Starting phenix.real_space_refine
on Tue Feb  3 16:07:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w1a_43717/02_2026/8w1a_43717.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w1a_43717/02_2026/8w1a_43717.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w1a_43717/02_2026/8w1a_43717.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w1a_43717/02_2026/8w1a_43717.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w1a_43717/02_2026/8w1a_43717.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w1a_43717/02_2026/8w1a_43717.map"
  }
  resolution = 2.89
  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=   0.052
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      32      5.16       5
     C    3084      2.51       5
     N     788      2.21       5
     O     760      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4664
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2317
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2317
          Classifications: {'peptide': 290}
          Link IDs: {'PTRANS': 7, 'TRANS': 282}
    Chain: "B"
      Number of atoms: 2347
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 294, 2347
          Classifications: {'peptide': 294}
          Link IDs: {'PTRANS': 7, 'TRANS': 286}
  Time building chain proxies: 1.22, per 1000 atoms: 0.26
  Number of scatterers: 4664
  At special positions: 0
  Unit cell: (86.46, 70.62, 75.9, 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      32     16.00
     O     760      8.00
     N     788      7.00
     C    3084      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 118 " - pdb=" SG  CYS A 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  39 " - pdb=" SG  CYS B 286 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 118 " - pdb=" SG  CYS B 196 " 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: 0.43
  Conformation dependent library (CDL) restraints added in 307.4 milliseconds
  

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1108

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 2 sheets defined
      86.5% alpha, 2.1% 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 46 through 75
    Processing helix  chain 'A' and resid 76 through 79
    Processing helix  chain 'A' and resid 80 through 109
      removed outlier: 3.601A  pdb=" N   LEU A  96 " --> pdb=" O   ASN A  92 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   SER A  97 " --> pdb=" O   SER A  93 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ILE A  98 " --> pdb=" O   LEU A  94 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   SER A  99 " --> pdb=" O   CYS A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 113
    Processing helix  chain 'A' and resid 114 through 149
      removed outlier: 3.920A  pdb=" N   ILE A 133 " --> pdb=" O   VAL A 129 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL A 147 " --> pdb=" O   ARG A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 156
    Processing helix  chain 'A' and resid 157 through 180
      removed outlier: 3.947A  pdb=" N   GLY A 161 " --> pdb=" O   LYS A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 202
      No H-bonds generated for 'chain 'A' and resid 200 through 202'
    Processing helix  chain 'A' and resid 203 through 220
      removed outlier: 3.534A  pdb=" N   ARG A 212 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 242
    Processing helix  chain 'A' and resid 250 through 264
      removed outlier: 3.856A  pdb=" N   VAL A 254 " --> pdb=" O   ARG A 250 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ALA A 255 " --> pdb=" O   GLY A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 279
    Processing helix  chain 'A' and resid 285 through 318
      removed outlier: 3.858A  pdb=" N   LEU A 301 " --> pdb=" O   ALA A 297 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU A 302 " --> pdb=" O   VAL A 298 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   SER A 307 " --> pdb=" O   GLN A 303 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   ALA A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      Proline residue:  A 311  - end of helix
      removed outlier: 3.634A  pdb=" N   TYR A 314 " --> pdb=" O   VAL A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 330
    Processing helix  chain 'B' and resid 46 through 74
    Processing helix  chain 'B' and resid 75 through 79
    Processing helix  chain 'B' and resid 80 through 109
      removed outlier: 3.773A  pdb=" N   ILE B  84 " --> pdb=" O   GLY B  80 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LEU B  85 " --> pdb=" O   ALA B  81 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   CYS B  90 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ILE B  98 " --> pdb=" O   LEU B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 113
    Processing helix  chain 'B' and resid 114 through 149
      removed outlier: 3.981A  pdb=" N   ILE B 133 " --> pdb=" O   VAL B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 156
    Processing helix  chain 'B' and resid 157 through 180
      removed outlier: 4.083A  pdb=" N   GLY B 161 " --> pdb=" O   LYS B 157 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL B 174 " --> pdb=" O   LEU B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 202
      No H-bonds generated for 'chain 'B' and resid 200 through 202'
    Processing helix  chain 'B' and resid 203 through 218
    Processing helix  chain 'B' and resid 220 through 241
    Processing helix  chain 'B' and resid 250 through 264
      removed outlier: 3.576A  pdb=" N   VAL B 256 " --> pdb=" O   VAL B 252 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   PHE B 261 " --> pdb=" O   VAL B 257 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 264 through 279
    Processing helix  chain 'B' and resid 285 through 317
      removed outlier: 4.099A  pdb=" N   LEU B 301 " --> pdb=" O   ALA B 297 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LEU B 302 " --> pdb=" O   VAL B 298 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   SER B 307 " --> pdb=" O   GLN B 303 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   ALA B 308 " --> pdb=" O   ALA B 304 " (cutoff:3.500A)
      Proline residue:  B 311  - end of helix
    Processing helix  chain 'B' and resid 318 through 331
      removed outlier: 3.683A  pdb=" N   SER B 331 " --> pdb=" O   GLY B 327 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187
    Processing sheet with id=AA2, first strand: chain 'B' and resid 184 through 187

    374 hydrogen bonds defined for protein.
    1095 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: 0.74

  Time building geometry restraints manager: 0.57 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1416
        1.35 -     1.46: 1233
        1.46 -     1.58: 2082
        1.58 -     1.70: 0
        1.70 -     1.82: 41
  Bond restraints: 4772
  Sorted by residual:
  bond pdb=" N   THR A  42 "
       pdb=" CA  THR A  42 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.25e+00
  bond pdb=" N   VAL B  38 "
       pdb=" CA  VAL B  38 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.72e+00
  bond pdb=" CA  ARG A 143 "
       pdb=" C   ARG A 143 "
    ideal  model  delta    sigma   weight residual
    1.523  1.539 -0.016 1.35e-02 5.49e+03 1.41e+00
  bond pdb=" CB  ASP A 178 "
       pdb=" CG  ASP A 178 "
    ideal  model  delta    sigma   weight residual
    1.516  1.537 -0.021 2.50e-02 1.60e+03 7.16e-01
  bond pdb=" CG  ARG A 212 "
       pdb=" CD  ARG A 212 "
    ideal  model  delta    sigma   weight residual
    1.520  1.542 -0.022 3.00e-02 1.11e+03 5.41e-01
  ... (remaining 4767 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 6363
        1.65 -     3.30: 113
        3.30 -     4.94: 20
        4.94 -     6.59: 4
        6.59 -     8.24: 2
  Bond angle restraints: 6502
  Sorted by residual:
  angle pdb=" N   VAL A 142 "
        pdb=" CA  VAL A 142 "
        pdb=" C   VAL A 142 "
      ideal   model   delta    sigma   weight residual
     110.72  116.77   -6.05 1.01e+00 9.80e-01 3.58e+01
  angle pdb=" N   TYR A 144 "
        pdb=" CA  TYR A 144 "
        pdb=" C   TYR A 144 "
      ideal   model   delta    sigma   weight residual
     111.07  105.20    5.87 1.07e+00 8.73e-01 3.01e+01
  angle pdb=" N   TYR A 144 "
        pdb=" CA  TYR A 144 "
        pdb=" CB  TYR A 144 "
      ideal   model   delta    sigma   weight residual
     110.01  116.21   -6.20 1.45e+00 4.76e-01 1.83e+01
  angle pdb=" CB  MET B 203 "
        pdb=" CG  MET B 203 "
        pdb=" SD  MET B 203 "
      ideal   model   delta    sigma   weight residual
     112.70  120.94   -8.24 3.00e+00 1.11e-01 7.54e+00
  angle pdb=" C   ARG A 143 "
        pdb=" CA  ARG A 143 "
        pdb=" CB  ARG A 143 "
      ideal   model   delta    sigma   weight residual
     110.67  105.88    4.79 1.92e+00 2.71e-01 6.23e+00
  ... (remaining 6497 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.66: 2516
       14.66 -    29.32: 191
       29.32 -    43.98: 68
       43.98 -    58.64: 16
       58.64 -    73.30: 2
  Dihedral angle restraints: 2793
    sinusoidal: 1073
      harmonic: 1720
  Sorted by residual:
  dihedral pdb=" CA  ASN B 202 "
           pdb=" C   ASN B 202 "
           pdb=" N   MET B 203 "
           pdb=" CA  MET B 203 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.41   18.59     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  ILE A 282 "
           pdb=" C   ILE A 282 "
           pdb=" N   ARG A 283 "
           pdb=" CA  ARG A 283 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.73  -18.27     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CG  ARG A 212 "
           pdb=" CD  ARG A 212 "
           pdb=" NE  ARG A 212 "
           pdb=" CZ  ARG A 212 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -40.72  -49.28     2      1.50e+01 4.44e-03 1.23e+01
  ... (remaining 2790 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 578
       0.037 -    0.074: 175
       0.074 -    0.110: 32
       0.110 -    0.147: 5
       0.147 -    0.184: 1
  Chirality restraints: 791
  Sorted by residual:
  chirality pdb=" CA  VAL A 142 "
            pdb=" N   VAL A 142 "
            pdb=" C   VAL A 142 "
            pdb=" CB  VAL A 142 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.26    0.18 2.00e-01 2.50e+01 8.47e-01
  chirality pdb=" CA  VAL B  38 "
            pdb=" N   VAL B  38 "
            pdb=" C   VAL B  38 "
            pdb=" CB  VAL B  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  chirality pdb=" CA  PRO A 311 "
            pdb=" N   PRO A 311 "
            pdb=" C   PRO A 311 "
            pdb=" CB  PRO A 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.39e-01
  ... (remaining 788 not shown)

  Planarity restraints: 773
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 212 "    0.150 9.50e-02 1.11e+02   6.77e-02 3.31e+00
        pdb=" NE  ARG A 212 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 212 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 212 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 212 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 235 "   -0.014 2.00e-02 2.50e+03   9.31e-03 2.17e+00
        pdb=" CG  TRP B 235 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 235 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 235 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 235 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 235 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 235 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 235 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 235 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 235 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 109 "    0.020 5.00e-02 4.00e+02   2.97e-02 1.41e+00
        pdb=" N   PRO A 110 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO A 110 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 110 "    0.017 5.00e-02 4.00e+02
  ... (remaining 770 not shown)

  Histogram of nonbonded interaction distances:
        2.49 -     2.97: 2338
        2.97 -     3.45: 5107
        3.45 -     3.94: 7505
        3.94 -     4.42: 8523
        4.42 -     4.90: 13987
  Nonbonded interactions: 37460
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 123 "
            pdb=" OG  SER A 176 "
     model   vdw
     2.492 3.040
  nonbonded pdb=" O   ASP A 178 "
            pdb=" OD1 ASP A 178 "
     model   vdw
     2.507 3.040
  nonbonded pdb=" C   ASN B  61 "
            pdb=" OD1 ASN B  61 "
     model   vdw
     2.525 3.270
  nonbonded pdb=" C   ASP A 178 "
            pdb=" OD1 ASP A 178 "
     model   vdw
     2.529 3.270
  nonbonded pdb=" O   GLY B  88 "
            pdb=" OD1 ASN B  92 "
     model   vdw
     2.543 3.040
  ... (remaining 37455 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and resid 42 through 331)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.270
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     6.680
  Find NCS groups from input model:        0.080
  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:6.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7183
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      :  0.003   0.034   4775  Z= 0.143
  Angle     :  0.596   8.240   6508  Z= 0.352
  Chirality :  0.036   0.184    791
  Planarity :  0.004   0.068    773
  Dihedral  : 12.485  73.304   1676
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.34 (0.35), residues: 580
  helix:  1.63 (0.24), residues: 458
  sheet: -3.00 (1.54), residues: 10
  loop : -1.85 (0.52), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 212 
 TYR   0.018   0.001   TYR B 267 
 PHE   0.015   0.001   PHE B 265 
 TRP   0.025   0.002   TRP B 235 
 HIS   0.003   0.001   HIS A 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 4772)
  covalent geometry    : angle       0.59471 ( 6502)
  SS BOND              : bond        0.00155 (    3)
  SS BOND              : angle       1.42068 (    6)
  hydrogen bonds       : bond        0.14821 (  374)
  hydrogen bonds       : angle       5.29989 ( 1095)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A  198 GLU cc_start: 0.6240 (mp0) cc_final: 0.5447 (tt0)
REVERT: A  203 MET cc_start: 0.5310 (mtm) cc_final: 0.4779 (mpp)
REVERT: A  289 ARG cc_start: 0.6410 (ttp-110) cc_final: 0.5723 (tpm170)
REVERT: A  326 TYR cc_start: 0.5284 (t80) cc_final: 0.4566 (t80)
REVERT: B  170 LEU cc_start: 0.7532 (mt) cc_final: 0.7241 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.6694
  time to fit residues: 29.8686
Evaluate side-chains
  37 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 24 optimal weight:    0.4980
   chunk 48 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  50 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.216711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.182120 restraints weight = 4525.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.4156 rms_B_bonded: 1.58
r_work: 0.3959 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7219
moved from start:          0.1096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4775  Z= 0.155
  Angle     :  0.592   9.269   6508  Z= 0.306
  Chirality :  0.039   0.126    791
  Planarity :  0.004   0.030    773
  Dihedral  :  4.113  17.504    656
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  :  6.59 %
    Favored  : 91.47 %
  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 are not related in a simple way.
  whole:  1.80 (0.35), residues: 580
  helix:  1.89 (0.24), residues: 464
  sheet: -3.07 (1.37), residues: 10
  loop : -1.51 (0.57), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 212 
 TYR   0.011   0.001   TYR B 314 
 PHE   0.014   0.002   PHE A 260 
 TRP   0.024   0.002   TRP B 235 
 HIS   0.003   0.001   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 4772)
  covalent geometry    : angle       0.59127 ( 6502)
  SS BOND              : bond        0.00205 (    3)
  SS BOND              : angle       1.29760 (    6)
  hydrogen bonds       : bond        0.06251 (  374)
  hydrogen bonds       : angle       4.08192 ( 1095)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.184 
Fit side-chains
REVERT: A  203 MET cc_start: 0.4963 (mtm) cc_final: 0.4479 (mpp)
REVERT: A  208 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.5980 (mmt180)
REVERT: A  289 ARG cc_start: 0.6425 (ttp-170) cc_final: 0.5696 (tpm170)
REVERT: A  326 TYR cc_start: 0.5302 (t80) cc_final: 0.4719 (t80)
REVERT: B  121 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6411 (tt0)
REVERT: B  170 LEU cc_start: 0.7586 (mt) cc_final: 0.7278 (tp)
  outliers start: 10
  outliers final: 7
  residues processed: 51
  average time/residue: 0.5344
  time to fit residues: 28.3824
Evaluate side-chains
  47 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 38
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  208 ARG
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain B residue  121 GLU
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  276 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 36 optimal weight:    7.9990
   chunk 37 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 54 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 271 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.216529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.181545 restraints weight = 4434.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.4152 rms_B_bonded: 1.57
r_work: 0.3959 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3828 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.1417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4775  Z= 0.148
  Angle     :  0.556   8.346   6508  Z= 0.289
  Chirality :  0.038   0.142    791
  Planarity :  0.004   0.035    773
  Dihedral  :  3.976  17.596    656
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  :  8.91 %
    Favored  : 88.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.02 (0.35), residues: 580
  helix:  2.08 (0.24), residues: 462
  sheet: -3.28 (0.96), residues: 10
  loop : -1.51 (0.57), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 212 
 TYR   0.012   0.001   TYR A 267 
 PHE   0.012   0.002   PHE B  72 
 TRP   0.018   0.001   TRP B 235 
 HIS   0.002   0.001   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 4772)
  covalent geometry    : angle       0.55495 ( 6502)
  SS BOND              : bond        0.00179 (    3)
  SS BOND              : angle       1.33369 (    6)
  hydrogen bonds       : bond        0.05882 (  374)
  hydrogen bonds       : angle       3.93275 ( 1095)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A  178 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.6411 (p0)
REVERT: A  185 ARG cc_start: 0.7960 (tmm-80) cc_final: 0.7157 (ttm-80)
REVERT: A  198 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7062 (mt-10)
REVERT: A  203 MET cc_start: 0.4978 (mtm) cc_final: 0.4325 (mpp)
REVERT: A  208 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.5706 (mmt180)
REVERT: A  289 ARG cc_start: 0.6552 (ttp-170) cc_final: 0.5701 (tpm170)
REVERT: A  326 TYR cc_start: 0.5292 (t80) cc_final: 0.4764 (t80)
REVERT: B  121 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6505 (tt0)
REVERT: B  170 LEU cc_start: 0.7690 (mt) cc_final: 0.7358 (tp)
  outliers start: 11
  outliers final: 6
  residues processed: 50
  average time/residue: 0.5539
  time to fit residues: 28.8675
Evaluate side-chains
  47 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 38
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  208 ARG
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain B residue  121 GLU
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  249 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 45 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 39 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4492 r_free = 0.4492 target = 0.213837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.178621 restraints weight = 4340.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.4159 rms_B_bonded: 1.58
r_work: 0.3974 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3845 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4775  Z= 0.140
  Angle     :  0.538   7.687   6508  Z= 0.278
  Chirality :  0.038   0.142    791
  Planarity :  0.004   0.036    773
  Dihedral  :  3.816  15.391    656
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 10.47 %
    Favored  : 87.79 %
  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 are not related in a simple way.
  whole:  2.18 (0.35), residues: 580
  helix:  2.18 (0.24), residues: 463
  sheet: -3.09 (0.97), residues: 10
  loop : -1.49 (0.57), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 212 
 TYR   0.010   0.001   TYR A  70 
 PHE   0.010   0.002   PHE B 260 
 TRP   0.016   0.001   TRP B 235 
 HIS   0.002   0.001   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 4772)
  covalent geometry    : angle       0.53693 ( 6502)
  SS BOND              : bond        0.00194 (    3)
  SS BOND              : angle       1.29005 (    6)
  hydrogen bonds       : bond        0.05588 (  374)
  hydrogen bonds       : angle       3.85406 ( 1095)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A  185 ARG cc_start: 0.7944 (tmm-80) cc_final: 0.7382 (ttm-80)
REVERT: A  203 MET cc_start: 0.5049 (mtm) cc_final: 0.4345 (mpp)
REVERT: A  326 TYR cc_start: 0.5240 (t80) cc_final: 0.4811 (t80)
REVERT: B  121 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6516 (tt0)
REVERT: B  170 LEU cc_start: 0.7637 (mt) cc_final: 0.7327 (tp)
  outliers start: 9
  outliers final: 7
  residues processed: 45
  average time/residue: 0.4445
  time to fit residues: 20.9796
Evaluate side-chains
  44 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 36
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain B residue  121 GLU
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  249 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 43 optimal weight:    6.9990
   chunk 6 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 40 optimal weight:    0.3980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4512 r_free = 0.4512 target = 0.216438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.181657 restraints weight = 4459.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.4161 rms_B_bonded: 1.58
r_work: 0.3970 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3840 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4775  Z= 0.139
  Angle     :  0.525   7.514   6508  Z= 0.275
  Chirality :  0.037   0.148    791
  Planarity :  0.004   0.038    773
  Dihedral  :  3.804  17.249    656
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 11.43 %
    Favored  : 86.43 %
  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 are not related in a simple way.
  whole:  2.25 (0.35), residues: 580
  helix:  2.24 (0.24), residues: 463
  sheet: -3.05 (0.94), residues: 10
  loop : -1.50 (0.58), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 212 
 TYR   0.015   0.001   TYR B 267 
 PHE   0.010   0.001   PHE B 260 
 TRP   0.014   0.001   TRP B 235 
 HIS   0.002   0.001   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 4772)
  covalent geometry    : angle       0.52379 ( 6502)
  SS BOND              : bond        0.00174 (    3)
  SS BOND              : angle       1.27825 (    6)
  hydrogen bonds       : bond        0.05544 (  374)
  hydrogen bonds       : angle       3.81712 ( 1095)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A  185 ARG cc_start: 0.8019 (tmm-80) cc_final: 0.7461 (ttm-80)
REVERT: A  198 GLU cc_start: 0.7579 (tt0) cc_final: 0.7260 (mt-10)
REVERT: A  203 MET cc_start: 0.5078 (mtm) cc_final: 0.4343 (mpp)
REVERT: A  326 TYR cc_start: 0.5293 (t80) cc_final: 0.4910 (t80)
REVERT: B   60 ILE cc_start: 0.8021 (mp) cc_final: 0.7751 (mm)
REVERT: B  121 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6522 (tt0)
REVERT: B  170 LEU cc_start: 0.7623 (mt) cc_final: 0.7365 (tp)
REVERT: B  203 MET cc_start: 0.6574 (mpp) cc_final: 0.6348 (mpm)
REVERT: B  208 ARG cc_start: 0.6406 (mtp85) cc_final: 0.6167 (mtp180)
  outliers start: 11
  outliers final: 7
  residues processed: 50
  average time/residue: 0.5337
  time to fit residues: 27.8926
Evaluate side-chains
  46 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain B residue  121 GLU
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  319 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 23 optimal weight:    0.5980
   chunk 36 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4489 r_free = 0.4489 target = 0.213438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.176334 restraints weight = 4442.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.4121 rms_B_bonded: 1.96
r_work: 0.3939 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7239
moved from start:          0.1928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4775  Z= 0.142
  Angle     :  0.529   7.531   6508  Z= 0.275
  Chirality :  0.038   0.149    791
  Planarity :  0.004   0.037    773
  Dihedral  :  3.781  15.634    656
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 11.43 %
    Favored  : 86.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.23 (0.35), residues: 580
  helix:  2.19 (0.24), residues: 466
  sheet: -3.07 (0.95), residues: 10
  loop : -1.43 (0.58), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 212 
 TYR   0.015   0.001   TYR B 267 
 PHE   0.011   0.001   PHE B 260 
 TRP   0.013   0.001   TRP B 235 
 HIS   0.002   0.001   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 4772)
  covalent geometry    : angle       0.52791 ( 6502)
  SS BOND              : bond        0.00183 (    3)
  SS BOND              : angle       1.28753 (    6)
  hydrogen bonds       : bond        0.05608 (  374)
  hydrogen bonds       : angle       3.80660 ( 1095)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 40
  time to evaluate  : 0.112 
Fit side-chains
REVERT: A  185 ARG cc_start: 0.7852 (tmm-80) cc_final: 0.7402 (ttm-80)
REVERT: A  198 GLU cc_start: 0.7361 (tt0) cc_final: 0.7028 (mt-10)
REVERT: A  203 MET cc_start: 0.5083 (mtm) cc_final: 0.4402 (mpp)
REVERT: A  326 TYR cc_start: 0.5380 (t80) cc_final: 0.5090 (t80)
REVERT: B   60 ILE cc_start: 0.8024 (mp) cc_final: 0.7761 (mm)
REVERT: B  121 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6447 (tt0)
REVERT: B  185 ARG cc_start: 0.6230 (OUTLIER) cc_final: 0.5122 (tmm-80)
REVERT: B  208 ARG cc_start: 0.6395 (mtp85) cc_final: 0.6181 (mtp180)
  outliers start: 12
  outliers final: 7
  residues processed: 49
  average time/residue: 0.4769
  time to fit residues: 24.3520
Evaluate side-chains
  47 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 38
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain B residue   41 MET
Chi-restraints excluded: chain B residue  121 GLU
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  185 ARG
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  319 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0040
   chunk 48 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 22 optimal weight:    0.3980
   chunk 50 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.5392

-------------------------------------------------------------------------------
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 = 0.4535 r_free = 0.4535 target = 0.218153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.184909 restraints weight = 4456.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.4170 rms_B_bonded: 2.05
r_work: 0.3951 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7242
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4775  Z= 0.128
  Angle     :  0.523   8.582   6508  Z= 0.269
  Chirality :  0.037   0.132    791
  Planarity :  0.003   0.037    773
  Dihedral  :  3.695  18.353    656
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 11.63 %
    Favored  : 85.47 %
  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 are not related in a simple way.
  whole:  2.45 (0.35), residues: 580
  helix:  2.37 (0.24), residues: 466
  sheet: -2.93 (0.96), residues: 10
  loop : -1.49 (0.57), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 212 
 TYR   0.016   0.001   TYR B 267 
 PHE   0.019   0.001   PHE B  72 
 TRP   0.013   0.001   TRP B 235 
 HIS   0.002   0.001   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 4772)
  covalent geometry    : angle       0.52206 ( 6502)
  SS BOND              : bond        0.00157 (    3)
  SS BOND              : angle       1.16658 (    6)
  hydrogen bonds       : bond        0.05102 (  374)
  hydrogen bonds       : angle       3.74054 ( 1095)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 43
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 ARG cc_start: 0.7963 (tmm-80) cc_final: 0.7490 (ttm-80)
REVERT: A  293 ASN cc_start: 0.7831 (m-40) cc_final: 0.7541 (m110)
REVERT: A  326 TYR cc_start: 0.5301 (t80) cc_final: 0.5059 (t80)
REVERT: B  121 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6450 (tt0)
REVERT: B  184 SER cc_start: 0.8368 (OUTLIER) cc_final: 0.8149 (m)
REVERT: B  204 THR cc_start: 0.6456 (OUTLIER) cc_final: 0.6148 (m)
  outliers start: 15
  outliers final: 9
  residues processed: 54
  average time/residue: 0.4047
  time to fit residues: 23.0249
Evaluate side-chains
  52 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 40
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain B residue   41 MET
Chi-restraints excluded: chain B residue  121 GLU
Chi-restraints excluded: chain B residue  142 VAL
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  319 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 47 optimal weight:    0.2980
   chunk 2 optimal weight:    0.5980
   chunk 43 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.7384

-------------------------------------------------------------------------------
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 = 0.4479 r_free = 0.4479 target = 0.212833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.177585 restraints weight = 4491.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.4150 rms_B_bonded: 1.62
r_work: 0.3951 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7241
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4775  Z= 0.143
  Angle     :  0.548  10.161   6508  Z= 0.279
  Chirality :  0.038   0.150    791
  Planarity :  0.004   0.038    773
  Dihedral  :  3.707  16.208    656
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 12.21 %
    Favored  : 85.47 %
  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 are not related in a simple way.
  whole:  2.35 (0.35), residues: 580
  helix:  2.34 (0.24), residues: 463
  sheet: -2.93 (0.98), residues: 10
  loop : -1.66 (0.55), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 212 
 TYR   0.016   0.001   TYR B 267 
 PHE   0.015   0.002   PHE B  72 
 TRP   0.012   0.001   TRP B 235 
 HIS   0.002   0.001   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 4772)
  covalent geometry    : angle       0.54664 ( 6502)
  SS BOND              : bond        0.00180 (    3)
  SS BOND              : angle       1.22905 (    6)
  hydrogen bonds       : bond        0.05492 (  374)
  hydrogen bonds       : angle       3.78053 ( 1095)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 38
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
REVERT: A  178 ASP cc_start: 0.7319 (t0) cc_final: 0.6333 (p0)
REVERT: A  185 ARG cc_start: 0.7900 (tmm-80) cc_final: 0.7436 (ttm-80)
REVERT: A  293 ASN cc_start: 0.7836 (m-40) cc_final: 0.7529 (m110)
REVERT: B  184 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.8224 (m)
REVERT: B  185 ARG cc_start: 0.6161 (OUTLIER) cc_final: 0.5115 (tmm-80)
REVERT: B  204 THR cc_start: 0.6480 (OUTLIER) cc_final: 0.6144 (m)
  outliers start: 12
  outliers final: 6
  residues processed: 47
  average time/residue: 0.4575
  time to fit residues: 22.4628
Evaluate side-chains
  46 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 37
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain B residue   41 MET
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  185 ARG
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  319 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   chunk 53 optimal weight:    0.8980
   chunk 54 optimal weight:    0.5980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.4453 r_free = 0.4453 target = 0.210398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.175589 restraints weight = 4384.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.4137 rms_B_bonded: 1.59
r_work: 0.3937 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3805 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
moved from start:          0.2156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4775  Z= 0.148
  Angle     :  0.556   8.718   6508  Z= 0.285
  Chirality :  0.038   0.156    791
  Planarity :  0.004   0.037    773
  Dihedral  :  3.765  17.520    656
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 12.60 %
    Favored  : 85.08 %
  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 are not related in a simple way.
  whole:  2.25 (0.35), residues: 580
  helix:  2.23 (0.24), residues: 466
  sheet: -2.62 (1.05), residues: 10
  loop : -1.62 (0.56), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 212 
 TYR   0.017   0.001   TYR B 267 
 PHE   0.011   0.002   PHE B 260 
 TRP   0.011   0.001   TRP B 235 
 HIS   0.002   0.001   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 4772)
  covalent geometry    : angle       0.55506 ( 6502)
  SS BOND              : bond        0.00165 (    3)
  SS BOND              : angle       1.23639 (    6)
  hydrogen bonds       : bond        0.05731 (  374)
  hydrogen bonds       : angle       3.82610 ( 1095)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 39
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 ARG cc_start: 0.8124 (tmm-80) cc_final: 0.7562 (ttm-80)
REVERT: B  184 SER cc_start: 0.8570 (OUTLIER) cc_final: 0.8343 (m)
REVERT: B  185 ARG cc_start: 0.6243 (OUTLIER) cc_final: 0.5101 (tmm-80)
REVERT: B  204 THR cc_start: 0.6503 (OUTLIER) cc_final: 0.6141 (m)
REVERT: B  208 ARG cc_start: 0.6473 (mtp85) cc_final: 0.6166 (mtp180)
  outliers start: 12
  outliers final: 6
  residues processed: 48
  average time/residue: 0.3804
  time to fit residues: 19.2764
Evaluate side-chains
  47 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 38
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  185 ARG
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  319 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 44 optimal weight:    0.0670
   chunk 21 optimal weight:    0.2980
   chunk 19 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 52 optimal weight:    0.6980
   chunk 53 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.5318

-------------------------------------------------------------------------------
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 = 0.4501 r_free = 0.4501 target = 0.215031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.180114 restraints weight = 4426.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.4160 rms_B_bonded: 1.63
r_work: 0.3971 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3839 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4775  Z= 0.129
  Angle     :  0.529   8.428   6508  Z= 0.274
  Chirality :  0.037   0.137    791
  Planarity :  0.003   0.036    773
  Dihedral  :  3.652  16.533    656
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 13.37 %
    Favored  : 84.69 %
  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 are not related in a simple way.
  whole:  2.43 (0.35), residues: 580
  helix:  2.36 (0.24), residues: 466
  sheet: -2.29 (1.07), residues: 10
  loop : -1.62 (0.56), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 212 
 TYR   0.017   0.001   TYR B 267 
 PHE   0.010   0.001   PHE B 260 
 TRP   0.011   0.001   TRP B 235 
 HIS   0.001   0.000   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 4772)
  covalent geometry    : angle       0.52761 ( 6502)
  SS BOND              : bond        0.00148 (    3)
  SS BOND              : angle       1.15525 (    6)
  hydrogen bonds       : bond        0.05127 (  374)
  hydrogen bonds       : angle       3.73979 ( 1095)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 ARG cc_start: 0.8125 (tmm-80) cc_final: 0.7564 (ttm-80)
REVERT: A  198 GLU cc_start: 0.7006 (tt0) cc_final: 0.6612 (tt0)
REVERT: A  293 ASN cc_start: 0.7856 (m-40) cc_final: 0.7578 (m110)
REVERT: B  184 SER cc_start: 0.8518 (OUTLIER) cc_final: 0.8300 (m)
REVERT: B  185 ARG cc_start: 0.6150 (OUTLIER) cc_final: 0.5027 (tmm-80)
REVERT: B  204 THR cc_start: 0.6467 (OUTLIER) cc_final: 0.6108 (m)
REVERT: B  208 ARG cc_start: 0.6424 (mtp85) cc_final: 0.6134 (mtp180)
  outliers start: 10
  outliers final: 5
  residues processed: 49
  average time/residue: 0.4662
  time to fit residues: 24.0631
Evaluate side-chains
  45 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  185 ARG
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  319 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 18 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4481 r_free = 0.4481 target = 0.212857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.178114 restraints weight = 4424.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.4146 rms_B_bonded: 1.61
r_work: 0.3950 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4775  Z= 0.144
  Angle     :  0.557  10.284   6508  Z= 0.286
  Chirality :  0.038   0.145    791
  Planarity :  0.004   0.037    773
  Dihedral  :  3.708  19.063    656
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 13.57 %
    Favored  : 84.11 %
  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 are not related in a simple way.
  whole:  2.29 (0.35), residues: 580
  helix:  2.26 (0.24), residues: 466
  sheet: -1.92 (1.17), residues: 10
  loop : -1.69 (0.56), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 212 
 TYR   0.018   0.001   TYR B 267 
 PHE   0.011   0.001   PHE B 260 
 TRP   0.011   0.001   TRP B 235 
 HIS   0.002   0.001   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 4772)
  covalent geometry    : angle       0.55553 ( 6502)
  SS BOND              : bond        0.00167 (    3)
  SS BOND              : angle       1.23335 (    6)
  hydrogen bonds       : bond        0.05525 (  374)
  hydrogen bonds       : angle       3.79665 ( 1095)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1486.18 seconds
wall clock time: 26 minutes 7.40 seconds (1567.40 seconds total)