Starting phenix.real_space_refine
on Fri Aug 22 14:19:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8s61_19754/08_2025/8s61_19754.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8s61_19754/08_2025/8s61_19754.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8s61_19754/08_2025/8s61_19754.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8s61_19754/08_2025/8s61_19754.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8s61_19754/08_2025/8s61_19754.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8s61_19754/08_2025/8s61_19754.cif"
  }
  resolution = 3.53
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.010
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      21      5.16       5
     C    2647      2.51       5
     N     624      2.21       5
     O     698      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3990
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 935
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "A"
      Number of atoms: 3037
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 380, 3037
          Classifications: {'peptide': 380}
          Link IDs: {'PTRANS': 13, 'TRANS': 366}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 18
          Unusual residues: {'VIB': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.07, per 1000 atoms: 0.27
  Number of scatterers: 3990
  At special positions: 0
  Unit cell: (92.13, 83.83, 75.53, 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      21     16.00
     O     698      8.00
     N     624      7.00
     C    2647      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.25
  Conformation dependent library (CDL) restraints added in 155.9 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  936

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 4 sheets defined
      60.2% alpha, 4.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 28
      removed outlier: 3.851A  pdb=" N   THR A  16 " --> pdb=" O   TRP A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 40
    Processing helix  chain 'A' and resid 47 through 52
    Processing helix  chain 'A' and resid 56 through 66
      removed outlier: 4.333A  pdb=" N   THR A  60 " --> pdb=" O   PHE A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 77
      removed outlier: 3.779A  pdb=" N   ASP A  75 " --> pdb=" O   PHE A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 97
      removed outlier: 4.386A  pdb=" N   VAL A  82 " --> pdb=" O   ARG A  78 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ILE A  83 " --> pdb=" O   TYR A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 119
      removed outlier: 3.566A  pdb=" N   GLN A 107 " --> pdb=" O   VAL A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 125
      removed outlier: 3.753A  pdb=" N   TYR A 124 " --> pdb=" O   GLU A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 131
      removed outlier: 4.206A  pdb=" N   SER A 129 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   VAL A 130 " --> pdb=" O   TYR A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 135
    Processing helix  chain 'A' and resid 136 through 162
      removed outlier: 3.528A  pdb=" N   VAL A 146 " --> pdb=" O   TYR A 142 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   THR A 147 " --> pdb=" O   CYS A 143 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LEU A 148 " --> pdb=" O   ARG A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 171
      No H-bonds generated for 'chain 'A' and resid 169 through 171'
    Processing helix  chain 'A' and resid 172 through 187
      removed outlier: 4.179A  pdb=" N   LEU A 185 " --> pdb=" O   SER A 181 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   PHE A 186 " --> pdb=" O   VAL A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 274
    Processing helix  chain 'A' and resid 275 through 298
      removed outlier: 3.571A  pdb=" N   TRP A 285 " --> pdb=" O   TRP A 281 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   GLN A 294 " --> pdb=" O   ALA A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 307
    Processing helix  chain 'A' and resid 315 through 335
      removed outlier: 3.529A  pdb=" N   GLU A 320 " --> pdb=" O   ASN A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 366
      removed outlier: 3.844A  pdb=" N   PHE A 352 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LEU A 362 " --> pdb=" O   GLY A 358 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   MET A 363 " --> pdb=" O   SER A 359 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   HIS A 364 " --> pdb=" O   LEU A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 395
      removed outlier: 3.621A  pdb=" N   LEU A 386 " --> pdb=" O   SER A 382 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   THR A 388 " --> pdb=" O   MET A 384 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   ILE A 389 " --> pdb=" O   LEU A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 426
      removed outlier: 4.381A  pdb=" N   ILE A 409 " --> pdb=" O   LEU A 405 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ASN A 410 " --> pdb=" O   VAL A 406 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   THR A 411 " --> pdb=" O   PHE A 407 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   LEU A 415 " --> pdb=" O   THR A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 452
      removed outlier: 4.182A  pdb=" N   PHE A 439 " --> pdb=" O   VAL A 435 " (cutoff:3.500A)
      removed outlier: 5.223A  pdb=" N   LEU A 440 " --> pdb=" O   SER A 436 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   VAL A 441 " --> pdb=" O   ILE A 437 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ALA A 447 " --> pdb=" O   GLY A 443 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ALA A 450 " --> pdb=" O   PHE A 446 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   GLY A 451 " --> pdb=" O   ALA A 447 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ILE A 452 " --> pdb=" O   VAL A 448 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7
      removed outlier: 3.549A  pdb=" N   SER B   7 " --> pdb=" O   SER B  21 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 47
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105
      removed outlier: 4.385A  pdb=" N   ARG B 104 " --> pdb=" O   GLN A 101 " (cutoff:3.500A)

    210 hydrogen bonds defined for protein.
    600 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: 0.60

  Time building geometry restraints manager: 0.34 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: 680
        1.33 -     1.45: 1184
        1.45 -     1.57: 2204
        1.57 -     1.69: 1
        1.69 -     1.81: 34
  Bond restraints: 4103
  Sorted by residual:
  bond pdb=" C5  VIB A 601 "
       pdb=" S1  VIB A 601 "
    ideal  model  delta    sigma   weight residual
    1.721  1.511  0.210 2.00e-02 2.50e+03 1.10e+02
  bond pdb=" C4  VIB A 601 "
       pdb=" N3  VIB A 601 "
    ideal  model  delta    sigma   weight residual
    1.385  1.570 -0.185 2.00e-02 2.50e+03 8.59e+01
  bond pdb=" C2A VIB A 601 "
       pdb=" N3A VIB A 601 "
    ideal  model  delta    sigma   weight residual
    1.323  1.483 -0.160 2.00e-02 2.50e+03 6.38e+01
  bond pdb=" C2A VIB A 601 "
       pdb=" N1A VIB A 601 "
    ideal  model  delta    sigma   weight residual
    1.331  1.483 -0.152 2.00e-02 2.50e+03 5.80e+01
  bond pdb=" C2  VIB A 601 "
       pdb=" S1  VIB A 601 "
    ideal  model  delta    sigma   weight residual
    1.670  1.537  0.133 2.00e-02 2.50e+03 4.42e+01
  ... (remaining 4098 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.30: 5564
        3.30 -     6.60: 29
        6.60 -     9.90: 1
        9.90 -    13.20: 0
       13.20 -    16.51: 1
  Bond angle restraints: 5595
  Sorted by residual:
  angle pdb=" C2  VIB A 601 "
        pdb=" S1  VIB A 601 "
        pdb=" C5  VIB A 601 "
      ideal   model   delta    sigma   weight residual
      91.25  107.76  -16.51 3.00e+00 1.11e-01 3.03e+01
  angle pdb=" N   ASN A 173 "
        pdb=" CA  ASN A 173 "
        pdb=" C   ASN A 173 "
      ideal   model   delta    sigma   weight residual
     112.23  105.56    6.67 1.26e+00 6.30e-01 2.80e+01
  angle pdb=" N   SER B  17 "
        pdb=" CA  SER B  17 "
        pdb=" C   SER B  17 "
      ideal   model   delta    sigma   weight residual
     110.41  115.36   -4.95 1.23e+00 6.61e-01 1.62e+01
  angle pdb=" N   ILE A 449 "
        pdb=" CA  ILE A 449 "
        pdb=" C   ILE A 449 "
      ideal   model   delta    sigma   weight residual
     112.80  108.41    4.39 1.15e+00 7.56e-01 1.46e+01
  angle pdb=" N   LEU A 160 "
        pdb=" CA  LEU A 160 "
        pdb=" C   LEU A 160 "
      ideal   model   delta    sigma   weight residual
     113.88  109.51    4.37 1.23e+00 6.61e-01 1.26e+01
  ... (remaining 5590 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 2033
       17.85 -    35.71: 224
       35.71 -    53.56: 61
       53.56 -    71.41: 11
       71.41 -    89.26: 4
  Dihedral angle restraints: 2333
    sinusoidal: 861
      harmonic: 1472
  Sorted by residual:
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  96 "
           pdb=" CB  CYS B  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  142.97  -49.97     1      1.00e+01 1.00e-02 3.43e+01
  dihedral pdb=" CA  ARG A  78 "
           pdb=" C   ARG A  78 "
           pdb=" N   TYR A  79 "
           pdb=" CA  TYR A  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.43  -19.57     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  TYR A 171 "
           pdb=" C   TYR A 171 "
           pdb=" N   LEU A 172 "
           pdb=" CA  LEU A 172 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.37   17.63     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 2330 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 417
       0.032 -    0.064: 145
       0.064 -    0.095: 47
       0.095 -    0.127: 17
       0.127 -    0.159: 4
  Chirality restraints: 630
  Sorted by residual:
  chirality pdb=" CA  ASN B  32 "
            pdb=" N   ASN B  32 "
            pdb=" C   ASN B  32 "
            pdb=" CB  ASN B  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.33e-01
  chirality pdb=" CA  ILE B  31 "
            pdb=" N   ILE B  31 "
            pdb=" C   ILE B  31 "
            pdb=" CB  ILE B  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.93e-01
  chirality pdb=" CA  ILE B 103 "
            pdb=" N   ILE B 103 "
            pdb=" C   ILE B 103 "
            pdb=" CB  ILE B 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.25e-01
  ... (remaining 627 not shown)

  Planarity restraints: 682
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  87 "    0.043 5.00e-02 4.00e+02   6.60e-02 6.97e+00
        pdb=" N   PRO B  88 "   -0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO B  88 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B  88 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 172 "    0.011 2.00e-02 2.50e+03   2.22e-02 4.93e+00
        pdb=" C   LEU A 172 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   LEU A 172 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ASN A 173 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B  73 "   -0.009 2.00e-02 2.50e+03   1.82e-02 3.33e+00
        pdb=" C   ASP B  73 "    0.032 2.00e-02 2.50e+03
        pdb=" O   ASP B  73 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ASN B  74 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 679 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 23
        2.57 -     3.16: 3363
        3.16 -     3.74: 5880
        3.74 -     4.32: 8341
        4.32 -     4.90: 14385
  Nonbonded interactions: 31992
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 320 "
            pdb=" O1  VIB A 601 "
     model   vdw
     1.994 3.040
  nonbonded pdb=" OE1 GLN A 159 "
            pdb=" OG  SER A 163 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   TYR A  76 "
            pdb=" NE2 HIS A 200 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" NH2 ARG A 277 "
            pdb=" O   GLN A 393 "
     model   vdw
     2.328 3.120
  nonbonded pdb=" OE1 GLU A 110 "
            pdb=" N4A VIB A 601 "
     model   vdw
     2.364 3.120
  ... (remaining 31987 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:             5.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.820
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
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      :  0.008   0.210   4104  Z= 0.454
  Angle     :  0.625  16.505   5597  Z= 0.349
  Chirality :  0.039   0.159    630
  Planarity :  0.004   0.066    682
  Dihedral  : 16.574  89.265   1394
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 19.48 %
    Favored  : 80.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.96 (0.38), residues: 496
  helix: -1.07 (0.31), residues: 280
  sheet: -2.36 (0.77), residues: 52
  loop : -0.96 (0.49), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  27 
 TYR   0.005   0.001   TYR B  47 
 PHE   0.014   0.001   PHE A 198 
 TRP   0.007   0.001   TRP B  53 
 HIS   0.003   0.001   HIS A 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00846 ( 4103)
  covalent geometry    : angle       0.62506 ( 5595)
  SS BOND              : bond        0.00348 (    1)
  SS BOND              : angle       0.86095 (    2)
  hydrogen bonds       : bond        0.26232 (  210)
  hydrogen bonds       : angle       9.20618 (  600)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A  198 PHE cc_start: 0.7743 (m-80) cc_final: 0.5705 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.0723
  time to fit residues: 4.4367
Evaluate side-chains
  47 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.2980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.137995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.127476 restraints weight = 4612.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.128445 restraints weight = 3880.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.129259 restraints weight = 3404.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.129259 restraints weight = 3048.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.129259 restraints weight = 3048.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.1435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4104  Z= 0.179
  Angle     :  0.593   5.663   5597  Z= 0.314
  Chirality :  0.042   0.169    630
  Planarity :  0.005   0.056    682
  Dihedral  :  5.681  63.697    556
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 18.53 %
    Favored  : 78.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.90 (0.39), residues: 496
  helix: -0.01 (0.32), residues: 282
  sheet: -1.32 (0.97), residues: 37
  loop : -1.24 (0.46), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 429 
 TYR   0.012   0.001   TYR A 280 
 PHE   0.013   0.001   PHE A 439 
 TRP   0.011   0.002   TRP A 284 
 HIS   0.003   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 4103)
  covalent geometry    : angle       0.59254 ( 5595)
  SS BOND              : bond        0.00687 (    1)
  SS BOND              : angle       1.33823 (    2)
  hydrogen bonds       : bond        0.05010 (  210)
  hydrogen bonds       : angle       4.77335 (  600)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.092 
Fit side-chains
REVERT: A   18 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7888 (mm)
REVERT: A  198 PHE cc_start: 0.7775 (m-80) cc_final: 0.6411 (t80)
  outliers start: 11
  outliers final: 4
  residues processed: 50
  average time/residue: 0.0618
  time to fit residues: 3.9974
Evaluate side-chains
  45 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  405 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0870
   chunk 14 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0010
   chunk 23 optimal weight:    1.9990
   chunk 30 optimal weight:    0.1980
   overall best weight:    0.4564

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.145475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.135133 restraints weight = 4565.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.135966 restraints weight = 3692.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.136777 restraints weight = 3203.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.136821 restraints weight = 2857.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.137556 restraints weight = 2820.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4104  Z= 0.155
  Angle     :  0.541   5.419   5597  Z= 0.287
  Chirality :  0.040   0.167    630
  Planarity :  0.004   0.058    682
  Dihedral  :  5.679  67.900    556
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 19.00 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.56 (0.39), residues: 496
  helix:  0.31 (0.33), residues: 282
  sheet: -1.00 (0.93), residues: 37
  loop : -1.21 (0.46), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 429 
 TYR   0.011   0.001   TYR A  14 
 PHE   0.012   0.001   PHE A 439 
 TRP   0.013   0.002   TRP A 284 
 HIS   0.002   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 4103)
  covalent geometry    : angle       0.54100 ( 5595)
  SS BOND              : bond        0.00613 (    1)
  SS BOND              : angle       1.27295 (    2)
  hydrogen bonds       : bond        0.04330 (  210)
  hydrogen bonds       : angle       4.20758 (  600)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 42
  time to evaluate  : 0.087 
Fit side-chains
REVERT: A   18 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7780 (mm)
REVERT: A  198 PHE cc_start: 0.7805 (m-80) cc_final: 0.6418 (t80)
  outliers start: 15
  outliers final: 7
  residues processed: 51
  average time/residue: 0.0517
  time to fit residues: 3.4657
Evaluate side-chains
  49 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  190 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 19 optimal weight:    0.3980
   chunk 9 optimal weight:    1.9990
   chunk 0 optimal weight:    0.3980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.142508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.132047 restraints weight = 4588.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.133028 restraints weight = 3804.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.133532 restraints weight = 3289.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.134331 restraints weight = 3012.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.134495 restraints weight = 2763.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   4104  Z= 0.197
  Angle     :  0.599   9.509   5597  Z= 0.307
  Chirality :  0.042   0.166    630
  Planarity :  0.004   0.059    682
  Dihedral  :  5.861  68.887    556
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 19.95 %
    Favored  : 76.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.63 (0.39), residues: 496
  helix:  0.26 (0.33), residues: 282
  sheet: -0.87 (0.94), residues: 35
  loop : -1.30 (0.45), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  29 
 TYR   0.010   0.001   TYR A  14 
 PHE   0.014   0.001   PHE A 439 
 TRP   0.014   0.002   TRP A 284 
 HIS   0.003   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 4103)
  covalent geometry    : angle       0.59849 ( 5595)
  SS BOND              : bond        0.00751 (    1)
  SS BOND              : angle       1.73346 (    2)
  hydrogen bonds       : bond        0.04418 (  210)
  hydrogen bonds       : angle       4.20960 (  600)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 43
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A   18 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7948 (mm)
REVERT: A  198 PHE cc_start: 0.7958 (m-80) cc_final: 0.6637 (t80)
REVERT: A  421 MET cc_start: 0.8424 (ttp) cc_final: 0.8186 (ptt)
  outliers start: 16
  outliers final: 11
  residues processed: 55
  average time/residue: 0.0665
  time to fit residues: 4.7473
Evaluate side-chains
  55 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   45 GLN
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  366 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 5 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9980
   chunk 3 optimal weight:    0.3980
   chunk 10 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0980
   chunk 27 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 0 optimal weight:    0.0870
   overall best weight:    0.3758

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.139414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.129259 restraints weight = 4535.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.130181 restraints weight = 3842.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.130622 restraints weight = 3360.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.131222 restraints weight = 3105.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.131222 restraints weight = 2813.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.2050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4104  Z= 0.134
  Angle     :  0.533   7.976   5597  Z= 0.275
  Chirality :  0.040   0.164    630
  Planarity :  0.004   0.056    682
  Dihedral  :  5.674  70.794    556
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 21.14 %
    Favored  : 76.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.39 (0.39), residues: 496
  helix:  0.46 (0.33), residues: 282
  sheet: -0.87 (0.90), residues: 37
  loop : -1.18 (0.46), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 402 
 TYR   0.013   0.001   TYR A  14 
 PHE   0.010   0.001   PHE A 439 
 TRP   0.012   0.001   TRP A 284 
 HIS   0.002   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 4103)
  covalent geometry    : angle       0.53299 ( 5595)
  SS BOND              : bond        0.00471 (    1)
  SS BOND              : angle       1.16228 (    2)
  hydrogen bonds       : bond        0.03801 (  210)
  hydrogen bonds       : angle       3.86960 (  600)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.100 
Fit side-chains
REVERT: A  198 PHE cc_start: 0.7948 (m-80) cc_final: 0.6566 (t80)
REVERT: A  384 MET cc_start: 0.8532 (tpp) cc_final: 0.8329 (mmt)
  outliers start: 11
  outliers final: 9
  residues processed: 49
  average time/residue: 0.0762
  time to fit residues: 4.7286
Evaluate side-chains
  50 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain A residue   45 GLN
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  366 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 47 optimal weight:    0.4980
   chunk 46 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.135257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.124803 restraints weight = 4725.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.125494 restraints weight = 3959.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.125494 restraints weight = 3530.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.125494 restraints weight = 3530.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.125494 restraints weight = 3530.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   4104  Z= 0.203
  Angle     :  0.599   8.026   5597  Z= 0.307
  Chirality :  0.042   0.163    630
  Planarity :  0.004   0.057    682
  Dihedral  :  5.879  69.470    556
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 21.62 %
    Favored  : 74.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.54 (0.39), residues: 496
  helix:  0.37 (0.33), residues: 282
  sheet: -0.81 (0.92), residues: 35
  loop : -1.33 (0.45), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  29 
 TYR   0.018   0.001   TYR A 336 
 PHE   0.015   0.001   PHE A 439 
 TRP   0.014   0.002   TRP A 284 
 HIS   0.003   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 ( 4103)
  covalent geometry    : angle       0.59804 ( 5595)
  SS BOND              : bond        0.00761 (    1)
  SS BOND              : angle       1.80267 (    2)
  hydrogen bonds       : bond        0.04351 (  210)
  hydrogen bonds       : angle       4.08840 (  600)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 45
  time to evaluate  : 0.167 
Fit side-chains
REVERT: A   18 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7932 (mm)
REVERT: A  198 PHE cc_start: 0.8100 (m-80) cc_final: 0.6646 (t80)
REVERT: A  384 MET cc_start: 0.8531 (tpp) cc_final: 0.8313 (mmt)
  outliers start: 15
  outliers final: 13
  residues processed: 56
  average time/residue: 0.0656
  time to fit residues: 4.7768
Evaluate side-chains
  58 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   45 GLN
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  366 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0870
   chunk 36 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   chunk 1 optimal weight:    0.0060
   overall best weight:    0.4174

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.134178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.124319 restraints weight = 4757.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.125102 restraints weight = 4009.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.125915 restraints weight = 3538.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.126252 restraints weight = 3194.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.126869 restraints weight = 2996.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4104  Z= 0.141
  Angle     :  0.540   7.026   5597  Z= 0.277
  Chirality :  0.040   0.164    630
  Planarity :  0.004   0.056    682
  Dihedral  :  5.714  70.854    556
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 21.38 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.43 (0.39), residues: 496
  helix:  0.50 (0.33), residues: 283
  sheet: -0.85 (0.83), residues: 43
  loop : -1.37 (0.46), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 277 
 TYR   0.018   0.001   TYR A 336 
 PHE   0.010   0.001   PHE A 439 
 TRP   0.012   0.001   TRP A 284 
 HIS   0.002   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 4103)
  covalent geometry    : angle       0.53943 ( 5595)
  SS BOND              : bond        0.00472 (    1)
  SS BOND              : angle       1.30314 (    2)
  hydrogen bonds       : bond        0.03793 (  210)
  hydrogen bonds       : angle       3.82407 (  600)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 44
  time to evaluate  : 0.128 
Fit side-chains
REVERT: B    4 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8290 (mp)
REVERT: A   18 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7791 (mm)
REVERT: A  198 PHE cc_start: 0.8053 (m-80) cc_final: 0.6617 (t80)
REVERT: A  384 MET cc_start: 0.8594 (tpp) cc_final: 0.8381 (mmt)
  outliers start: 17
  outliers final: 14
  residues processed: 57
  average time/residue: 0.0545
  time to fit residues: 4.0844
Evaluate side-chains
  58 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 42
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   45 GLN
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  381 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 41 optimal weight:    0.5980
   chunk 24 optimal weight:    0.2980
   chunk 42 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0970
   chunk 13 optimal weight:    0.4980
   chunk 39 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.4178

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.134379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.124692 restraints weight = 4637.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.125403 restraints weight = 3965.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.126151 restraints weight = 3524.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.126833 restraints weight = 3183.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.126835 restraints weight = 2981.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.2325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4104  Z= 0.141
  Angle     :  0.533   6.820   5597  Z= 0.274
  Chirality :  0.040   0.162    630
  Planarity :  0.004   0.055    682
  Dihedral  :  5.664  69.930    556
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 21.85 %
    Favored  : 74.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.32 (0.39), residues: 496
  helix:  0.56 (0.33), residues: 283
  sheet: -0.71 (0.83), residues: 43
  loop : -1.27 (0.46), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  72 
 TYR   0.018   0.001   TYR A 336 
 PHE   0.011   0.001   PHE A 439 
 TRP   0.012   0.001   TRP A 284 
 HIS   0.002   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 4103)
  covalent geometry    : angle       0.53220 ( 5595)
  SS BOND              : bond        0.00496 (    1)
  SS BOND              : angle       1.31926 (    2)
  hydrogen bonds       : bond        0.03756 (  210)
  hydrogen bonds       : angle       3.76828 (  600)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 44
  time to evaluate  : 0.164 
Fit side-chains
REVERT: B    4 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8286 (mp)
REVERT: A   18 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7802 (mm)
REVERT: A  198 PHE cc_start: 0.8063 (m-80) cc_final: 0.6653 (t80)
REVERT: A  384 MET cc_start: 0.8621 (tpp) cc_final: 0.8354 (mmt)
  outliers start: 17
  outliers final: 14
  residues processed: 57
  average time/residue: 0.0729
  time to fit residues: 5.3634
Evaluate side-chains
  59 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 43
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   45 GLN
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  381 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0470
   chunk 41 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 49 optimal weight:    0.2980
   chunk 23 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.5278

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.133885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.123767 restraints weight = 4732.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.124483 restraints weight = 4006.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.124483 restraints weight = 3570.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.124483 restraints weight = 3570.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.124483 restraints weight = 3570.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.2286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4104  Z= 0.165
  Angle     :  0.558   6.976   5597  Z= 0.286
  Chirality :  0.041   0.162    630
  Planarity :  0.004   0.055    682
  Dihedral  :  5.760  69.264    556
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 21.62 %
    Favored  : 74.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.36 (0.39), residues: 496
  helix:  0.52 (0.33), residues: 283
  sheet: -0.71 (0.82), residues: 43
  loop : -1.29 (0.46), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 277 
 TYR   0.019   0.001   TYR A 336 
 PHE   0.013   0.001   PHE A 439 
 TRP   0.012   0.002   TRP A 284 
 HIS   0.002   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 4103)
  covalent geometry    : angle       0.55776 ( 5595)
  SS BOND              : bond        0.00610 (    1)
  SS BOND              : angle       1.55921 (    2)
  hydrogen bonds       : bond        0.04011 (  210)
  hydrogen bonds       : angle       3.87318 (  600)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 43
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A   18 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7825 (mm)
REVERT: A  198 PHE cc_start: 0.8116 (m-80) cc_final: 0.6744 (t80)
REVERT: A  384 MET cc_start: 0.8604 (tpp) cc_final: 0.8341 (mmt)
REVERT: A  385 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8864 (tt)
  outliers start: 18
  outliers final: 16
  residues processed: 58
  average time/residue: 0.0605
  time to fit residues: 4.5648
Evaluate side-chains
  60 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 42
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   45 GLN
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  381 SER
Chi-restraints excluded: chain A residue  385 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 14 optimal weight:    0.3980
   chunk 3 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0980
   chunk 9 optimal weight:    0.7980
   chunk 19 optimal weight:    0.2980
   overall best weight:    0.4580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.142000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.131479 restraints weight = 4590.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.132419 restraints weight = 3825.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.133308 restraints weight = 3353.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.133309 restraints weight = 3049.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.133309 restraints weight = 3048.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.2366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4104  Z= 0.150
  Angle     :  0.540   6.720   5597  Z= 0.277
  Chirality :  0.040   0.163    630
  Planarity :  0.004   0.055    682
  Dihedral  :  5.704  69.710    556
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 21.14 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.28 (0.39), residues: 496
  helix:  0.57 (0.33), residues: 283
  sheet: -0.63 (0.82), residues: 43
  loop : -1.24 (0.46), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 277 
 TYR   0.013   0.001   TYR A 459 
 PHE   0.011   0.001   PHE A 439 
 TRP   0.011   0.001   TRP A 284 
 HIS   0.002   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 4103)
  covalent geometry    : angle       0.53936 ( 5595)
  SS BOND              : bond        0.00535 (    1)
  SS BOND              : angle       1.40072 (    2)
  hydrogen bonds       : bond        0.03825 (  210)
  hydrogen bonds       : angle       3.83594 (  600)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 43
  time to evaluate  : 0.121 
Fit side-chains
REVERT: B    4 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8277 (mp)
REVERT: A   18 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7840 (mm)
REVERT: A  198 PHE cc_start: 0.8128 (m-80) cc_final: 0.6831 (t80)
REVERT: A  384 MET cc_start: 0.8615 (tpp) cc_final: 0.8358 (mmt)
REVERT: A  385 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8783 (tt)
  outliers start: 19
  outliers final: 15
  residues processed: 59
  average time/residue: 0.0577
  time to fit residues: 4.3777
Evaluate side-chains
  60 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 42
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   45 GLN
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  381 SER
Chi-restraints excluded: chain A residue  385 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 1 optimal weight:    0.4980
   chunk 0 optimal weight:    0.0970
   chunk 35 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.6778

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.140740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.129977 restraints weight = 4607.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.130589 restraints weight = 3876.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.130589 restraints weight = 3491.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.130589 restraints weight = 3491.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.130589 restraints weight = 3491.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   4104  Z= 0.198
  Angle     :  0.591   7.112   5597  Z= 0.302
  Chirality :  0.042   0.163    630
  Planarity :  0.004   0.056    682
  Dihedral  :  5.886  68.996    556
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 21.14 %
    Favored  : 74.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.39), residues: 496
  helix:  0.48 (0.32), residues: 282
  sheet: -0.94 (0.75), residues: 50
  loop : -1.31 (0.47), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 277 
 TYR   0.014   0.001   TYR A 459 
 PHE   0.014   0.001   PHE A 439 
 TRP   0.012   0.001   TRP A 284 
 HIS   0.003   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 ( 4103)
  covalent geometry    : angle       0.58956 ( 5595)
  SS BOND              : bond        0.00745 (    1)
  SS BOND              : angle       1.88249 (    2)
  hydrogen bonds       : bond        0.04222 (  210)
  hydrogen bonds       : angle       4.02396 (  600)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 796.45 seconds
wall clock time: 14 minutes 28.46 seconds (868.46 seconds total)