Starting phenix.real_space_refine
on Wed Sep 17 07:21:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zl9_38897/09_2025/8zl9_38897.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zl9_38897/09_2025/8zl9_38897.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zl9_38897/09_2025/8zl9_38897.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zl9_38897/09_2025/8zl9_38897.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zl9_38897/09_2025/8zl9_38897.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zl9_38897/09_2025/8zl9_38897.cif"
  }
  resolution = 4.36
  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=  -0.001 sd=   0.059
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      30      5.16       5
     C    4208      2.51       5
     N    1171      2.21       5
     O    1235      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6644
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 926
          Classifications: {'peptide': 122}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 117}
    Chain: "B"
      Number of atoms: 875
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 875
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 102}
    Chain: "C"
      Number of atoms: 1276
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 160, 1276
          Classifications: {'peptide': 160}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 143}
          Chain breaks: 4
    Chain: "D"
      Number of atoms: 1608
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1608
          Classifications: {'peptide': 202}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 181}
          Chain breaks: 5
    Chain: "E"
      Number of atoms: 1959
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 244, 1959
          Classifications: {'peptide': 244}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 220}
          Chain breaks: 4
  Time building chain proxies: 1.74, per 1000 atoms: 0.26
  Number of scatterers: 6644
  At special positions: 0
  Unit cell: (105.93, 90.95, 102.72, 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      30     16.00
     O    1235      8.00
     N    1171      7.00
     C    4208      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  35 " - pdb=" SG  CYS A  50 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 102 " - pdb=" SG  CYS A 107 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  92 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.49
  Conformation dependent library (CDL) restraints added in 347.1 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1540

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 17 sheets defined
      3.2% alpha, 15.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'B' and resid 83 through 87
      removed outlier: 3.553A  pdb=" N   ASP B  86 " --> pdb=" O   GLU B  83 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ALA B  87 " --> pdb=" O   ALA B  84 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 83 through 87'
    Processing helix  chain 'C' and resid 130 through 132
      No H-bonds generated for 'chain 'C' and resid 130 through 132'
    Processing helix  chain 'D' and resid 129 through 133
      removed outlier: 4.022A  pdb=" N   GLY D 132 " --> pdb=" O   GLY D 129 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLN D 133 " --> pdb=" O   ALA D 130 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 129 through 133'
    Processing helix  chain 'E' and resid 130 through 132
      No H-bonds generated for 'chain 'E' and resid 130 through 132'
    Processing helix  chain 'E' and resid 182 through 186
    Processing helix  chain 'E' and resid 482 through 487
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7
      removed outlier: 3.659A  pdb=" N   SER A   7 " --> pdb=" O   SER A  21 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39
    Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 71
    Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 94
      removed outlier: 3.964A  pdb=" N   TYR A  94 " --> pdb=" O   VAL A 116 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   VAL A 116 " --> pdb=" O   TYR A  94 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 7
      removed outlier: 3.801A  pdb=" N   ALA B  19 " --> pdb=" O   ILE B  79 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ILE B  79 " --> pdb=" O   ALA B  19 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   PHE B  75 " --> pdb=" O   CYS B  23 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13
      removed outlier: 3.916A  pdb=" N   GLY B  88 " --> pdb=" O   LEU B 108 " (cutoff:3.500A)
      removed outlier: 7.805A  pdb=" N   TRP B  39 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   LEU B  51 " --> pdb=" O   TRP B  39 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ASN B  57 " --> pdb=" O   TYR B  53 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 126 through 128
    Processing sheet with id=AA8, first strand: chain 'C' and resid 157 through 158
    Processing sheet with id=AA9, first strand: chain 'C' and resid 241 through 244
      removed outlier: 3.640A  pdb=" N   ASP C 305 " --> pdb=" O   CYS C 243 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 313 through 314
    Processing sheet with id=AB2, first strand: chain 'D' and resid 154 through 158
      removed outlier: 4.137A  pdb=" N   VAL D 154 " --> pdb=" O   SER D 379 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   PHE D 375 " --> pdb=" O   VAL D 158 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LYS D 394 " --> pdb=" O   VAL D 376 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 154 through 158
      removed outlier: 4.137A  pdb=" N   VAL D 154 " --> pdb=" O   SER D 379 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   PHE D 375 " --> pdb=" O   VAL D 158 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   ARG D 389 " --> pdb=" O   SER D 521 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 241 through 242
      removed outlier: 3.514A  pdb=" N   VAL D 310 " --> pdb=" O   TYR E 312 " (cutoff:3.500A)
      removed outlier: 4.773A  pdb=" N   TYR E 312 " --> pdb=" O   VAL D 310 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 496 through 498
    Processing sheet with id=AB6, first strand: chain 'E' and resid 125 through 128
      removed outlier: 3.536A  pdb=" N   THR E 125 " --> pdb=" O   PHE E 137 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 375 through 377
    Processing sheet with id=AB8, first strand: chain 'E' and resid 492 through 498

    86 hydrogen bonds defined for protein.
    195 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: 0.73

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1413
        1.33 -     1.45: 1743
        1.45 -     1.58: 3639
        1.58 -     1.70: 0
        1.70 -     1.82: 39
  Bond restraints: 6834
  Sorted by residual:
  bond pdb=" C   PHE D 137 "
       pdb=" N   PRO D 138 "
    ideal  model  delta    sigma   weight residual
    1.332  1.364 -0.032 1.33e-02 5.65e+03 5.79e+00
  bond pdb=" N   PRO D 138 "
       pdb=" CA  PRO D 138 "
    ideal  model  delta    sigma   weight residual
    1.466  1.495 -0.029 1.23e-02 6.61e+03 5.48e+00
  bond pdb=" C   PRO D 138 "
       pdb=" O   PRO D 138 "
    ideal  model  delta    sigma   weight residual
    1.233  1.204  0.028 1.23e-02 6.61e+03 5.32e+00
  bond pdb=" C   LEU E 515 "
       pdb=" N   PRO E 516 "
    ideal  model  delta    sigma   weight residual
    1.334  1.385 -0.052 2.34e-02 1.83e+03 4.85e+00
  bond pdb=" C   PRO E 531 "
       pdb=" O   PRO E 531 "
    ideal  model  delta    sigma   weight residual
    1.235  1.208  0.027 1.30e-02 5.92e+03 4.21e+00
  ... (remaining 6829 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.59: 9025
        2.59 -     5.19: 227
        5.19 -     7.78: 36
        7.78 -    10.37: 8
       10.37 -    12.96: 3
  Bond angle restraints: 9299
  Sorted by residual:
  angle pdb=" N   PRO D 138 "
        pdb=" CA  PRO D 138 "
        pdb=" C   PRO D 138 "
      ideal   model   delta    sigma   weight residual
     111.11  124.07  -12.96 1.59e+00 3.96e-01 6.65e+01
  angle pdb=" C   THR D 136 "
        pdb=" N   PHE D 137 "
        pdb=" CA  PHE D 137 "
      ideal   model   delta    sigma   weight residual
     122.85  115.30    7.55 1.10e+00 8.26e-01 4.71e+01
  angle pdb=" C   PRO D 138 "
        pdb=" CA  PRO D 138 "
        pdb=" CB  PRO D 138 "
      ideal   model   delta    sigma   weight residual
     111.39  102.76    8.63 1.28e+00 6.10e-01 4.54e+01
  angle pdb=" C   PHE D 137 "
        pdb=" CA  PHE D 137 "
        pdb=" CB  PHE D 137 "
      ideal   model   delta    sigma   weight residual
     111.27  120.71   -9.44 1.47e+00 4.63e-01 4.13e+01
  angle pdb=" C   ARG E 511 "
        pdb=" N   ASP E 512 "
        pdb=" CA  ASP E 512 "
      ideal   model   delta    sigma   weight residual
     121.54  133.32  -11.78 1.91e+00 2.74e-01 3.80e+01
  ... (remaining 9294 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 3616
       17.93 -    35.87: 356
       35.87 -    53.80: 57
       53.80 -    71.73: 6
       71.73 -    89.67: 9
  Dihedral angle restraints: 4044
    sinusoidal: 1642
      harmonic: 2402
  Sorted by residual:
  dihedral pdb=" CA  MET A 109 "
           pdb=" C   MET A 109 "
           pdb=" N   ASP A 110 "
           pdb=" CA  ASP A 110 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -134.41  -45.59     0      5.00e+00 4.00e-02 8.31e+01
  dihedral pdb=" CB  CYS A 102 "
           pdb=" SG  CYS A 102 "
           pdb=" SG  CYS A 107 "
           pdb=" CB  CYS A 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -163.06   77.06     1      1.00e+01 1.00e-02 7.45e+01
  dihedral pdb=" CB  CYS A  35 "
           pdb=" SG  CYS A  35 "
           pdb=" SG  CYS A  50 "
           pdb=" CB  CYS A  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -160.35   74.35     1      1.00e+01 1.00e-02 7.01e+01
  ... (remaining 4041 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 727
       0.054 -    0.108: 170
       0.108 -    0.162: 62
       0.162 -    0.217: 7
       0.217 -    0.271: 6
  Chirality restraints: 972
  Sorted by residual:
  chirality pdb=" CB  THR A  91 "
            pdb=" CA  THR A  91 "
            pdb=" OG1 THR A  91 "
            pdb=" CG2 THR A  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.28    0.27 2.00e-01 2.50e+01 1.83e+00
  chirality pdb=" CB  THR E 513 "
            pdb=" CA  THR E 513 "
            pdb=" OG1 THR E 513 "
            pdb=" CG2 THR E 513 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.29    0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CA  PRO D 138 "
            pdb=" N   PRO D 138 "
            pdb=" C   PRO D 138 "
            pdb=" CB  PRO D 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.25 2.00e-01 2.50e+01 1.58e+00
  ... (remaining 969 not shown)

  Planarity restraints: 1223
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU E 515 "   -0.051 5.00e-02 4.00e+02   7.60e-02 9.25e+00
        pdb=" N   PRO E 516 "    0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO E 516 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO E 516 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C 159 "    0.048 5.00e-02 4.00e+02   7.26e-02 8.44e+00
        pdb=" N   PRO C 160 "   -0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO C 160 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO C 160 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 511 "   -0.215 9.50e-02 1.11e+02   9.67e-02 6.04e+00
        pdb=" NE  ARG C 511 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 511 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 511 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 511 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1220 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1116
        2.77 -     3.31: 5859
        3.31 -     3.84: 11071
        3.84 -     4.37: 11863
        4.37 -     4.90: 20066
  Nonbonded interactions: 49975
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 100 "
            pdb=" OG  SER E 387 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" OD1 ASN D 390 "
            pdb=" OG  SER D 521 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OG1 THR B  56 "
            pdb=" OD1 ASN B  57 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   PRO B   8 "
            pdb=" OG1 THR B 106 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OG1 THR B   5 "
            pdb=" O   ARG B  24 "
     model   vdw
     2.286 3.040
  ... (remaining 49970 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.110
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.410
  Find NCS groups from input model:        0.020
  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:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5197
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      :  0.005   0.067   6838  Z= 0.222
  Angle     :  1.007  12.964   9307  Z= 0.549
  Chirality :  0.058   0.271    972
  Planarity :  0.009   0.097   1223
  Dihedral  : 14.246  89.668   2492
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  7.61 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.55 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.40 %

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 aren not related in a simple way.
  whole: -2.34 (0.27), residues: 802
  helix: -4.35 (0.70), residues: 12
  sheet: -0.61 (0.38), residues: 171
  loop : -1.94 (0.23), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG C 392 
 TYR   0.032   0.002   TYR D 155 
 PHE   0.031   0.003   PHE A  29 
 TRP   0.032   0.003   TRP B 100 
 HIS   0.004   0.001   HIS E 503 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 6834)
  covalent geometry    : angle       1.00551 ( 9299)
  SS BOND              : bond        0.00509 (    4)
  SS BOND              : angle       2.23700 (    8)
  hydrogen bonds       : bond        0.28950 (   82)
  hydrogen bonds       : angle      11.16141 (  195)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  319 THR cc_start: 0.8307 (m) cc_final: 0.8024 (p)
REVERT: C  509 GLN cc_start: 0.6261 (OUTLIER) cc_final: 0.5994 (mm-40)
  outliers start: 1
  outliers final: 0
  residues processed: 116
  average time/residue: 0.0861
  time to fit residues: 13.4857
Evaluate side-chains
  86 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0060
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.0570
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    1.3718

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
A  82 GLN
B  57 ASN
D 315 ASN
** D 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 509 GLN
E 127 GLN
E 483 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4745 r_free = 0.4745 target = 0.222288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.205283 restraints weight = 15212.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.207375 restraints weight = 12034.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.208544 restraints weight = 9949.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4607 r_free = 0.4607 target = 0.209999 restraints weight = 8716.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.210829 restraints weight = 7616.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.4605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5500
moved from start:          0.1916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6838  Z= 0.180
  Angle     :  0.743   9.917   9307  Z= 0.384
  Chirality :  0.047   0.178    972
  Planarity :  0.008   0.078   1223
  Dihedral  :  6.522  35.843    913
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 19.40
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  8.98 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  5.76 %
    Favored  : 93.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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 aren not related in a simple way.
  whole: -2.38 (0.28), residues: 802
  helix: -4.38 (0.49), residues: 12
  sheet: -0.91 (0.34), residues: 201
  loop : -1.90 (0.24), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 392 
 TYR   0.030   0.002   TYR A 103 
 PHE   0.016   0.003   PHE E 381 
 TRP   0.026   0.002   TRP A 112 
 HIS   0.004   0.001   HIS E 502 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 6834)
  covalent geometry    : angle       0.74027 ( 9299)
  SS BOND              : bond        0.00716 (    4)
  SS BOND              : angle       2.23037 (    8)
  hydrogen bonds       : bond        0.04394 (   82)
  hydrogen bonds       : angle       8.01701 (  195)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 106
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   21 ILE cc_start: 0.7570 (mp) cc_final: 0.7281 (mp)
REVERT: B   25 SER cc_start: 0.6350 (p) cc_final: 0.5989 (m)
REVERT: B   75 PHE cc_start: 0.2880 (m-80) cc_final: 0.2049 (m-80)
REVERT: C  319 THR cc_start: 0.8295 (m) cc_final: 0.8011 (p)
REVERT: D  509 GLN cc_start: -0.1531 (OUTLIER) cc_final: -0.1764 (mm110)
REVERT: E  230 GLN cc_start: 0.7126 (pm20) cc_final: 0.6564 (pp30)
REVERT: E  482 HIS cc_start: 0.6131 (m-70) cc_final: 0.5703 (m90)
  outliers start: 3
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0816
  time to fit residues: 12.3167
Evaluate side-chains
  90 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 25 optimal weight:    7.9990
   chunk 36 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 7 optimal weight:   10.0000
   chunk 65 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0470
   chunk 4 optimal weight:    0.0270
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
B  35 ASN
D 315 ASN
** D 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 114 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4799 r_free = 0.4799 target = 0.227480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4596 r_free = 0.4596 target = 0.209433 restraints weight = 15010.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4630 r_free = 0.4630 target = 0.212209 restraints weight = 11021.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4653 r_free = 0.4653 target = 0.214283 restraints weight = 8585.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.215847 restraints weight = 7081.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4686 r_free = 0.4686 target = 0.217042 restraints weight = 5961.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.4691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5295
moved from start:          0.2191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6838  Z= 0.119
  Angle     :  0.653   7.563   9307  Z= 0.335
  Chirality :  0.046   0.174    972
  Planarity :  0.007   0.082   1223
  Dihedral  :  5.948  36.445    913
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  6.98 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.74 %
    Favored  : 97.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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 aren not related in a simple way.
  whole: -2.28 (0.28), residues: 802
  helix: -3.73 (0.83), residues: 12
  sheet: -0.96 (0.31), residues: 234
  loop : -1.81 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 307 
 TYR   0.015   0.001   TYR A 103 
 PHE   0.010   0.002   PHE E 371 
 TRP   0.017   0.002   TRP B  36 
 HIS   0.003   0.000   HIS D 482 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6834)
  covalent geometry    : angle       0.65165 ( 9299)
  SS BOND              : bond        0.00382 (    4)
  SS BOND              : angle       1.54385 (    8)
  hydrogen bonds       : bond        0.03434 (   82)
  hydrogen bonds       : angle       7.21198 (  195)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 MET cc_start: 0.3796 (ttm) cc_final: 0.3233 (ttm)
REVERT: B   21 ILE cc_start: 0.7594 (mp) cc_final: 0.7333 (mp)
REVERT: B   25 SER cc_start: 0.6182 (p) cc_final: 0.5888 (m)
REVERT: C  319 THR cc_start: 0.8278 (m) cc_final: 0.7985 (p)
REVERT: E  230 GLN cc_start: 0.7287 (pm20) cc_final: 0.6869 (pp30)
REVERT: E  482 HIS cc_start: 0.6001 (m-70) cc_final: 0.5575 (m90)
  outliers start: 1
  outliers final: 0
  residues processed: 116
  average time/residue: 0.0893
  time to fit residues: 13.9230
Evaluate side-chains
  88 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 80 optimal weight:    0.8980
   chunk 38 optimal weight:    5.9990
   chunk 79 optimal weight:    3.9990
   chunk 74 optimal weight:    0.3980
   chunk 81 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0980
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
D 315 ASN
** D 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4780 r_free = 0.4780 target = 0.225626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.208330 restraints weight = 14998.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4610 r_free = 0.4610 target = 0.210657 restraints weight = 11394.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4631 r_free = 0.4631 target = 0.212484 restraints weight = 9178.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4646 r_free = 0.4646 target = 0.213762 restraints weight = 7682.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4659 r_free = 0.4659 target = 0.214823 restraints weight = 6663.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.4656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5355
moved from start:          0.2520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6838  Z= 0.124
  Angle     :  0.645   8.049   9307  Z= 0.330
  Chirality :  0.046   0.304    972
  Planarity :  0.007   0.083   1223
  Dihedral  :  5.729  34.418    913
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 16.16
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  9.10 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.61 %
    Favored  : 97.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.40 %

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 aren not related in a simple way.
  whole: -2.18 (0.28), residues: 802
  helix: -3.55 (0.89), residues: 12
  sheet: -0.85 (0.32), residues: 233
  loop : -1.77 (0.26), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  38 
 TYR   0.017   0.001   TYR A 103 
 PHE   0.012   0.002   PHE E 371 
 TRP   0.016   0.002   TRP A  47 
 HIS   0.004   0.001   HIS E 484 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6834)
  covalent geometry    : angle       0.64370 ( 9299)
  SS BOND              : bond        0.00507 (    4)
  SS BOND              : angle       1.57712 (    8)
  hydrogen bonds       : bond        0.03126 (   82)
  hydrogen bonds       : angle       6.70672 (  195)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.8075 (ptp90) cc_final: 0.7866 (ptp90)
REVERT: A  109 MET cc_start: 0.4234 (ttm) cc_final: 0.3663 (ttm)
REVERT: B   21 ILE cc_start: 0.7525 (mp) cc_final: 0.7221 (mp)
REVERT: B   25 SER cc_start: 0.5968 (p) cc_final: 0.5688 (m)
REVERT: C  319 THR cc_start: 0.8397 (m) cc_final: 0.8138 (p)
REVERT: E  230 GLN cc_start: 0.7403 (pm20) cc_final: 0.7016 (pp30)
REVERT: E  482 HIS cc_start: 0.5879 (m-70) cc_final: 0.5490 (m90)
  outliers start: 1
  outliers final: 0
  residues processed: 111
  average time/residue: 0.0805
  time to fit residues: 12.1380
Evaluate side-chains
  91 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 72 optimal weight:    0.3980
   chunk 51 optimal weight:    5.9990
   chunk 48 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0470
   chunk 66 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    1.0282

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

Flipped N/Q/H residues before XYZ refinement:
** B  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 123 GLN
D 315 ASN
** D 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4747 r_free = 0.4747 target = 0.222543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4578 r_free = 0.4578 target = 0.208281 restraints weight = 15538.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4592 r_free = 0.4592 target = 0.209508 restraints weight = 12534.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4610 r_free = 0.4610 target = 0.210901 restraints weight = 10768.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4623 r_free = 0.4623 target = 0.212013 restraints weight = 9355.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.4626 r_free = 0.4626 target = 0.212273 restraints weight = 8204.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.4625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5434
moved from start:          0.2857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6838  Z= 0.142
  Angle     :  0.670   8.910   9307  Z= 0.342
  Chirality :  0.046   0.168    972
  Planarity :  0.007   0.077   1223
  Dihedral  :  5.793  34.647    913
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 17.09
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  9.73 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.33 %
    Favored  : 97.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.40 %

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 aren not related in a simple way.
  whole: -2.17 (0.28), residues: 802
  helix: -3.72 (0.80), residues: 12
  sheet: -0.93 (0.32), residues: 224
  loop : -1.70 (0.26), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 511 
 TYR   0.019   0.001   TYR A 103 
 PHE   0.011   0.002   PHE E 393 
 TRP   0.019   0.002   TRP A  47 
 HIS   0.003   0.001   HIS D 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 6834)
  covalent geometry    : angle       0.66832 ( 9299)
  SS BOND              : bond        0.00594 (    4)
  SS BOND              : angle       1.82018 (    8)
  hydrogen bonds       : bond        0.03189 (   82)
  hydrogen bonds       : angle       6.62443 (  195)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.8020 (ptp90) cc_final: 0.7797 (ptp90)
REVERT: A   48 LEU cc_start: 0.6681 (mt) cc_final: 0.6236 (mt)
REVERT: A  109 MET cc_start: 0.4169 (ttm) cc_final: 0.3550 (ttm)
REVERT: B   21 ILE cc_start: 0.7289 (mp) cc_final: 0.6965 (mp)
REVERT: C  319 THR cc_start: 0.8437 (m) cc_final: 0.8171 (p)
REVERT: E  230 GLN cc_start: 0.7497 (pm20) cc_final: 0.7151 (pp30)
REVERT: E  482 HIS cc_start: 0.5747 (m-70) cc_final: 0.5337 (m-70)
  outliers start: 1
  outliers final: 0
  residues processed: 113
  average time/residue: 0.0855
  time to fit residues: 13.1395
Evaluate side-chains
  94 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0030
   chunk 5 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 82 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.7192

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

Flipped N/Q/H residues before XYZ refinement:
** B  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 503 HIS
D 315 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4780 r_free = 0.4780 target = 0.226178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4651 r_free = 0.4651 target = 0.215369 restraints weight = 15677.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4661 r_free = 0.4661 target = 0.216310 restraints weight = 13235.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4674 r_free = 0.4674 target = 0.217269 restraints weight = 11494.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4679 r_free = 0.4679 target = 0.217797 restraints weight = 10254.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.4682 r_free = 0.4682 target = 0.218041 restraints weight = 9342.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.4669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5332
moved from start:          0.3076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6838  Z= 0.121
  Angle     :  0.638   7.407   9307  Z= 0.324
  Chirality :  0.046   0.260    972
  Planarity :  0.006   0.074   1223
  Dihedral  :  5.632  36.529    913
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 16.93
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.35 %
    Favored  : 90.52 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  1.37 %
    Favored  : 98.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.40 %

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 aren not related in a simple way.
  whole: -2.11 (0.28), residues: 802
  helix: -3.53 (0.88), residues: 12
  sheet: -0.97 (0.33), residues: 214
  loop : -1.62 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 392 
 TYR   0.016   0.001   TYR A 103 
 PHE   0.023   0.002   PHE D 393 
 TRP   0.031   0.002   TRP B  36 
 HIS   0.009   0.001   HIS C 503 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6834)
  covalent geometry    : angle       0.63667 ( 9299)
  SS BOND              : bond        0.00495 (    4)
  SS BOND              : angle       1.60539 (    8)
  hydrogen bonds       : bond        0.02938 (   82)
  hydrogen bonds       : angle       6.33907 (  195)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 GLU cc_start: 0.2418 (tm-30) cc_final: 0.1730 (tm-30)
REVERT: A  109 MET cc_start: 0.3471 (ttm) cc_final: 0.3022 (ttm)
REVERT: B   21 ILE cc_start: 0.7317 (mp) cc_final: 0.7017 (mp)
REVERT: C  319 THR cc_start: 0.8401 (m) cc_final: 0.8125 (p)
REVERT: E  482 HIS cc_start: 0.5606 (m-70) cc_final: 0.5224 (m90)
  outliers start: 1
  outliers final: 0
  residues processed: 111
  average time/residue: 0.0813
  time to fit residues: 12.3231
Evaluate side-chains
  91 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0060
   chunk 68 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 52 optimal weight:    0.7980
   chunk 78 optimal weight:    2.9990
   chunk 69 optimal weight:   10.0000
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
** B  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 503 HIS
D 315 ASN
D 480 ASN
** E 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4777 r_free = 0.4777 target = 0.225764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4647 r_free = 0.4647 target = 0.214937 restraints weight = 15799.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4655 r_free = 0.4655 target = 0.215667 restraints weight = 13375.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4669 r_free = 0.4669 target = 0.216733 restraints weight = 11896.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.4673 r_free = 0.4673 target = 0.217044 restraints weight = 10574.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4673 r_free = 0.4673 target = 0.217044 restraints weight = 9891.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.4658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5352
moved from start:          0.3261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6838  Z= 0.122
  Angle     :  0.644   7.514   9307  Z= 0.325
  Chirality :  0.046   0.229    972
  Planarity :  0.006   0.071   1223
  Dihedral  :  5.626  35.398    913
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 17.09
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.98 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  1.92 %
    Favored  : 97.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.40 %

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 aren not related in a simple way.
  whole: -2.09 (0.28), residues: 802
  helix: -3.36 (0.92), residues: 12
  sheet: -0.84 (0.34), residues: 206
  loop : -1.66 (0.26), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  38 
 TYR   0.024   0.001   TYR E 155 
 PHE   0.018   0.002   PHE D 393 
 TRP   0.027   0.002   TRP B  36 
 HIS   0.009   0.001   HIS C 503 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6834)
  covalent geometry    : angle       0.64278 ( 9299)
  SS BOND              : bond        0.00523 (    4)
  SS BOND              : angle       1.62991 (    8)
  hydrogen bonds       : bond        0.02896 (   82)
  hydrogen bonds       : angle       6.29505 (  195)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 GLU cc_start: 0.2621 (tm-30) cc_final: 0.2278 (tm-30)
REVERT: A   38 ARG cc_start: 0.7957 (ptp90) cc_final: 0.7573 (ptp90)
REVERT: A  109 MET cc_start: 0.3376 (ttm) cc_final: 0.2936 (ttm)
REVERT: B   21 ILE cc_start: 0.7307 (mp) cc_final: 0.7008 (mp)
REVERT: C  319 THR cc_start: 0.8387 (m) cc_final: 0.8094 (p)
REVERT: E  482 HIS cc_start: 0.5437 (m-70) cc_final: 0.5106 (m-70)
  outliers start: 2
  outliers final: 0
  residues processed: 105
  average time/residue: 0.0811
  time to fit residues: 11.5226
Evaluate side-chains
  91 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 28 optimal weight:    0.4980
   chunk 31 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 47 optimal weight:    0.8980
   chunk 62 optimal weight:    6.9990
   chunk 49 optimal weight:    0.8980
   chunk 71 optimal weight:    4.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** B  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 315 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4757 r_free = 0.4757 target = 0.223746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4631 r_free = 0.4631 target = 0.213378 restraints weight = 16003.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4641 r_free = 0.4641 target = 0.214240 restraints weight = 13752.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4644 r_free = 0.4644 target = 0.214568 restraints weight = 12204.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4645 r_free = 0.4645 target = 0.214577 restraints weight = 11346.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4655 r_free = 0.4655 target = 0.215348 restraints weight = 11322.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.4640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5408
moved from start:          0.3471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6838  Z= 0.141
  Angle     :  0.670   7.436   9307  Z= 0.339
  Chirality :  0.047   0.208    972
  Planarity :  0.007   0.071   1223
  Dihedral  :  5.727  34.656    913
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 17.24
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.48 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.82 %
    Favored  : 99.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.40 %

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 aren not related in a simple way.
  whole: -2.08 (0.29), residues: 802
  helix: -3.51 (0.94), residues: 12
  sheet: -0.77 (0.35), residues: 200
  loop : -1.66 (0.25), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  38 
 TYR   0.018   0.001   TYR D 155 
 PHE   0.017   0.002   PHE D 393 
 TRP   0.021   0.002   TRP B  36 
 HIS   0.003   0.001   HIS E 502 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 6834)
  covalent geometry    : angle       0.66828 ( 9299)
  SS BOND              : bond        0.00605 (    4)
  SS BOND              : angle       1.94343 (    8)
  hydrogen bonds       : bond        0.03077 (   82)
  hydrogen bonds       : angle       6.34290 (  195)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 MET cc_start: 0.3738 (ttm) cc_final: 0.3491 (ttm)
REVERT: B   21 ILE cc_start: 0.7288 (mp) cc_final: 0.6963 (mp)
REVERT: C  319 THR cc_start: 0.8470 (m) cc_final: 0.8179 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 104
  average time/residue: 0.0797
  time to fit residues: 11.4140
Evaluate side-chains
  92 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 74 optimal weight:    7.9990
   chunk 41 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0980
   chunk 42 optimal weight:    0.0980
   chunk 3 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
D 315 ASN
E 483 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4784 r_free = 0.4784 target = 0.226653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4662 r_free = 0.4662 target = 0.215847 restraints weight = 16117.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4661 r_free = 0.4661 target = 0.216073 restraints weight = 17113.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4670 r_free = 0.4670 target = 0.216981 restraints weight = 14992.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4676 r_free = 0.4676 target = 0.217520 restraints weight = 12373.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4678 r_free = 0.4678 target = 0.217770 restraints weight = 11182.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.4662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5344
moved from start:          0.3541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6838  Z= 0.116
  Angle     :  0.647   9.313   9307  Z= 0.324
  Chirality :  0.046   0.196    972
  Planarity :  0.006   0.070   1223
  Dihedral  :  5.551  35.917    913
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 16.16
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  9.10 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.69 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.40 %

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 aren not related in a simple way.
  whole: -2.04 (0.29), residues: 802
  helix: -3.45 (1.03), residues: 12
  sheet: -0.82 (0.35), residues: 200
  loop : -1.61 (0.25), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  38 
 TYR   0.015   0.001   TYR D 155 
 PHE   0.014   0.002   PHE D 393 
 TRP   0.023   0.002   TRP B  36 
 HIS   0.002   0.000   HIS D 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6834)
  covalent geometry    : angle       0.64597 ( 9299)
  SS BOND              : bond        0.00516 (    4)
  SS BOND              : angle       1.63185 (    8)
  hydrogen bonds       : bond        0.02873 (   82)
  hydrogen bonds       : angle       6.09923 (  195)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 MET cc_start: 0.4007 (ttm) cc_final: 0.3792 (ttm)
REVERT: B   21 ILE cc_start: 0.7271 (mp) cc_final: 0.7015 (mp)
REVERT: C  319 THR cc_start: 0.8434 (m) cc_final: 0.8114 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 104
  average time/residue: 0.0830
  time to fit residues: 11.6279
Evaluate side-chains
  85 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 20 optimal weight:    0.0070
   chunk 1 optimal weight:    0.0370
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 72 optimal weight:    5.9990
   chunk 45 optimal weight:    0.0030
   chunk 21 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   chunk 8 optimal weight:    6.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.5288

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

Flipped N/Q/H residues before XYZ refinement:
D 315 ASN
E 483 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4792 r_free = 0.4792 target = 0.227527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4675 r_free = 0.4675 target = 0.217062 restraints weight = 16030.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4675 r_free = 0.4675 target = 0.217532 restraints weight = 17146.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4683 r_free = 0.4683 target = 0.218324 restraints weight = 15075.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.218822 restraints weight = 12285.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4689 r_free = 0.4689 target = 0.218920 restraints weight = 10991.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.4675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5294
moved from start:          0.3708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6838  Z= 0.114
  Angle     :  0.645  10.213   9307  Z= 0.321
  Chirality :  0.046   0.194    972
  Planarity :  0.006   0.068   1223
  Dihedral  :  5.435  36.528    913
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 14.62
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.10 %
    Favored  : 90.77 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.14 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.40 %

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 aren not related in a simple way.
  whole: -1.98 (0.29), residues: 802
  helix: -3.44 (1.06), residues: 12
  sheet: -0.75 (0.34), residues: 217
  loop : -1.58 (0.26), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  38 
 TYR   0.015   0.001   TYR D 155 
 PHE   0.014   0.001   PHE D 393 
 TRP   0.023   0.002   TRP B  36 
 HIS   0.002   0.000   HIS D 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 6834)
  covalent geometry    : angle       0.64233 ( 9299)
  SS BOND              : bond        0.00437 (    4)
  SS BOND              : angle       1.95493 (    8)
  hydrogen bonds       : bond        0.02658 (   82)
  hydrogen bonds       : angle       5.98833 (  195)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   21 ILE cc_start: 0.7318 (mp) cc_final: 0.6992 (mp)
REVERT: C  319 THR cc_start: 0.8443 (m) cc_final: 0.8137 (p)
REVERT: C  524 ASP cc_start: 0.5977 (m-30) cc_final: 0.5774 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 102
  average time/residue: 0.0849
  time to fit residues: 11.7961
Evaluate side-chains
  83 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 67 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0570
   chunk 35 optimal weight:    0.0570
   chunk 48 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 38 optimal weight:    5.9990
   chunk 57 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
C 503 HIS
D 315 ASN
E 483 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4790 r_free = 0.4790 target = 0.227432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4673 r_free = 0.4673 target = 0.216958 restraints weight = 15801.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4671 r_free = 0.4671 target = 0.217183 restraints weight = 16021.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4679 r_free = 0.4679 target = 0.217914 restraints weight = 14049.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.218856 restraints weight = 12099.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4689 r_free = 0.4689 target = 0.218919 restraints weight = 10478.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.4674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5290
moved from start:          0.3845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6838  Z= 0.113
  Angle     :  0.635   7.518   9307  Z= 0.317
  Chirality :  0.046   0.182    972
  Planarity :  0.006   0.070   1223
  Dihedral  :  5.378  36.706    913
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 14.70
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.73 %
    Favored  : 91.02 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.14 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.40 %

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 aren not related in a simple way.
  whole: -1.86 (0.29), residues: 802
  helix: -3.39 (1.07), residues: 12
  sheet: -0.64 (0.34), residues: 212
  loop : -1.51 (0.26), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E 511 
 TYR   0.014   0.001   TYR D 155 
 PHE   0.029   0.002   PHE D 393 
 TRP   0.026   0.002   TRP A  47 
 HIS   0.002   0.000   HIS D 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 6834)
  covalent geometry    : angle       0.63385 ( 9299)
  SS BOND              : bond        0.00543 (    4)
  SS BOND              : angle       1.47520 (    8)
  hydrogen bonds       : bond        0.02668 (   82)
  hydrogen bonds       : angle       5.95633 (  195)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1160.30 seconds
wall clock time: 20 minutes 51.77 seconds (1251.77 seconds total)