Starting phenix.real_space_refine
on Tue Feb  3 15:34:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hj1_52208/02_2026/9hj1_52208.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hj1_52208/02_2026/9hj1_52208.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hj1_52208/02_2026/9hj1_52208.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hj1_52208/02_2026/9hj1_52208.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hj1_52208/02_2026/9hj1_52208.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hj1_52208/02_2026/9hj1_52208.map"
  }
  resolution = 2.9
  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=   0.006
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      19      5.16       5
     C    2874      2.51       5
     N     741      2.21       5
     O     793      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  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: 4427
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2062
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 2062
          Classifications: {'peptide': 255}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 241}
    Chain: "B"
      Number of atoms: 2293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2293
          Classifications: {'peptide': 285}
          Link IDs: {'PTRANS': 19, 'TRANS': 265}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 72
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
  Time building chain proxies: 1.12, per 1000 atoms: 0.25
  Number of scatterers: 4427
  At special positions: 0
  Unit cell: (78.315, 85.125, 69.235, 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      19     16.00
     O     793      8.00
     N     741      7.00
     C    2874      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.27
  Conformation dependent library (CDL) restraints added in 99.2 milliseconds
  

  1074 Ramachandran restraints generated.
    537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1048

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 4 sheets defined
      57.6% alpha, 7.5% 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 178 through 193
      removed outlier: 4.040A  pdb=" N   VAL A 191 " --> pdb=" O   ARG A 187 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LYS A 192 " --> pdb=" O   GLU A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 203
      removed outlier: 4.248A  pdb=" N   LYS A 202 " --> pdb=" O   GLY A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 225
    Processing helix  chain 'A' and resid 228 through 246
    Processing helix  chain 'A' and resid 252 through 269
    Processing helix  chain 'A' and resid 274 through 282
    Processing helix  chain 'A' and resid 287 through 303
    Processing helix  chain 'A' and resid 310 through 320
      removed outlier: 3.559A  pdb=" N   PHE A 314 " --> pdb=" O   THR A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 343
      removed outlier: 3.577A  pdb=" N   LEU A 341 " --> pdb=" O   GLY A 337 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ILE A 342 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   ASP A 343 " --> pdb=" O   LEU A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 348
      removed outlier: 3.758A  pdb=" N   TYR A 347 " --> pdb=" O   ASP A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 368
    Processing helix  chain 'A' and resid 373 through 381
    Processing helix  chain 'A' and resid 387 through 400
    Processing helix  chain 'A' and resid 407 through 413
    Processing helix  chain 'A' and resid 414 through 419
      removed outlier: 6.280A  pdb=" N   LYS A 417 " --> pdb=" O   LYS A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 424
    Processing helix  chain 'B' and resid 45 through 56
    Processing helix  chain 'B' and resid 87 through 94
    Processing helix  chain 'B' and resid 100 through 121
    Processing helix  chain 'B' and resid 129 through 131
      No H-bonds generated for 'chain 'B' and resid 129 through 131'
    Processing helix  chain 'B' and resid 145 through 149
      removed outlier: 4.345A  pdb=" N   LEU B 148 " --> pdb=" O   ASP B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 175
    Processing helix  chain 'B' and resid 182 through 199
    Processing helix  chain 'B' and resid 207 through 220
    Processing helix  chain 'B' and resid 247 through 252
    Processing helix  chain 'B' and resid 256 through 267
    Processing helix  chain 'B' and resid 276 through 282
      removed outlier: 3.703A  pdb=" N   ALA B 282 " --> pdb=" O   LYS B 278 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 287
    Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 11
      removed outlier: 5.611A  pdb=" N   LYS B   6 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   ARG B  22 " --> pdb=" O   LYS B   6 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   VAL B  18 " --> pdb=" O   ILE B  10 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   TYR B  19 " --> pdb=" O   LEU B  32 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   GLU B  81 " --> pdb=" O   LEU B  66 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   LEU B  66 " --> pdb=" O   GLU B  81 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 85 through 86
      removed outlier: 4.041A  pdb=" N   ALA B 140 " --> pdb=" O   ASN B 136 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 123 through 124
    Processing sheet with id=AA4, first strand: chain 'B' and resid 156 through 157
      removed outlier: 4.541A  pdb=" N   VAL B 156 " --> pdb=" O   TYR B 180 " (cutoff:3.500A)

    222 hydrogen bonds defined for protein.
    639 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: 0.59

  Time building geometry restraints manager: 0.37 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1395
        1.34 -     1.46: 798
        1.46 -     1.57: 2308
        1.57 -     1.69: 0
        1.69 -     1.81: 32
  Bond restraints: 4533
  Sorted by residual:
  bond pdb=" CB  VAL B 230 "
       pdb=" CG2 VAL B 230 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 8.21e-01
  bond pdb=" CB  ASN B 136 "
       pdb=" CG  ASN B 136 "
    ideal  model  delta    sigma   weight residual
    1.516  1.536 -0.020 2.50e-02 1.60e+03 6.14e-01
  bond pdb=" CB  PRO A 346 "
       pdb=" CG  PRO A 346 "
    ideal  model  delta    sigma   weight residual
    1.506  1.531 -0.025 3.90e-02 6.57e+02 4.13e-01
  bond pdb=" C   PRO B 253 "
       pdb=" N   PRO B 254 "
    ideal  model  delta    sigma   weight residual
    1.335  1.342 -0.008 1.19e-02 7.06e+03 4.12e-01
  bond pdb=" CB  VAL A 367 "
       pdb=" CG2 VAL A 367 "
    ideal  model  delta    sigma   weight residual
    1.521  1.500  0.021 3.30e-02 9.18e+02 4.11e-01
  ... (remaining 4528 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 6019
        1.21 -     2.42: 87
        2.42 -     3.63: 32
        3.63 -     4.84: 5
        4.84 -     6.04: 1
  Bond angle restraints: 6144
  Sorted by residual:
  angle pdb=" N   ARG B 126 "
        pdb=" CA  ARG B 126 "
        pdb=" CB  ARG B 126 "
      ideal   model   delta    sigma   weight residual
     113.65  110.40    3.25 1.47e+00 4.63e-01 4.89e+00
  angle pdb=" N   PRO B 253 "
        pdb=" CA  PRO B 253 "
        pdb=" C   PRO B 253 "
      ideal   model   delta    sigma   weight residual
     110.70  113.08   -2.38 1.22e+00 6.72e-01 3.82e+00
  angle pdb=" CA  PRO B 253 "
        pdb=" C   PRO B 253 "
        pdb=" N   PRO B 254 "
      ideal   model   delta    sigma   weight residual
     117.93  120.21   -2.28 1.20e+00 6.94e-01 3.60e+00
  angle pdb=" N   LEU B  67 "
        pdb=" CA  LEU B  67 "
        pdb=" C   LEU B  67 "
      ideal   model   delta    sigma   weight residual
     111.69  113.68   -1.99 1.23e+00 6.61e-01 2.63e+00
  angle pdb=" CA  ASN B 136 "
        pdb=" CB  ASN B 136 "
        pdb=" CG  ASN B 136 "
      ideal   model   delta    sigma   weight residual
     112.60  114.19   -1.59 1.00e+00 1.00e+00 2.52e+00
  ... (remaining 6139 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.55: 2297
       16.55 -    33.10: 318
       33.10 -    49.65: 86
       49.65 -    66.20: 24
       66.20 -    82.75: 15
  Dihedral angle restraints: 2740
    sinusoidal: 1123
      harmonic: 1617
  Sorted by residual:
  dihedral pdb=" CA  GLY B 153 "
           pdb=" C   GLY B 153 "
           pdb=" N   VAL B 154 "
           pdb=" CA  VAL B 154 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.74   16.26     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" N   LEU B 124 "
           pdb=" CA  LEU B 124 "
           pdb=" CB  LEU B 124 "
           pdb=" CG  LEU B 124 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.61   58.61     3      1.50e+01 4.44e-03 9.47e+00
  dihedral pdb=" CA  GLU A 428 "
           pdb=" CB  GLU A 428 "
           pdb=" CG  GLU A 428 "
           pdb=" CD  GLU A 428 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.59  -58.41     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 2737 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 449
       0.028 -    0.056: 154
       0.056 -    0.084: 60
       0.084 -    0.113: 25
       0.113 -    0.141: 6
  Chirality restraints: 694
  Sorted by residual:
  chirality pdb=" CA  VAL B 154 "
            pdb=" N   VAL B 154 "
            pdb=" C   VAL B 154 "
            pdb=" CB  VAL B 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.95e-01
  chirality pdb=" CA  ILE B  99 "
            pdb=" N   ILE B  99 "
            pdb=" C   ILE B  99 "
            pdb=" CB  ILE B  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.80e-01
  chirality pdb=" CA  ILE B  63 "
            pdb=" N   ILE B  63 "
            pdb=" C   ILE B  63 "
            pdb=" CB  ILE B  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  ... (remaining 691 not shown)

  Planarity restraints: 773
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 345 "   -0.022 5.00e-02 4.00e+02   3.37e-02 1.82e+00
        pdb=" N   PRO A 346 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 346 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 346 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 252 "    0.019 5.00e-02 4.00e+02   2.81e-02 1.27e+00
        pdb=" N   PRO B 253 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO B 253 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 253 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B  60 "   -0.018 5.00e-02 4.00e+02   2.74e-02 1.20e+00
        pdb=" N   PRO B  61 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO B  61 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B  61 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 770 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1059
        2.79 -     3.32: 4153
        3.32 -     3.85: 7863
        3.85 -     4.37: 9458
        4.37 -     4.90: 15831
  Nonbonded interactions: 38364
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 247 "
            pdb=" OG  SER B 249 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" OH  TYR A 238 "
            pdb=" O   LEU A 306 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" OG1 THR B 165 "
            pdb=" N   LEU B 166 "
     model   vdw
     2.299 3.120
  nonbonded pdb=" OH  TYR B 168 "
            pdb=" OE1 GLU B 195 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" OH  TYR A 365 "
            pdb=" OD1 ASN A 431 "
     model   vdw
     2.325 3.040
  ... (remaining 38359 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.240
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.190
  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:7.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4533  Z= 0.093
  Angle     :  0.433   6.044   6144  Z= 0.225
  Chirality :  0.037   0.141    694
  Planarity :  0.004   0.034    773
  Dihedral  : 17.806  82.753   1692
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 21.36 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  1.92 (0.37), residues: 537
  helix:  2.37 (0.33), residues: 273
  sheet: -0.44 (0.95), residues: 34
  loop :  0.28 (0.41), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  36 
 TYR   0.017   0.001   TYR B 236 
 PHE   0.016   0.001   PHE B 152 
 TRP   0.010   0.001   TRP A 372 
 HIS   0.004   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 4533)
  covalent geometry    : angle       0.43276 ( 6144)
  hydrogen bonds       : bond        0.14105 (  222)
  hydrogen bonds       : angle       5.83093 (  639)

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

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

  1074 Ramachandran restraints generated.
    537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1074 Ramachandran restraints generated.
    537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.106 
Fit side-chains
REVERT: A  180 GLU cc_start: 0.7641 (tt0) cc_final: 0.6930 (mp0)
REVERT: A  202 LYS cc_start: 0.8178 (ttmt) cc_final: 0.7953 (mppt)
REVERT: A  207 THR cc_start: 0.8532 (p) cc_final: 0.8284 (p)
REVERT: A  216 ASP cc_start: 0.8465 (t70) cc_final: 0.7868 (t70)
REVERT: A  294 MET cc_start: 0.8908 (tpp) cc_final: 0.8502 (tpt)
REVERT: A  347 TYR cc_start: 0.8514 (m-80) cc_final: 0.7738 (m-80)
REVERT: B  135 ILE cc_start: 0.8440 (mt) cc_final: 0.8210 (pt)
REVERT: B  145 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8011 (m-30)
REVERT: B  200 ARG cc_start: 0.7791 (mtp-110) cc_final: 0.6941 (ptt-90)
REVERT: B  273 LYS cc_start: 0.8523 (mtmt) cc_final: 0.8190 (mmpt)
  outliers start: 9
  outliers final: 4
  residues processed: 83
  average time/residue: 0.4342
  time to fit residues: 37.2748
Evaluate side-chains
  80 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue  122 ARG
Chi-restraints excluded: chain B residue  145 ASP
Chi-restraints excluded: chain B residue  225 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    6.9990
   chunk 26 optimal weight:    0.0050
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.6996

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

Flipped N/Q/H residues before XYZ refinement:
A 431 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.121855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.101167 restraints weight = 4988.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 1.47
r_work: 0.2857 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2721 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.0707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4533  Z= 0.112
  Angle     :  0.464   6.025   6144  Z= 0.241
  Chirality :  0.039   0.142    694
  Planarity :  0.004   0.037    773
  Dihedral  :  4.942  52.821    603
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 19.51 %
    Favored  : 77.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  1.71 (0.37), residues: 537
  helix:  2.25 (0.32), residues: 278
  sheet: -1.30 (1.11), residues: 24
  loop :  0.11 (0.40), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 274 
 TYR   0.008   0.001   TYR A 413 
 PHE   0.016   0.001   PHE B 152 
 TRP   0.010   0.001   TRP A 372 
 HIS   0.003   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 4533)
  covalent geometry    : angle       0.46419 ( 6144)
  hydrogen bonds       : bond        0.03901 (  222)
  hydrogen bonds       : angle       4.82518 (  639)

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

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

  1074 Ramachandran restraints generated.
    537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1074 Ramachandran restraints generated.
    537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.112 
Fit side-chains
REVERT: A  180 GLU cc_start: 0.7632 (tt0) cc_final: 0.6903 (mp0)
REVERT: A  200 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.6103 (mpt)
REVERT: A  202 LYS cc_start: 0.8212 (ttmt) cc_final: 0.7932 (mppt)
REVERT: A  209 SER cc_start: 0.8851 (OUTLIER) cc_final: 0.8598 (t)
REVERT: A  216 ASP cc_start: 0.8500 (t70) cc_final: 0.7942 (t70)
REVERT: A  294 MET cc_start: 0.8972 (tpp) cc_final: 0.8586 (tpt)
REVERT: A  417 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8123 (ttmp)
REVERT: B  200 ARG cc_start: 0.7748 (mtp-110) cc_final: 0.6928 (ptt-90)
REVERT: B  247 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.7013 (t70)
REVERT: B  273 LYS cc_start: 0.8487 (mtmt) cc_final: 0.8143 (mmpt)
  outliers start: 17
  outliers final: 7
  residues processed: 91
  average time/residue: 0.4877
  time to fit residues: 46.0497
Evaluate side-chains
  89 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  417 LYS
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  122 ARG
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  261 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0270
   chunk 20 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.6440

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

Flipped N/Q/H residues before XYZ refinement:
B  23 ASN
B 268 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.122051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.102060 restraints weight = 4984.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 1.48
r_work: 0.2865 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2730 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.0932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4533  Z= 0.104
  Angle     :  0.452   6.051   6144  Z= 0.233
  Chirality :  0.038   0.141    694
  Planarity :  0.004   0.038    773
  Dihedral  :  4.739  52.995    599
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 19.92 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  1.73 (0.37), residues: 537
  helix:  2.28 (0.32), residues: 278
  sheet: -1.34 (1.13), residues: 24
  loop :  0.10 (0.41), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 250 
 TYR   0.011   0.001   TYR A 280 
 PHE   0.015   0.001   PHE B 152 
 TRP   0.008   0.001   TRP A 372 
 HIS   0.003   0.001   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 4533)
  covalent geometry    : angle       0.45201 ( 6144)
  hydrogen bonds       : bond        0.03599 (  222)
  hydrogen bonds       : angle       4.62428 (  639)

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

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

  1074 Ramachandran restraints generated.
    537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1074 Ramachandran restraints generated.
    537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A  180 GLU cc_start: 0.7552 (tt0) cc_final: 0.6867 (mp0)
REVERT: A  200 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.6027 (mpt)
REVERT: A  202 LYS cc_start: 0.8114 (ttmt) cc_final: 0.7781 (mppt)
REVERT: A  209 SER cc_start: 0.8868 (OUTLIER) cc_final: 0.8622 (t)
REVERT: A  216 ASP cc_start: 0.8481 (t70) cc_final: 0.7949 (t70)
REVERT: A  224 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8026 (tp30)
REVERT: A  277 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7026 (mt-10)
REVERT: A  294 MET cc_start: 0.8951 (tpp) cc_final: 0.8609 (tpt)
REVERT: A  388 LYS cc_start: 0.8051 (ttmt) cc_final: 0.7760 (tptt)
REVERT: B   23 ASN cc_start: 0.7372 (t0) cc_final: 0.7047 (t0)
REVERT: B   65 LYS cc_start: 0.7967 (ttpp) cc_final: 0.7344 (tmtm)
REVERT: B  200 ARG cc_start: 0.7734 (mtp-110) cc_final: 0.6919 (ptt-90)
REVERT: B  247 ASP cc_start: 0.7244 (OUTLIER) cc_final: 0.7028 (t70)
REVERT: B  273 LYS cc_start: 0.8460 (mtmt) cc_final: 0.8145 (mmpt)
  outliers start: 17
  outliers final: 6
  residues processed: 92
  average time/residue: 0.5350
  time to fit residues: 50.9807
Evaluate side-chains
  88 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  224 GLU
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  122 ARG
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  261 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0670
   chunk 45 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 23 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 16 optimal weight:    0.4980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
A 312 ASN
B 268 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.122348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.102468 restraints weight = 4997.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 1.47
r_work: 0.2875 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2740 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.1014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4533  Z= 0.097
  Angle     :  0.441   5.986   6144  Z= 0.227
  Chirality :  0.038   0.141    694
  Planarity :  0.004   0.039    773
  Dihedral  :  4.701  53.320    599
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 20.33 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  1.75 (0.38), residues: 537
  helix:  2.35 (0.32), residues: 278
  sheet: -1.40 (1.12), residues: 24
  loop :  0.04 (0.41), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 250 
 TYR   0.007   0.001   TYR A 413 
 PHE   0.015   0.001   PHE B 152 
 TRP   0.007   0.001   TRP A 372 
 HIS   0.003   0.001   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 4533)
  covalent geometry    : angle       0.44080 ( 6144)
  hydrogen bonds       : bond        0.03313 (  222)
  hydrogen bonds       : angle       4.50894 (  639)

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

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

  1074 Ramachandran restraints generated.
    537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1074 Ramachandran restraints generated.
    537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A  180 GLU cc_start: 0.7554 (tt0) cc_final: 0.6842 (mp0)
REVERT: A  200 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.6057 (mpt)
REVERT: A  202 LYS cc_start: 0.8115 (ttmt) cc_final: 0.7897 (mppt)
REVERT: A  209 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8647 (t)
REVERT: A  216 ASP cc_start: 0.8454 (t70) cc_final: 0.7933 (t70)
REVERT: A  224 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8015 (tp30)
REVERT: A  277 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7061 (mt-10)
REVERT: A  294 MET cc_start: 0.8878 (tpp) cc_final: 0.8535 (tpt)
REVERT: A  388 LYS cc_start: 0.8018 (ttmt) cc_final: 0.7719 (tptt)
REVERT: B   23 ASN cc_start: 0.7296 (t0) cc_final: 0.6970 (t0)
REVERT: B   65 LYS cc_start: 0.7888 (ttpp) cc_final: 0.7317 (tmtm)
REVERT: B  200 ARG cc_start: 0.7713 (mtp-110) cc_final: 0.6927 (ptt-90)
REVERT: B  247 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.7038 (t70)
REVERT: B  273 LYS cc_start: 0.8455 (mtmt) cc_final: 0.8128 (mmpt)
  outliers start: 15
  outliers final: 6
  residues processed: 87
  average time/residue: 0.4978
  time to fit residues: 44.8408
Evaluate side-chains
  86 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  224 GLU
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain B residue   46 SER
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  122 ARG
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  247 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 15 optimal weight:    0.5980
   chunk 1 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 312 ASN
B 268 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.121755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.101805 restraints weight = 5001.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 1.48
r_work: 0.2859 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2723 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.1124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4533  Z= 0.107
  Angle     :  0.453   6.012   6144  Z= 0.233
  Chirality :  0.038   0.140    694
  Planarity :  0.004   0.038    773
  Dihedral  :  4.695  54.361    598
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 20.74 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  1.72 (0.37), residues: 537
  helix:  2.32 (0.32), residues: 278
  sheet: -1.39 (1.13), residues: 24
  loop :  0.02 (0.41), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 274 
 TYR   0.014   0.001   TYR A 280 
 PHE   0.015   0.001   PHE B 152 
 TRP   0.008   0.001   TRP A 372 
 HIS   0.003   0.001   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 4533)
  covalent geometry    : angle       0.45283 ( 6144)
  hydrogen bonds       : bond        0.03378 (  222)
  hydrogen bonds       : angle       4.49460 (  639)

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

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

  1074 Ramachandran restraints generated.
    537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1074 Ramachandran restraints generated.
    537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A  180 GLU cc_start: 0.7552 (tt0) cc_final: 0.6820 (mp0)
REVERT: A  200 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.6059 (mpt)
REVERT: A  202 LYS cc_start: 0.8102 (ttmt) cc_final: 0.7758 (mppt)
REVERT: A  209 SER cc_start: 0.8930 (OUTLIER) cc_final: 0.8698 (t)
REVERT: A  216 ASP cc_start: 0.8469 (t70) cc_final: 0.7939 (t70)
REVERT: A  224 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8019 (tp30)
REVERT: A  277 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7068 (mt-10)
REVERT: A  294 MET cc_start: 0.9020 (tpp) cc_final: 0.8570 (tpt)
REVERT: A  388 LYS cc_start: 0.8022 (ttmt) cc_final: 0.7731 (tptt)
REVERT: B   23 ASN cc_start: 0.7303 (t0) cc_final: 0.6967 (t0)
REVERT: B   65 LYS cc_start: 0.7899 (ttpp) cc_final: 0.7321 (tmtm)
REVERT: B  200 ARG cc_start: 0.7696 (mtp-110) cc_final: 0.6894 (ptt-90)
REVERT: B  273 LYS cc_start: 0.8466 (mtmt) cc_final: 0.8130 (mmpt)
  outliers start: 14
  outliers final: 6
  residues processed: 86
  average time/residue: 0.4806
  time to fit residues: 42.9348
Evaluate side-chains
  83 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  224 GLU
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  122 ARG
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  226 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 46 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0770
   overall best weight:    0.7138

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

Flipped N/Q/H residues before XYZ refinement:
A 312 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.121952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.102020 restraints weight = 5088.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 1.49
r_work: 0.2863 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2728 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.1118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4533  Z= 0.103
  Angle     :  0.449   6.061   6144  Z= 0.230
  Chirality :  0.038   0.140    694
  Planarity :  0.004   0.038    773
  Dihedral  :  4.687  54.706    598
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 20.33 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  1.72 (0.37), residues: 537
  helix:  2.32 (0.32), residues: 278
  sheet: -1.41 (1.12), residues: 24
  loop :  0.02 (0.41), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 274 
 TYR   0.008   0.001   TYR B 168 
 PHE   0.015   0.001   PHE B 152 
 TRP   0.008   0.001   TRP A 372 
 HIS   0.003   0.001   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 4533)
  covalent geometry    : angle       0.44850 ( 6144)
  hydrogen bonds       : bond        0.03282 (  222)
  hydrogen bonds       : angle       4.46727 (  639)

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

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

  1074 Ramachandran restraints generated.
    537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1074 Ramachandran restraints generated.
    537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A  180 GLU cc_start: 0.7564 (tt0) cc_final: 0.6847 (mp0)
REVERT: A  200 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.6020 (mpt)
REVERT: A  202 LYS cc_start: 0.8200 (ttmt) cc_final: 0.7903 (mppt)
REVERT: A  209 SER cc_start: 0.8935 (OUTLIER) cc_final: 0.8701 (t)
REVERT: A  216 ASP cc_start: 0.8463 (t70) cc_final: 0.7939 (t70)
REVERT: A  224 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8014 (tp30)
REVERT: A  277 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7032 (mt-10)
REVERT: A  294 MET cc_start: 0.9020 (tpp) cc_final: 0.8552 (tpt)
REVERT: A  388 LYS cc_start: 0.8027 (ttmt) cc_final: 0.7739 (tptt)
REVERT: B   23 ASN cc_start: 0.7307 (t0) cc_final: 0.7012 (t0)
REVERT: B   65 LYS cc_start: 0.7830 (ttpp) cc_final: 0.7258 (tmtm)
REVERT: B  200 ARG cc_start: 0.7709 (mtp-110) cc_final: 0.6921 (ptt-90)
REVERT: B  273 LYS cc_start: 0.8482 (mtmt) cc_final: 0.8131 (mmpt)
  outliers start: 16
  outliers final: 8
  residues processed: 84
  average time/residue: 0.5275
  time to fit residues: 45.9015
Evaluate side-chains
  85 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  224 GLU
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain B residue    2 GLU
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  122 ARG
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  261 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 35 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 312 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.121599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.101740 restraints weight = 5075.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 1.45
r_work: 0.2861 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2727 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.1174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4533  Z= 0.108
  Angle     :  0.452   6.066   6144  Z= 0.232
  Chirality :  0.038   0.140    694
  Planarity :  0.004   0.038    773
  Dihedral  :  4.705  55.149    598
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 20.53 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  1.70 (0.37), residues: 537
  helix:  2.29 (0.32), residues: 278
  sheet: -1.39 (1.12), residues: 24
  loop :  0.03 (0.40), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 274 
 TYR   0.015   0.001   TYR A 280 
 PHE   0.015   0.001   PHE B 152 
 TRP   0.008   0.001   TRP A 372 
 HIS   0.003   0.001   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 4533)
  covalent geometry    : angle       0.45244 ( 6144)
  hydrogen bonds       : bond        0.03332 (  222)
  hydrogen bonds       : angle       4.46819 (  639)

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

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

  1074 Ramachandran restraints generated.
    537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1074 Ramachandran restraints generated.
    537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.107 
Fit side-chains
REVERT: A  180 GLU cc_start: 0.7596 (tt0) cc_final: 0.6868 (mp0)
REVERT: A  200 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.6018 (mpt)
REVERT: A  202 LYS cc_start: 0.8216 (ttmt) cc_final: 0.7995 (mppt)
REVERT: A  209 SER cc_start: 0.8908 (OUTLIER) cc_final: 0.8664 (t)
REVERT: A  216 ASP cc_start: 0.8490 (t70) cc_final: 0.7962 (t70)
REVERT: A  224 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8060 (tp30)
REVERT: A  277 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7064 (mt-10)
REVERT: A  294 MET cc_start: 0.9045 (tpp) cc_final: 0.8573 (tpt)
REVERT: A  388 LYS cc_start: 0.8072 (ttmt) cc_final: 0.7777 (tptt)
REVERT: B   23 ASN cc_start: 0.7324 (t0) cc_final: 0.7030 (t0)
REVERT: B   65 LYS cc_start: 0.7865 (ttpp) cc_final: 0.7302 (tmtm)
REVERT: B  200 ARG cc_start: 0.7717 (mtp-110) cc_final: 0.6931 (ptt-90)
REVERT: B  273 LYS cc_start: 0.8479 (mtmt) cc_final: 0.8152 (mmpt)
  outliers start: 14
  outliers final: 7
  residues processed: 84
  average time/residue: 0.4817
  time to fit residues: 41.9482
Evaluate side-chains
  85 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  224 GLU
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain B residue    2 GLU
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  122 ARG
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  261 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 50 optimal weight:   10.0000
   chunk 42 optimal weight:    5.9990
   chunk 41 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 31 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 312 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.121537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.101548 restraints weight = 5012.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 1.49
r_work: 0.2858 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2721 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.1167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4533  Z= 0.109
  Angle     :  0.456   6.067   6144  Z= 0.234
  Chirality :  0.038   0.140    694
  Planarity :  0.004   0.039    773
  Dihedral  :  4.711  55.244    598
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 20.53 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  1.69 (0.37), residues: 537
  helix:  2.28 (0.32), residues: 278
  sheet: -1.40 (1.12), residues: 24
  loop :  0.04 (0.40), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 274 
 TYR   0.010   0.001   TYR A 347 
 PHE   0.015   0.001   PHE B 152 
 TRP   0.008   0.001   TRP A 372 
 HIS   0.003   0.001   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 4533)
  covalent geometry    : angle       0.45630 ( 6144)
  hydrogen bonds       : bond        0.03322 (  222)
  hydrogen bonds       : angle       4.47437 (  639)

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

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

  1074 Ramachandran restraints generated.
    537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1074 Ramachandran restraints generated.
    537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A  180 GLU cc_start: 0.7576 (tt0) cc_final: 0.6837 (mp0)
REVERT: A  200 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.5991 (mpt)
REVERT: A  202 LYS cc_start: 0.8207 (ttmt) cc_final: 0.7971 (mppt)
REVERT: A  209 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8652 (t)
REVERT: A  216 ASP cc_start: 0.8477 (t70) cc_final: 0.7948 (t70)
REVERT: A  224 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8041 (tp30)
REVERT: A  277 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7041 (mt-10)
REVERT: A  294 MET cc_start: 0.9039 (tpp) cc_final: 0.8557 (tpt)
REVERT: A  388 LYS cc_start: 0.7992 (ttmt) cc_final: 0.7702 (tptt)
REVERT: B   23 ASN cc_start: 0.7305 (t0) cc_final: 0.7005 (t0)
REVERT: B   65 LYS cc_start: 0.7867 (ttpp) cc_final: 0.7282 (tmtm)
REVERT: B  200 ARG cc_start: 0.7647 (mtp-110) cc_final: 0.6869 (ptt-90)
REVERT: B  273 LYS cc_start: 0.8486 (mtmt) cc_final: 0.8132 (mmpt)
  outliers start: 15
  outliers final: 9
  residues processed: 86
  average time/residue: 0.4443
  time to fit residues: 39.6954
Evaluate side-chains
  85 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  224 GLU
Chi-restraints excluded: chain A residue  261 MET
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain B residue    2 GLU
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  122 ARG
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  261 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 33 optimal weight:    0.2980
   chunk 15 optimal weight:    4.9990
   chunk 25 optimal weight:   10.0000
   chunk 43 optimal weight:    0.8980
   chunk 16 optimal weight:    0.3980
   overall best weight:    1.5184

-------------------------------------------------------------------------------
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 = 0.3219 r_free = 0.3219 target = 0.118924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.098813 restraints weight = 5083.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 1.50
r_work: 0.2818 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2680 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.1177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4533  Z= 0.154
  Angle     :  0.502   6.132   6144  Z= 0.256
  Chirality :  0.040   0.147    694
  Planarity :  0.004   0.039    773
  Dihedral  :  4.879  55.920    598
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 21.15 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  1.57 (0.37), residues: 537
  helix:  2.19 (0.32), residues: 274
  sheet: -1.40 (1.12), residues: 24
  loop : -0.01 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 126 
 TYR   0.012   0.001   TYR A 347 
 PHE   0.016   0.002   PHE B 152 
 TRP   0.009   0.001   TRP A 372 
 HIS   0.003   0.001   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 4533)
  covalent geometry    : angle       0.50242 ( 6144)
  hydrogen bonds       : bond        0.03783 (  222)
  hydrogen bonds       : angle       4.61461 (  639)

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

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

  1074 Ramachandran restraints generated.
    537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1074 Ramachandran restraints generated.
    537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.178 
Fit side-chains
REVERT: A  180 GLU cc_start: 0.7601 (tt0) cc_final: 0.6867 (mp0)
REVERT: A  200 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.6007 (mpt)
REVERT: A  202 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7872 (mppt)
REVERT: A  209 SER cc_start: 0.8935 (OUTLIER) cc_final: 0.8686 (t)
REVERT: A  216 ASP cc_start: 0.8497 (t70) cc_final: 0.7979 (t70)
REVERT: A  224 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8031 (tp30)
REVERT: A  294 MET cc_start: 0.9056 (tpp) cc_final: 0.8600 (tpt)
REVERT: A  388 LYS cc_start: 0.8041 (ttmt) cc_final: 0.7744 (tptt)
REVERT: B   65 LYS cc_start: 0.8105 (ttpp) cc_final: 0.7465 (tmtm)
REVERT: B  200 ARG cc_start: 0.7731 (mtp-110) cc_final: 0.6849 (ptt-90)
REVERT: B  273 LYS cc_start: 0.8524 (mtmt) cc_final: 0.8154 (mmpt)
  outliers start: 12
  outliers final: 7
  residues processed: 83
  average time/residue: 0.4927
  time to fit residues: 42.4170
Evaluate side-chains
  84 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  224 GLU
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain B residue    2 GLU
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  122 ARG
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  261 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 24 optimal weight:    6.9990
   chunk 14 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B  23 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.120834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.100873 restraints weight = 5056.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.2995 rms_B_bonded: 1.49
r_work: 0.2848 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2709 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.1207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4533  Z= 0.111
  Angle     :  0.464   6.046   6144  Z= 0.237
  Chirality :  0.039   0.140    694
  Planarity :  0.004   0.039    773
  Dihedral  :  4.768  55.243    598
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 20.94 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  1.60 (0.37), residues: 537
  helix:  2.24 (0.32), residues: 276
  sheet: -1.39 (1.10), residues: 24
  loop : -0.04 (0.39), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 122 
 TYR   0.014   0.001   TYR A 280 
 PHE   0.016   0.001   PHE B 152 
 TRP   0.009   0.001   TRP A 372 
 HIS   0.003   0.001   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 4533)
  covalent geometry    : angle       0.46403 ( 6144)
  hydrogen bonds       : bond        0.03366 (  222)
  hydrogen bonds       : angle       4.48325 (  639)

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

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

  1074 Ramachandran restraints generated.
    537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1074 Ramachandran restraints generated.
    537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A  180 GLU cc_start: 0.7577 (tt0) cc_final: 0.6836 (mp0)
REVERT: A  200 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.6028 (mpt)
REVERT: A  202 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7854 (mppt)
REVERT: A  209 SER cc_start: 0.8918 (OUTLIER) cc_final: 0.8674 (t)
REVERT: A  216 ASP cc_start: 0.8495 (t70) cc_final: 0.7945 (t70)
REVERT: A  224 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8045 (tp30)
REVERT: A  294 MET cc_start: 0.9037 (tpp) cc_final: 0.8535 (tpt)
REVERT: A  388 LYS cc_start: 0.8008 (ttmt) cc_final: 0.7709 (tptt)
REVERT: B   23 ASN cc_start: 0.7332 (t0) cc_final: 0.6965 (t0)
REVERT: B   65 LYS cc_start: 0.8039 (ttpp) cc_final: 0.7414 (tmtm)
REVERT: B  200 ARG cc_start: 0.7719 (mtp-110) cc_final: 0.6883 (ptt-90)
REVERT: B  273 LYS cc_start: 0.8508 (mtmt) cc_final: 0.8129 (mmpt)
  outliers start: 13
  outliers final: 8
  residues processed: 84
  average time/residue: 0.4569
  time to fit residues: 39.7716
Evaluate side-chains
  84 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  224 GLU
Chi-restraints excluded: chain A residue  261 MET
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain B residue    2 GLU
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  122 ARG
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  261 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 31 optimal weight:    9.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 312 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.121212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.101241 restraints weight = 5040.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 1.49
r_work: 0.2867 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2730 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.1194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4533  Z= 0.108
  Angle     :  0.459   6.072   6144  Z= 0.234
  Chirality :  0.039   0.140    694
  Planarity :  0.004   0.040    773
  Dihedral  :  4.746  55.411    598
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 20.74 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  1.60 (0.37), residues: 537
  helix:  2.25 (0.32), residues: 276
  sheet: -1.36 (1.10), residues: 24
  loop : -0.05 (0.39), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 274 
 TYR   0.016   0.001   TYR A 280 
 PHE   0.016   0.001   PHE B 152 
 TRP   0.008   0.001   TRP A 372 
 HIS   0.003   0.001   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 4533)
  covalent geometry    : angle       0.45920 ( 6144)
  hydrogen bonds       : bond        0.03286 (  222)
  hydrogen bonds       : angle       4.46212 (  639)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1500.38 seconds
wall clock time: 26 minutes 19.77 seconds (1579.77 seconds total)