pdb=" O   ARG I 197 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 202 through 206
    Processing helix  chain 'I' and resid 208 through 224
    Processing helix  chain 'I' and resid 228 through 234
      removed outlier: 3.684A  pdb=" N   LEU I 232 " --> pdb=" O   MET I 228 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 243 through 262
    Processing helix  chain 'I' and resid 266 through 283
    Processing helix  chain 'J' and resid 56 through 67
    Processing helix  chain 'J' and resid 98 through 104
    Processing helix  chain 'J' and resid 110 through 131
    Processing helix  chain 'J' and resid 139 through 141
      No H-bonds generated for 'chain 'J' and resid 139 through 141'
    Processing helix  chain 'J' and resid 155 through 159
      removed outlier: 4.506A  pdb=" N   LEU J 158 " --> pdb=" O   ASP J 155 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 175 through 179
    Processing helix  chain 'J' and resid 180 through 185
    Processing helix  chain 'J' and resid 192 through 209
      removed outlier: 3.654A  pdb=" N   ALA J 198 " --> pdb=" O   VAL J 194 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 217 through 230
    Processing helix  chain 'J' and resid 239 through 243
    Processing helix  chain 'J' and resid 256 through 261
    Processing helix  chain 'J' and resid 265 through 276
    Processing helix  chain 'J' and resid 285 through 291
    Processing helix  chain 'J' and resid 292 through 297
      removed outlier: 3.649A  pdb=" N   SER J 296 " --> pdb=" O   MET J 292 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 303 through 307
    Processing sheet with id=AA1, first strand: chain 'J' and resid 14 through 20
      removed outlier: 6.098A  pdb=" N   VAL J  26 " --> pdb=" O   LEU J  18 " (cutoff:3.500A)
      removed outlier: 7.275A  pdb=" N   ASP J  92 " --> pdb=" O   LEU J  77 " (cutoff:3.500A)
      removed outlier: 7.975A  pdb=" N   LEU J  77 " --> pdb=" O   ASP J  92 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97
    Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134

    276 hydrogen bonds defined for protein.
    762 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: 1.53

  Time building geometry restraints manager: 1.63 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1237
        1.33 -     1.45: 1023
        1.45 -     1.57: 2919
        1.57 -     1.69: 0
        1.69 -     1.81: 49
  Bond restraints: 5228
  Sorted by residual:
  bond pdb=" C08AX50 J 401 "
       pdb=" N09AX50 J 401 "
    ideal  model  delta    sigma   weight residual
    1.338  1.484 -0.146 2.00e-02 2.50e+03 5.33e+01
  bond pdb=" C18AX50 J 401 "
       pdb=" N19AX50 J 401 "
    ideal  model  delta    sigma   weight residual
    1.351  1.495 -0.144 2.00e-02 2.50e+03 5.20e+01
  bond pdb=" C08BX58 J 402 "
       pdb=" N09BX58 J 402 "
    ideal  model  delta    sigma   weight residual
    1.342  1.458 -0.116 2.00e-02 2.50e+03 3.36e+01
  bond pdb=" C18BX58 J 402 "
       pdb=" N19BX58 J 402 "
    ideal  model  delta    sigma   weight residual
    1.358  1.460 -0.102 2.00e-02 2.50e+03 2.60e+01
  bond pdb=" C30BX58 J 402 "
       pdb=" N07BX58 J 402 "
    ideal  model  delta    sigma   weight residual
    1.383  1.302  0.081 2.00e-02 2.50e+03 1.66e+01
  ... (remaining 5223 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 6870
        1.71 -     3.41: 163
        3.41 -     5.12: 31
        5.12 -     6.82: 9
        6.82 -     8.53: 6
  Bond angle restraints: 7079
  Sorted by residual:
  angle pdb=" CA  LYS I  29 "
        pdb=" CB  LYS I  29 "
        pdb=" CG  LYS I  29 "
      ideal   model   delta    sigma   weight residual
     114.10  122.63   -8.53 2.00e+00 2.50e-01 1.82e+01
  angle pdb=" CG  ARG I 279 "
        pdb=" CD  ARG I 279 "
        pdb=" NE  ARG I 279 "
      ideal   model   delta    sigma   weight residual
     112.00  119.81   -7.81 2.20e+00 2.07e-01 1.26e+01
  angle pdb=" CA  TYR I  91 "
        pdb=" CB  TYR I  91 "
        pdb=" CG  TYR I  91 "
      ideal   model   delta    sigma   weight residual
     113.90  108.41    5.49 1.80e+00 3.09e-01 9.30e+00
  angle pdb=" CB  MET J  94 "
        pdb=" CG  MET J  94 "
        pdb=" SD  MET J  94 "
      ideal   model   delta    sigma   weight residual
     112.70  120.99   -8.29 3.00e+00 1.11e-01 7.64e+00
  angle pdb=" C18BX58 J 402 "
        pdb=" N19BX58 J 402 "
        pdb=" C20BX58 J 402 "
      ideal   model   delta    sigma   weight residual
     125.44  117.87    7.57 3.00e+00 1.11e-01 6.37e+00
  ... (remaining 7074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.67: 2765
       17.67 -    35.33: 303
       35.33 -    52.99: 76
       52.99 -    70.66: 18
       70.66 -    88.32: 11
  Dihedral angle restraints: 3173
    sinusoidal: 1339
      harmonic: 1834
  Sorted by residual:
  dihedral pdb=" CA  THR J 175 "
           pdb=" C   THR J 175 "
           pdb=" N   ARG J 176 "
           pdb=" CA  ARG J 176 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.37  -18.63     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CA  TYR I  91 "
           pdb=" C   TYR I  91 "
           pdb=" N   LEU I  92 "
           pdb=" CA  LEU I  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.87   17.13     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  THR I 176 "
           pdb=" C   THR I 176 "
           pdb=" N   ARG I 177 "
           pdb=" CA  ARG I 177 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.05  -16.95     0      5.00e+00 4.00e-02 1.15e+01
  ... (remaining 3170 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 490
       0.032 -    0.064: 184
       0.064 -    0.096: 70
       0.096 -    0.128: 24
       0.128 -    0.160: 6
  Chirality restraints: 774
  Sorted by residual:
  chirality pdb=" C21BX58 J 402 "
            pdb=" C23BX58 J 402 "
            pdb=" C27BX58 J 402 "
            pdb=" O22BX58 J 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.63    2.47    0.16 2.00e-01 2.50e+01 6.42e-01
  chirality pdb=" CA  TYR I  91 "
            pdb=" N   TYR I  91 "
            pdb=" C   TYR I  91 "
            pdb=" CB  TYR I  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.09e-01
  chirality pdb=" CA  PRO I 101 "
            pdb=" N   PRO I 101 "
            pdb=" C   PRO I 101 "
            pdb=" CB  PRO I 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.92e-01
  ... (remaining 771 not shown)

  Planarity restraints: 898
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG I 279 "    0.258 9.50e-02 1.11e+02   1.16e-01 8.25e+00
        pdb=" NE  ARG I 279 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG I 279 "    0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG I 279 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG I 279 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP I 116 "   -0.010 2.00e-02 2.50e+03   1.94e-02 3.78e+00
        pdb=" CG  ASP I 116 "    0.034 2.00e-02 2.50e+03
        pdb=" OD1 ASP I 116 "   -0.012 2.00e-02 2.50e+03
        pdb=" OD2 ASP I 116 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG I 165 "    0.024 5.00e-02 4.00e+02   3.68e-02 2.17e+00
        pdb=" N   PRO I 166 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO I 166 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO I 166 "    0.021 5.00e-02 4.00e+02
  ... (remaining 895 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 262
        2.73 -     3.27: 5428
        3.27 -     3.81: 9509
        3.81 -     4.36: 11586
        4.36 -     4.90: 18900
  Nonbonded interactions: 45685
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU J  62 "
            pdb=" O   HOH J 501 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" OD1 ASP J 104 "
            pdb=" OG  SER J 106 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   HOH J 532 "
            pdb=" O   HOH J 533 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OG1 THR J 231 "
            pdb=" O   LYS J 250 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OD2 ASP J  97 "
            pdb=" O   HOH J 502 "
     model   vdw
     2.256 3.040
  ... (remaining 45680 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=0.29 max=1.00 mean=0.99
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:             2.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     17.440
  Find NCS groups from input model:        0.060
  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:14.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
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   0.146   5228  Z= 0.302
  Angle     :  0.689   8.526   7079  Z= 0.325
  Chirality :  0.042   0.160    774
  Planarity :  0.006   0.116    898
  Dihedral  : 16.691  88.324   1985
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.47 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 17.82 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.44 (0.34), residues: 612
  helix:  1.67 (0.28), residues: 334
  sheet:  0.37 (1.51), residues: 15
  loop :  0.15 (0.39), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP J 132 
 HIS   0.005   0.001   HIS J 258 
 PHE   0.015   0.002   PHE I  30 
 TYR   0.023   0.002   TYR I  91 
 ARG   0.005   0.000   ARG H 268 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13269 (  276)
  hydrogen bonds       : angle       6.12240 (  762)
  covalent geometry    : bond        0.00626 ( 5228)
  covalent geometry    : angle       0.68906 ( 7079)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 8
  residues processed: 93
  average time/residue: 1.4175
  time to fit residues: 136.6590
Evaluate side-chains
  92 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  171 LEU
Chi-restraints excluded: chain I residue  218 LEU
Chi-restraints excluded: chain I residue  230 SER
Chi-restraints excluded: chain I residue  242 ARG
Chi-restraints excluded: chain I residue  254 SER
Chi-restraints excluded: chain I residue  274 LYS
Chi-restraints excluded: chain J residue  242 SER
Chi-restraints excluded: chain J residue  248 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 47 optimal weight:    0.8980
   chunk 18 optimal weight:    7.9990
   chunk 29 optimal weight:    4.9990
   chunk 35 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
H 307 GLN
I 136 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 258 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.180097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.153874 restraints weight = 16779.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3863 rms_B_bonded: 1.99
r_work: 0.3732 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3632 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3627
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3627 r_free = 0.3627    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3627 r_free = 0.3627    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3627
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.0707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5228  Z= 0.127
  Angle     :  0.545   7.402   7079  Z= 0.280
  Chirality :  0.040   0.139    774
  Planarity :  0.005   0.038    898
  Dihedral  :  5.851  59.467    750
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.14 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 16.55 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.85 (0.35), residues: 612
  helix:  1.95 (0.29), residues: 344
  sheet:  0.01 (1.51), residues: 15
  loop :  0.41 (0.40), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP I  11 
 HIS   0.004   0.001   HIS J 131 
 PHE   0.016   0.002   PHE J  91 
 TYR   0.021   0.002   TYR I  91 
 ARG   0.002   0.000   ARG I 279 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04783 (  276)
  hydrogen bonds       : angle       4.78110 (  762)
  covalent geometry    : bond        0.00275 ( 5228)
  covalent geometry    : angle       0.54509 ( 7079)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
  outliers start: 10
  outliers final: 1
  residues processed: 93
  average time/residue: 1.9361
  time to fit residues: 185.8039
Evaluate side-chains
  86 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  218 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 7 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 30 optimal weight:    8.9990
   chunk 20 optimal weight:    1.9990
   chunk 56 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   chunk 23 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
H 307 GLN
I 136 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 258 HIS
J 297 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.176988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.155275 restraints weight = 19541.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3883 rms_B_bonded: 2.04
r_work: 0.3669 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3665
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3665 r_free = 0.3665    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3665 r_free = 0.3665    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3665
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.0652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   5228  Z= 0.216
  Angle     :  0.666   8.914   7079  Z= 0.340
  Chirality :  0.044   0.147    774
  Planarity :  0.006   0.041    898
  Dihedral  :  5.725  59.091    736
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.63 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 17.82 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.24 (0.34), residues: 612
  helix:  1.44 (0.28), residues: 343
  sheet:  0.16 (1.62), residues: 15
  loop :  0.12 (0.39), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP I  11 
 HIS   0.006   0.002   HIS J 131 
 PHE   0.019   0.003   PHE J 156 
 TYR   0.028   0.002   TYR I  91 
 ARG   0.004   0.001   ARG I  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05713 (  276)
  hydrogen bonds       : angle       5.02428 (  762)
  covalent geometry    : bond        0.00487 ( 5228)
  covalent geometry    : angle       0.66602 ( 7079)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.560 
Fit side-chains
REVERT: H  276 ARG cc_start: 0.6199 (OUTLIER) cc_final: 0.5571 (ttt-90)
REVERT: I  250 ASP cc_start: 0.6289 (m-30) cc_final: 0.5985 (m-30)
REVERT: J  169 TYR cc_start: 0.6394 (m-80) cc_final: 0.5899 (m-80)
  outliers start: 7
  outliers final: 2
  residues processed: 93
  average time/residue: 1.6739
  time to fit residues: 160.8051
Evaluate side-chains
  91 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 88
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  276 ARG
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain I residue  218 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 54 optimal weight:    4.9990
   chunk 60 optimal weight:    0.0970
   chunk 55 optimal weight:    0.9990
   chunk 50 optimal weight:    5.9990
   chunk 51 optimal weight:    0.7980
   chunk 6 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
H 307 GLN
I 136 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 258 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.179550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.157030 restraints weight = 18050.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3908 rms_B_bonded: 2.17
r_work: 0.3709 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3704
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3704 r_free = 0.3704    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3704 r_free = 0.3704    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3704
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.0831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5228  Z= 0.122
  Angle     :  0.543   7.411   7079  Z= 0.278
  Chirality :  0.040   0.143    774
  Planarity :  0.004   0.038    898
  Dihedral  :  5.455  59.571    736
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  0.98 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 18.18 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.74 (0.35), residues: 612
  helix:  1.87 (0.29), residues: 345
  sheet:  0.19 (1.55), residues: 15
  loop :  0.31 (0.40), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP I  11 
 HIS   0.004   0.001   HIS J 258 
 PHE   0.014   0.002   PHE I  30 
 TYR   0.021   0.002   TYR I  91 
 ARG   0.002   0.000   ARG J 179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04542 (  276)
  hydrogen bonds       : angle       4.64684 (  762)
  covalent geometry    : bond        0.00263 ( 5228)
  covalent geometry    : angle       0.54277 ( 7079)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.596 
Fit side-chains
REVERT: H  251 LEU cc_start: 0.5517 (OUTLIER) cc_final: 0.5270 (tp)
REVERT: H  276 ARG cc_start: 0.6164 (OUTLIER) cc_final: 0.5563 (ttt-90)
REVERT: I  138 LYS cc_start: 0.7152 (ttmm) cc_final: 0.6902 (mttm)
REVERT: J   11 ARG cc_start: 0.5777 (ptt-90) cc_final: 0.5182 (ttt90)
REVERT: J  169 TYR cc_start: 0.6306 (m-80) cc_final: 0.5829 (m-80)
  outliers start: 8
  outliers final: 2
  residues processed: 92
  average time/residue: 1.7808
  time to fit residues: 170.0063
Evaluate side-chains
  93 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 89
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  251 LEU
Chi-restraints excluded: chain H residue  276 ARG
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain I residue  218 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 28 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 6 optimal weight:    6.9990
   chunk 51 optimal weight:    0.2980
   chunk 1 optimal weight:    0.1980
   chunk 21 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   chunk 34 optimal weight:    7.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
H 307 GLN
I 136 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 258 HIS
J 297 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.178945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.155444 restraints weight = 20056.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3887 rms_B_bonded: 2.46
r_work: 0.3690 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3686
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3686 r_free = 0.3686    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3686 r_free = 0.3686    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3686
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.0789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5228  Z= 0.137
  Angle     :  0.562   7.703   7079  Z= 0.287
  Chirality :  0.040   0.141    774
  Planarity :  0.005   0.038    898
  Dihedral  :  5.481  59.861    736
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.47 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 17.82 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.68 (0.35), residues: 612
  helix:  1.81 (0.29), residues: 345
  sheet:  0.46 (1.56), residues: 15
  loop :  0.28 (0.40), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP I  11 
 HIS   0.005   0.001   HIS J 131 
 PHE   0.015   0.002   PHE J  91 
 TYR   0.022   0.002   TYR I  91 
 ARG   0.002   0.000   ARG H 268 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04720 (  276)
  hydrogen bonds       : angle       4.67084 (  762)
  covalent geometry    : bond        0.00303 ( 5228)
  covalent geometry    : angle       0.56196 ( 7079)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.567 
Fit side-chains
REVERT: H  251 LEU cc_start: 0.5521 (OUTLIER) cc_final: 0.5294 (tp)
REVERT: H  276 ARG cc_start: 0.6157 (OUTLIER) cc_final: 0.5506 (ttt-90)
REVERT: I  138 LYS cc_start: 0.7148 (ttmm) cc_final: 0.6893 (mttm)
REVERT: J   11 ARG cc_start: 0.5780 (ptt-90) cc_final: 0.5172 (ttt90)
REVERT: J  169 TYR cc_start: 0.6335 (m-80) cc_final: 0.5831 (m-80)
  outliers start: 12
  outliers final: 4
  residues processed: 96
  average time/residue: 1.4843
  time to fit residues: 147.6399
Evaluate side-chains
  94 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  251 LEU
Chi-restraints excluded: chain H residue  276 ARG
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain I residue  218 LEU
Chi-restraints excluded: chain I residue  227 THR
Chi-restraints excluded: chain J residue  248 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 18 optimal weight:    0.3980
   chunk 33 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 51 optimal weight:    0.5980
   chunk 57 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
H 307 GLN
I 136 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 258 HIS
J 297 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.179140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.155774 restraints weight = 17408.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3891 rms_B_bonded: 2.30
r_work: 0.3714 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3616 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3611
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3611 r_free = 0.3611    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3611 r_free = 0.3611    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3611
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.0854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5228  Z= 0.131
  Angle     :  0.560   7.598   7079  Z= 0.285
  Chirality :  0.040   0.141    774
  Planarity :  0.005   0.039    898
  Dihedral  :  5.435  59.857    736
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.14 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 18.36 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.72 (0.35), residues: 612
  helix:  1.84 (0.29), residues: 345
  sheet:  0.62 (1.58), residues: 15
  loop :  0.31 (0.40), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP I  11 
 HIS   0.005   0.001   HIS J 131 
 PHE   0.014   0.002   PHE J  91 
 TYR   0.022   0.002   TYR I  91 
 ARG   0.002   0.000   ARG H 268 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04612 (  276)
  hydrogen bonds       : angle       4.62657 (  762)
  covalent geometry    : bond        0.00289 ( 5228)
  covalent geometry    : angle       0.56030 ( 7079)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.614 
Fit side-chains
REVERT: H  276 ARG cc_start: 0.6115 (OUTLIER) cc_final: 0.5499 (ttt-90)
REVERT: J   11 ARG cc_start: 0.5803 (ptt-90) cc_final: 0.5124 (ttt90)
REVERT: J   83 HIS cc_start: 0.6201 (OUTLIER) cc_final: 0.5850 (m-70)
REVERT: J  169 TYR cc_start: 0.6385 (m-80) cc_final: 0.5795 (m-80)
  outliers start: 9
  outliers final: 3
  residues processed: 90
  average time/residue: 1.4393
  time to fit residues: 134.4317
Evaluate side-chains
  91 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  276 ARG
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain I residue  218 LEU
Chi-restraints excluded: chain I residue  237 MET
Chi-restraints excluded: chain J residue   83 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 3 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 53 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   chunk 41 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
H 307 GLN
I 136 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 258 HIS
J 297 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.179161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.155800 restraints weight = 21097.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.3892 rms_B_bonded: 2.56
r_work: 0.3692 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3688
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3688 r_free = 0.3688    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3688 r_free = 0.3688    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3688
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.0850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5228  Z= 0.132
  Angle     :  0.568   7.697   7079  Z= 0.289
  Chirality :  0.040   0.140    774
  Planarity :  0.005   0.038    898
  Dihedral  :  5.421  59.933    736
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.14 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 18.55 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.73 (0.35), residues: 612
  helix:  1.84 (0.29), residues: 345
  sheet:  0.76 (1.60), residues: 15
  loop :  0.31 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP I  11 
 HIS   0.005   0.001   HIS J 131 
 PHE   0.016   0.002   PHE J  17 
 TYR   0.022   0.002   TYR I  91 
 ARG   0.003   0.000   ARG H 268 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04583 (  276)
  hydrogen bonds       : angle       4.59873 (  762)
  covalent geometry    : bond        0.00294 ( 5228)
  covalent geometry    : angle       0.56808 ( 7079)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.572 
Fit side-chains
REVERT: H  276 ARG cc_start: 0.6121 (OUTLIER) cc_final: 0.5474 (ttt-90)
REVERT: J   11 ARG cc_start: 0.5832 (ptt-90) cc_final: 0.5204 (ttt90)
REVERT: J   83 HIS cc_start: 0.5963 (OUTLIER) cc_final: 0.5623 (m-70)
REVERT: J  169 TYR cc_start: 0.6304 (m-80) cc_final: 0.5802 (m-80)
  outliers start: 8
  outliers final: 5
  residues processed: 89
  average time/residue: 1.4829
  time to fit residues: 136.7885
Evaluate side-chains
  88 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  276 ARG
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain I residue  218 LEU
Chi-restraints excluded: chain I residue  227 THR
Chi-restraints excluded: chain I residue  237 MET
Chi-restraints excluded: chain J residue   83 HIS
Chi-restraints excluded: chain J residue  248 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 30 optimal weight:   10.0000
   chunk 9 optimal weight:    8.9990
   chunk 36 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
H 307 GLN
I 136 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 258 HIS
J 297 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.179196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.156250 restraints weight = 18714.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3896 rms_B_bonded: 2.21
r_work: 0.3710 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3615 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3609
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3609 r_free = 0.3609    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3609 r_free = 0.3609    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3609
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.0943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5228  Z= 0.132
  Angle     :  0.576   8.010   7079  Z= 0.291
  Chirality :  0.040   0.140    774
  Planarity :  0.005   0.038    898
  Dihedral  :  5.456  59.884    736
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.14 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 18.55 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.74 (0.35), residues: 612
  helix:  1.84 (0.29), residues: 345
  sheet:  0.81 (1.58), residues: 15
  loop :  0.32 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP I  11 
 HIS   0.005   0.001   HIS J 131 
 PHE   0.019   0.002   PHE J  17 
 TYR   0.022   0.002   TYR I  91 
 ARG   0.003   0.000   ARG H 268 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04561 (  276)
  hydrogen bonds       : angle       4.58620 (  762)
  covalent geometry    : bond        0.00294 ( 5228)
  covalent geometry    : angle       0.57627 ( 7079)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.631 
Fit side-chains
REVERT: H  276 ARG cc_start: 0.6131 (OUTLIER) cc_final: 0.5525 (ttt-90)
REVERT: J   11 ARG cc_start: 0.5827 (ptt-90) cc_final: 0.5150 (ttt90)
REVERT: J   83 HIS cc_start: 0.6143 (OUTLIER) cc_final: 0.5794 (m-70)
REVERT: J  169 TYR cc_start: 0.6400 (m-80) cc_final: 0.5798 (m-80)
  outliers start: 8
  outliers final: 5
  residues processed: 88
  average time/residue: 1.6236
  time to fit residues: 147.7937
Evaluate side-chains
  87 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  276 ARG
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain I residue  218 LEU
Chi-restraints excluded: chain I residue  227 THR
Chi-restraints excluded: chain I residue  237 MET
Chi-restraints excluded: chain J residue   83 HIS
Chi-restraints excluded: chain J residue  248 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 34 optimal weight:    7.9990
   chunk 25 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 38 optimal weight:    9.9990
   chunk 7 optimal weight:    1.9990
   chunk 51 optimal weight:    0.1980
   chunk 42 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
H 307 GLN
I 136 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 258 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.179253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.155290 restraints weight = 12896.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3884 rms_B_bonded: 1.74
r_work: 0.3761 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3663 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3659
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3659 r_free = 0.3659    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3659 r_free = 0.3659    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3659
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.0909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5228  Z= 0.133
  Angle     :  0.583   8.226   7079  Z= 0.295
  Chirality :  0.040   0.140    774
  Planarity :  0.005   0.038    898
  Dihedral  :  5.476  59.905    736
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.14 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 18.91 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.70 (0.34), residues: 612
  helix:  1.83 (0.29), residues: 345
  sheet:  0.64 (1.72), residues: 9
  loop :  0.27 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP I  11 
 HIS   0.005   0.001   HIS J 131 
 PHE   0.021   0.002   PHE J  17 
 TYR   0.022   0.002   TYR I  91 
 ARG   0.003   0.000   ARG H 268 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04547 (  276)
  hydrogen bonds       : angle       4.56915 (  762)
  covalent geometry    : bond        0.00297 ( 5228)
  covalent geometry    : angle       0.58294 ( 7079)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.578 
Fit side-chains
REVERT: H  276 ARG cc_start: 0.6131 (OUTLIER) cc_final: 0.5505 (ttt-90)
REVERT: J   11 ARG cc_start: 0.5809 (ptt-90) cc_final: 0.5173 (ttt90)
REVERT: J   83 HIS cc_start: 0.6014 (OUTLIER) cc_final: 0.5675 (m-70)
REVERT: J  169 TYR cc_start: 0.6363 (m-80) cc_final: 0.5808 (m-80)
  outliers start: 7
  outliers final: 4
  residues processed: 86
  average time/residue: 1.5057
  time to fit residues: 134.3406
Evaluate side-chains
  89 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  276 ARG
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain I residue  218 LEU
Chi-restraints excluded: chain I residue  227 THR
Chi-restraints excluded: chain J residue   83 HIS
Chi-restraints excluded: chain J residue  248 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 56 optimal weight:    5.9990
   chunk 21 optimal weight:    0.0670
   chunk 12 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 33 optimal weight:    0.2980
   chunk 26 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0670
   chunk 58 optimal weight:    0.0980
   chunk 34 optimal weight:    0.4980
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.2056

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

Flipped N/Q/H residues before XYZ refinement:
H 307 GLN
I 136 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 258 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.183459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.160959 restraints weight = 20750.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3953 rms_B_bonded: 2.75
r_work: 0.3742 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3738
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3738 r_free = 0.3738    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3738 r_free = 0.3738    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3738
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.1405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5228  Z= 0.102
  Angle     :  0.520   6.611   7079  Z= 0.263
  Chirality :  0.039   0.142    774
  Planarity :  0.004   0.040    898
  Dihedral  :  5.235  58.940    736
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.14 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 20.00 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.35), residues: 612
  helix:  2.21 (0.29), residues: 340
  sheet:  0.72 (1.46), residues: 15
  loop :  0.44 (0.40), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP I  11 
 HIS   0.005   0.001   HIS J 258 
 PHE   0.021   0.001   PHE J  17 
 TYR   0.018   0.001   TYR I  60 
 ARG   0.003   0.000   ARG H 268 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03683 (  276)
  hydrogen bonds       : angle       4.28174 (  762)
  covalent geometry    : bond        0.00222 ( 5228)
  covalent geometry    : angle       0.51978 ( 7079)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 93
  time to evaluate  : 0.625 
Fit side-chains
REVERT: I  138 LYS cc_start: 0.7133 (ttmm) cc_final: 0.6856 (mttm)
REVERT: J   11 ARG cc_start: 0.5832 (ptt-90) cc_final: 0.5122 (ttt180)
REVERT: J   83 HIS cc_start: 0.6012 (OUTLIER) cc_final: 0.5673 (m-70)
REVERT: J  169 TYR cc_start: 0.6269 (m-80) cc_final: 0.5640 (m-80)
  outliers start: 2
  outliers final: 1
  residues processed: 95
  average time/residue: 1.4348
  time to fit residues: 141.3471
Evaluate side-chains
  85 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 83
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  218 LEU
Chi-restraints excluded: chain J residue   83 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 38 optimal weight:   10.0000
   chunk 50 optimal weight:    1.9990
   chunk 3 optimal weight:    9.9990
   chunk 5 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 55 optimal weight:    0.1980
   chunk 31 optimal weight:    4.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
H 307 GLN
I 136 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 258 HIS
J 297 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.179394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.155469 restraints weight = 22675.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3887 rms_B_bonded: 2.84
r_work: 0.3690 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3686
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3686 r_free = 0.3686    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3686 r_free = 0.3686    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3686
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.1191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5228  Z= 0.143
  Angle     :  0.582   7.578   7079  Z= 0.293
  Chirality :  0.041   0.139    774
  Planarity :  0.005   0.038    898
  Dihedral  :  5.413  59.762    736
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.14 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 19.64 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.88 (0.35), residues: 612
  helix:  1.96 (0.29), residues: 345
  sheet:  0.61 (1.45), residues: 15
  loop :  0.39 (0.40), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP J 132 
 HIS   0.005   0.001   HIS J 131 
 PHE   0.024   0.002   PHE J  17 
 TYR   0.023   0.002   TYR I  91 
 ARG   0.005   0.000   ARG I  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04614 (  276)
  hydrogen bonds       : angle       4.52201 (  762)
  covalent geometry    : bond        0.00320 ( 5228)
  covalent geometry    : angle       0.58182 ( 7079)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6019.75 seconds
wall clock time: 104 minutes 24.05 seconds (6264.05 seconds total)