Starting phenix.real_space_refine
on Fri Aug 22 20:35:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ug4_42213/08_2025/8ug4_42213.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ug4_42213/08_2025/8ug4_42213.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ug4_42213/08_2025/8ug4_42213.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ug4_42213/08_2025/8ug4_42213.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ug4_42213/08_2025/8ug4_42213.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ug4_42213/08_2025/8ug4_42213.cif"
  }
  resolution = 3.02
  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=   0.004
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      52      5.16       5
     C    5182      2.51       5
     N    1270      2.21       5
     O    1298      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7802
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3901
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 486, 3891
          Classifications: {'peptide': 486}
          Link IDs: {'PTRANS': 8, 'TRANS': 477}
          Chain breaks: 3
      Conformer: "B"
        Number of residues, atoms: 486, 3891
          Classifications: {'peptide': 486}
          Link IDs: {'PTRANS': 8, 'TRANS': 477}
          Chain breaks: 3
          bond proxies already assigned to first conformer: 3975
  Restraints were copied for chains:
    B
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AHIS A 567 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS A 567 " occ=0.50
    residue:
      pdb=" N  AHIS B 567 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS B 567 " occ=0.50
  Time building chain proxies: 3.76, per 1000 atoms: 0.48
  Number of scatterers: 7802
  At special positions: 0
  Unit cell: (100.43, 92.13, 90.47, 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      52     16.00
     O    1298      8.00
     N    1270      7.00
     C    5182      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: 0.66
  Conformation dependent library (CDL) restraints added in 727.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1828

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 2 sheets defined
      77.8% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 57 through 86
    Processing helix  chain 'A' and resid 93 through 119
    Processing helix  chain 'A' and resid 122 through 136
    Processing helix  chain 'A' and resid 158 through 186
    Processing helix  chain 'A' and resid 190 through 213
      removed outlier: 3.765A  pdb=" N   ILE A 194 " --> pdb=" O   LYS A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 268
      removed outlier: 3.890A  pdb=" N   ALA A 251 " --> pdb=" O   ALA A 247 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LYS A 252 " --> pdb=" O   LYS A 248 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ALA A 253 " --> pdb=" O   GLN A 249 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   HIS A 254 " --> pdb=" O   GLU A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
    Processing helix  chain 'A' and resid 314 through 340
      removed outlier: 3.632A  pdb=" N   PHE A 318 " --> pdb=" O   ASP A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 389
      removed outlier: 3.589A  pdb=" N   PHE A 389 " --> pdb=" O   MET A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 395
    Processing helix  chain 'A' and resid 395 through 425
    Processing helix  chain 'A' and resid 436 through 467
      removed outlier: 4.273A  pdb=" N   GLU A 440 " --> pdb=" O   GLU A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 499
    Processing helix  chain 'A' and resid 504 through 510
    Processing helix  chain 'A' and resid 513 through 535
    Processing helix  chain 'A' and resid 544 through 549
    Processing helix  chain 'A' and resid 563 through 579
    Processing helix  chain 'B' and resid 57 through 86
    Processing helix  chain 'B' and resid 93 through 119
    Processing helix  chain 'B' and resid 122 through 136
    Processing helix  chain 'B' and resid 158 through 186
    Processing helix  chain 'B' and resid 190 through 213
      removed outlier: 3.765A  pdb=" N   ILE B 194 " --> pdb=" O   LYS B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 268
      removed outlier: 3.890A  pdb=" N   ALA B 251 " --> pdb=" O   ALA B 247 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LYS B 252 " --> pdb=" O   LYS B 248 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ALA B 253 " --> pdb=" O   GLN B 249 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   HIS B 254 " --> pdb=" O   GLU B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 312
    Processing helix  chain 'B' and resid 314 through 340
      removed outlier: 3.632A  pdb=" N   PHE B 318 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 389
      removed outlier: 3.589A  pdb=" N   PHE B 389 " --> pdb=" O   MET B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 389 through 395
    Processing helix  chain 'B' and resid 395 through 425
    Processing helix  chain 'B' and resid 436 through 467
      removed outlier: 4.272A  pdb=" N   GLU B 440 " --> pdb=" O   GLU B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 474 through 499
    Processing helix  chain 'B' and resid 504 through 510
    Processing helix  chain 'B' and resid 513 through 535
    Processing helix  chain 'B' and resid 544 through 549
    Processing helix  chain 'B' and resid 563 through 579
    Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 429
    Processing sheet with id=AA2, first strand: chain 'B' and resid 428 through 429

    614 hydrogen bonds defined for protein.
    1820 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.29

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1357
        1.33 -     1.45: 2158
        1.45 -     1.57: 4401
        1.57 -     1.69: 0
        1.69 -     1.81: 82
  Bond restraints: 7998
  Sorted by residual:
  bond pdb=" CA  SER A 396 "
       pdb=" CB  SER A 396 "
    ideal  model  delta    sigma   weight residual
    1.531  1.481  0.049 1.59e-02 3.96e+03 9.65e+00
  bond pdb=" CA  SER B 396 "
       pdb=" CB  SER B 396 "
    ideal  model  delta    sigma   weight residual
    1.531  1.481  0.049 1.59e-02 3.96e+03 9.65e+00
  bond pdb=" N   ILE B 146 "
       pdb=" CA  ILE B 146 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.12e-02 7.97e+03 9.61e+00
  bond pdb=" N   ILE A 146 "
       pdb=" CA  ILE A 146 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.12e-02 7.97e+03 9.59e+00
  bond pdb=" N   VAL B 219 "
       pdb=" CA  VAL B 219 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.25e-02 6.40e+03 8.89e+00
  ... (remaining 7993 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.35: 10110
        1.35 -     2.70: 551
        2.70 -     4.05: 124
        4.05 -     5.40: 25
        5.40 -     6.75: 8
  Bond angle restraints: 10818
  Sorted by residual:
  angle pdb=" CA BHIS A 567 "
        pdb=" CB BHIS A 567 "
        pdb=" CG BHIS A 567 "
      ideal   model   delta    sigma   weight residual
     113.80  107.05    6.75 1.00e+00 1.00e+00 4.56e+01
  angle pdb=" CA BHIS B 567 "
        pdb=" CB BHIS B 567 "
        pdb=" CG BHIS B 567 "
      ideal   model   delta    sigma   weight residual
     113.80  107.06    6.74 1.00e+00 1.00e+00 4.54e+01
  angle pdb=" N   LEU B 400 "
        pdb=" CA  LEU B 400 "
        pdb=" C   LEU B 400 "
      ideal   model   delta    sigma   weight residual
     111.14  106.86    4.28 1.08e+00 8.57e-01 1.57e+01
  angle pdb=" N   VAL B 437 "
        pdb=" CA  VAL B 437 "
        pdb=" C   VAL B 437 "
      ideal   model   delta    sigma   weight residual
     112.76  107.75    5.01 1.27e+00 6.20e-01 1.55e+01
  angle pdb=" N   LEU A 400 "
        pdb=" CA  LEU A 400 "
        pdb=" C   LEU A 400 "
      ideal   model   delta    sigma   weight residual
     111.14  106.88    4.26 1.08e+00 8.57e-01 1.55e+01
  ... (remaining 10813 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 4105
       17.85 -    35.69: 435
       35.69 -    53.53: 66
       53.53 -    71.38: 12
       71.38 -    89.22: 8
  Dihedral angle restraints: 4626
    sinusoidal: 1784
      harmonic: 2842
  Sorted by residual:
  dihedral pdb=" CD  ARG A 133 "
           pdb=" NE  ARG A 133 "
           pdb=" CZ  ARG A 133 "
           pdb=" NH1 ARG A 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   65.82  -65.82     1      1.00e+01 1.00e-02 5.67e+01
  dihedral pdb=" CD  ARG B 133 "
           pdb=" NE  ARG B 133 "
           pdb=" CZ  ARG B 133 "
           pdb=" NH1 ARG B 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   65.78  -65.78     1      1.00e+01 1.00e-02 5.66e+01
  dihedral pdb=" N   LEU A 306 "
           pdb=" C   LEU A 306 "
           pdb=" CA  LEU A 306 "
           pdb=" CB  LEU A 306 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  113.75    9.05     0      2.50e+00 1.60e-01 1.31e+01
  ... (remaining 4623 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1064
       0.066 -    0.132: 141
       0.132 -    0.198: 35
       0.198 -    0.264: 8
       0.264 -    0.331: 4
  Chirality restraints: 1252
  Sorted by residual:
  chirality pdb=" CA  LEU A 306 "
            pdb=" N   LEU A 306 "
            pdb=" C   LEU A 306 "
            pdb=" CB  LEU A 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.84   -0.33 2.00e-01 2.50e+01 2.73e+00
  chirality pdb=" CA  LEU B 306 "
            pdb=" N   LEU B 306 "
            pdb=" C   LEU B 306 "
            pdb=" CB  LEU B 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.84   -0.33 2.00e-01 2.50e+01 2.70e+00
  chirality pdb=" CA  LEU B 400 "
            pdb=" N   LEU B 400 "
            pdb=" C   LEU B 400 "
            pdb=" CB  LEU B 400 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.27 2.00e-01 2.50e+01 1.89e+00
  ... (remaining 1249 not shown)

  Planarity restraints: 1294
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 133 "   -1.003 9.50e-02 1.11e+02   4.49e-01 1.22e+02
        pdb=" NE  ARG A 133 "    0.060 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 133 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 133 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 133 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 133 "   -1.002 9.50e-02 1.11e+02   4.49e-01 1.22e+02
        pdb=" NE  ARG B 133 "    0.060 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 133 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 133 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 133 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA BHIS B 567 "   -0.024 2.00e-02 2.50e+03   4.85e-02 2.35e+01
        pdb=" C  BHIS B 567 "    0.084 2.00e-02 2.50e+03
        pdb=" O  BHIS B 567 "   -0.031 2.00e-02 2.50e+03
        pdb=" N   SER B 568 "   -0.029 2.00e-02 2.50e+03
  ... (remaining 1291 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 875
        2.75 -     3.28: 8130
        3.28 -     3.82: 14096
        3.82 -     4.36: 15823
        4.36 -     4.90: 27639
  Nonbonded interactions: 66563
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 512 "
            pdb=" OH  TYR B 580 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" O   PRO A 512 "
            pdb=" OH  TYR A 580 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" O   ILE A  99 "
            pdb=" OG  SER A 103 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   ILE B  99 "
            pdb=" OG  SER B 103 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   ASP A 314 "
            pdb=" OG1 THR A 317 "
     model   vdw
     2.350 3.040
  ... (remaining 66558 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 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:             2.130
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.180
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   7998  Z= 0.375
  Angle     :  0.726   6.749  10818  Z= 0.505
  Chirality :  0.055   0.331   1252
  Planarity :  0.018   0.449   1294
  Dihedral  : 14.721  89.224   2798
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.83 (0.27), residues: 962
  helix:  2.10 (0.18), residues: 724
  sheet:  None (None), residues: 0
  loop : -1.70 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 565 
 TYR   0.017   0.002   TYR B 101 
 PHE   0.018   0.001   PHE B 542 
 TRP   0.006   0.001   TRP B 338 
 HIS   0.005   0.001   HIS B 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00575 ( 7998)
  covalent geometry    : angle       0.72621 (10818)
  hydrogen bonds       : bond        0.10986 (  614)
  hydrogen bonds       : angle       4.56484 ( 1820)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.7867 (t80) cc_final: 0.7575 (t80)
REVERT: A  436 GLU cc_start: 0.6713 (tp30) cc_final: 0.6420 (tp30)
REVERT: B  181 PHE cc_start: 0.7825 (t80) cc_final: 0.7568 (t80)
REVERT: B  436 GLU cc_start: 0.6691 (tp30) cc_final: 0.6418 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1051
  time to fit residues: 17.1461
Evaluate side-chains
  101 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    0.0170
   chunk 74 optimal weight:    9.9990
   overall best weight:    0.7020

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

Flipped N/Q/H residues before XYZ refinement:
** A 567 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.140425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.095284 restraints weight = 23818.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 2.95
r_work: 0.2925 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2831
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2831 r_free = 0.2831    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2830 r_free = 0.2830    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2830
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.1106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   7998  Z= 0.120
  Angle     :  0.449   7.054  10818  Z= 0.254
  Chirality :  0.038   0.215   1252
  Planarity :  0.003   0.030   1294
  Dihedral  :  3.404  13.289   1058
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  6.53 %
    Favored  : 92.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.78 (0.27), residues: 962
  helix:  2.77 (0.18), residues: 722
  sheet:  None (None), residues: 0
  loop : -1.24 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 133 
 TYR   0.016   0.001   TYR A 101 
 PHE   0.010   0.001   PHE B  63 
 TRP   0.005   0.001   TRP A 576 
 HIS   0.002   0.001   HIS A 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 7998)
  covalent geometry    : angle       0.44925 (10818)
  hydrogen bonds       : bond        0.04479 (  614)
  hydrogen bonds       : angle       3.61332 ( 1820)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 115
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.8108 (t80) cc_final: 0.7765 (t80)
REVERT: A  430 ARG cc_start: 0.8291 (ptt90) cc_final: 0.7838 (ptt180)
REVERT: B  181 PHE cc_start: 0.8127 (t80) cc_final: 0.7803 (t80)
REVERT: B  430 ARG cc_start: 0.8278 (ptt90) cc_final: 0.7842 (ptt180)
  outliers start: 6
  outliers final: 4
  residues processed: 117
  average time/residue: 0.0860
  time to fit residues: 13.8749
Evaluate side-chains
  110 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 106
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain B residue  432 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 50 optimal weight:    0.5980
   chunk 46 optimal weight:    0.7980
   chunk 88 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   overall best weight:    1.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A 567 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 567 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.135837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.091062 restraints weight = 23488.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 2.90
r_work: 0.2858 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2766
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2766 r_free = 0.2766    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2766 r_free = 0.2766    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2766
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.1298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7998  Z= 0.183
  Angle     :  0.499   7.612  10818  Z= 0.279
  Chirality :  0.040   0.204   1252
  Planarity :  0.003   0.032   1294
  Dihedral  :  3.519  13.551   1058
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  8.91 %
    Favored  : 89.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.58 (0.26), residues: 962
  helix:  2.63 (0.18), residues: 722
  sheet:  None (None), residues: 0
  loop : -1.32 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 133 
 TYR   0.019   0.002   TYR B 453 
 PHE   0.013   0.001   PHE A  63 
 TRP   0.006   0.001   TRP B 239 
 HIS   0.004   0.001   HIS B 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 7998)
  covalent geometry    : angle       0.49858 (10818)
  hydrogen bonds       : bond        0.04893 (  614)
  hydrogen bonds       : angle       3.62916 ( 1820)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A  266 TYR cc_start: 0.6622 (m-10) cc_final: 0.6393 (m-80)
REVERT: A  436 GLU cc_start: 0.6958 (tp30) cc_final: 0.6755 (tp30)
REVERT: B  181 PHE cc_start: 0.8140 (t80) cc_final: 0.7902 (t80)
REVERT: B  266 TYR cc_start: 0.6579 (m-10) cc_final: 0.6356 (m-80)
REVERT: B  436 GLU cc_start: 0.6968 (tp30) cc_final: 0.6761 (tp30)
  outliers start: 10
  outliers final: 4
  residues processed: 111
  average time/residue: 0.0819
  time to fit residues: 12.7180
Evaluate side-chains
  107 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 103
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  539 SER
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain B residue  539 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 57 optimal weight:    9.9990
   chunk 67 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0770
   chunk 89 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.7138

-------------------------------------------------------------------------------
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 = 0.3676 r_free = 0.3676 target = 0.138876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.096395 restraints weight = 15512.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 2.42
r_work: 0.2959 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2961
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2961 r_free = 0.2961    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2961 r_free = 0.2961    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2961
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.1491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   7998  Z= 0.113
  Angle     :  0.414   4.315  10818  Z= 0.236
  Chirality :  0.037   0.165   1252
  Planarity :  0.003   0.033   1294
  Dihedral  :  3.329  14.225   1058
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  9.74 %
    Favored  : 89.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.94 (0.26), residues: 962
  helix:  2.87 (0.18), residues: 722
  sheet:  None (None), residues: 0
  loop : -1.14 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 430 
 TYR   0.014   0.001   TYR A 101 
 PHE   0.010   0.001   PHE A  63 
 TRP   0.007   0.001   TRP A 338 
 HIS   0.002   0.001   HIS B 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 7998)
  covalent geometry    : angle       0.41378 (10818)
  hydrogen bonds       : bond        0.04204 (  614)
  hydrogen bonds       : angle       3.48782 ( 1820)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.8080 (t80) cc_final: 0.7849 (t80)
REVERT: A  430 ARG cc_start: 0.8312 (ptt90) cc_final: 0.7699 (ptt180)
REVERT: B  181 PHE cc_start: 0.8099 (t80) cc_final: 0.7865 (t80)
REVERT: B  430 ARG cc_start: 0.8279 (ptt90) cc_final: 0.7681 (ptt180)
  outliers start: 7
  outliers final: 4
  residues processed: 109
  average time/residue: 0.0947
  time to fit residues: 14.1327
Evaluate side-chains
  106 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 102
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain B residue  432 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 89 optimal weight:    4.9990
   chunk 54 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 21 optimal weight:   10.0000
   chunk 84 optimal weight:    1.9990
   chunk 92 optimal weight:    9.9990
   chunk 76 optimal weight:    8.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN
B 261 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.138051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.093755 restraints weight = 21876.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 2.81
r_work: 0.2896 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2913
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2913 r_free = 0.2913    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2913 r_free = 0.2913    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2913
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.1547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   7998  Z= 0.136
  Angle     :  0.431   4.505  10818  Z= 0.245
  Chirality :  0.038   0.146   1252
  Planarity :  0.003   0.034   1294
  Dihedral  :  3.406  15.020   1058
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  9.74 %
    Favored  : 89.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.86 (0.26), residues: 962
  helix:  2.78 (0.18), residues: 722
  sheet:  None (None), residues: 0
  loop : -1.03 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 430 
 TYR   0.017   0.001   TYR B 101 
 PHE   0.011   0.001   PHE A  63 
 TRP   0.006   0.001   TRP B 239 
 HIS   0.002   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7998)
  covalent geometry    : angle       0.43089 (10818)
  hydrogen bonds       : bond        0.04414 (  614)
  hydrogen bonds       : angle       3.49083 ( 1820)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.296 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.8115 (t80) cc_final: 0.7891 (t80)
REVERT: A  261 GLN cc_start: 0.7227 (mm-40) cc_final: 0.6935 (mm-40)
REVERT: A  430 ARG cc_start: 0.8405 (ptt90) cc_final: 0.7795 (ptt180)
REVERT: B  181 PHE cc_start: 0.8158 (t80) cc_final: 0.7933 (t80)
REVERT: B  261 GLN cc_start: 0.7242 (mm-40) cc_final: 0.6955 (mm-40)
REVERT: B  430 ARG cc_start: 0.8393 (ptt90) cc_final: 0.7790 (ptt180)
  outliers start: 10
  outliers final: 4
  residues processed: 103
  average time/residue: 0.0867
  time to fit residues: 12.2556
Evaluate side-chains
  101 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  217 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 8 optimal weight:   10.0000
   chunk 12 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 30 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 66 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   chunk 56 optimal weight:   10.0000
   overall best weight:    2.3186

-------------------------------------------------------------------------------
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 = 0.3641 r_free = 0.3641 target = 0.136091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.097092 restraints weight = 28794.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3100 rms_B_bonded: 4.38
r_work: 0.2781 rms_B_bonded: 4.62 restraints_weight: 0.5000
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2727
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2727 r_free = 0.2727    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2727 r_free = 0.2727    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2727
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
moved from start:          0.1673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   7998  Z= 0.210
  Angle     :  0.497   4.679  10818  Z= 0.280
  Chirality :  0.040   0.148   1252
  Planarity :  0.003   0.035   1294
  Dihedral  :  3.656  15.579   1058
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  9.50 %
    Favored  : 89.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.41 (0.26), residues: 962
  helix:  2.40 (0.18), residues: 726
  sheet:  None (None), residues: 0
  loop : -1.05 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 133 
 TYR   0.021   0.002   TYR B 101 
 PHE   0.014   0.001   PHE B  63 
 TRP   0.006   0.001   TRP A  89 
 HIS   0.004   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 ( 7998)
  covalent geometry    : angle       0.49684 (10818)
  hydrogen bonds       : bond        0.04999 (  614)
  hydrogen bonds       : angle       3.66112 ( 1820)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A   91 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8382 (p)
REVERT: A  181 PHE cc_start: 0.8221 (t80) cc_final: 0.7994 (t80)
REVERT: B  179 GLU cc_start: 0.8221 (tp30) cc_final: 0.7802 (mm-30)
REVERT: B  181 PHE cc_start: 0.8206 (t80) cc_final: 0.7987 (t80)
REVERT: B  554 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8463 (tt)
  outliers start: 12
  outliers final: 7
  residues processed: 102
  average time/residue: 0.0817
  time to fit residues: 11.5009
Evaluate side-chains
  104 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  539 SER
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  539 SER
Chi-restraints excluded: chain B residue  554 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 61 optimal weight:    8.9990
   chunk 46 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 25 optimal weight:    0.2980
   chunk 17 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 18 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 261 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.139573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.101342 restraints weight = 32943.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 4.99
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3109
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3109
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   7998  Z= 0.113
  Angle     :  0.417   4.676  10818  Z= 0.237
  Chirality :  0.036   0.123   1252
  Planarity :  0.003   0.035   1294
  Dihedral  :  3.379  15.302   1058
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  9.98 %
    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 aren not related in a simple way.
  whole:  2.90 (0.26), residues: 962
  helix:  2.80 (0.18), residues: 722
  sheet:  None (None), residues: 0
  loop : -0.98 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 430 
 TYR   0.014   0.001   TYR B 101 
 PHE   0.010   0.001   PHE A  63 
 TRP   0.009   0.001   TRP B 338 
 HIS   0.002   0.001   HIS B 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 7998)
  covalent geometry    : angle       0.41697 (10818)
  hydrogen bonds       : bond        0.04202 (  614)
  hydrogen bonds       : angle       3.48507 ( 1820)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.7808 (t80) cc_final: 0.7605 (t80)
REVERT: A  260 LYS cc_start: 0.7260 (mptt) cc_final: 0.6386 (mmmt)
REVERT: A  430 ARG cc_start: 0.8249 (ptt90) cc_final: 0.7713 (ptt180)
REVERT: B  181 PHE cc_start: 0.7793 (t80) cc_final: 0.7583 (t80)
REVERT: B  261 GLN cc_start: 0.7172 (mm-40) cc_final: 0.6936 (mm-40)
REVERT: B  430 ARG cc_start: 0.8262 (ptt90) cc_final: 0.7711 (ptt180)
REVERT: B  554 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8487 (tt)
  outliers start: 9
  outliers final: 6
  residues processed: 100
  average time/residue: 0.0918
  time to fit residues: 12.3523
Evaluate side-chains
  103 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain B residue  266 TYR
Chi-restraints excluded: chain B residue  554 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 9 optimal weight:    8.9990
   chunk 25 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 95 optimal weight:    4.9990
   chunk 21 optimal weight:   10.0000
   chunk 37 optimal weight:    0.2980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.139888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.094704 restraints weight = 20942.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 2.80
r_work: 0.2930 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2929
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2929
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.1748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7998  Z= 0.116
  Angle     :  0.416   4.999  10818  Z= 0.236
  Chirality :  0.037   0.123   1252
  Planarity :  0.003   0.035   1294
  Dihedral  :  3.364  16.232   1058
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 10.21 %
    Favored  : 88.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.97 (0.26), residues: 962
  helix:  2.85 (0.18), residues: 722
  sheet:  None (None), residues: 0
  loop : -0.96 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 430 
 TYR   0.016   0.001   TYR B 101 
 PHE   0.009   0.001   PHE A  63 
 TRP   0.007   0.001   TRP A 338 
 HIS   0.002   0.001   HIS A 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 7998)
  covalent geometry    : angle       0.41571 (10818)
  hydrogen bonds       : bond        0.04211 (  614)
  hydrogen bonds       : angle       3.44913 ( 1820)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.307 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.8122 (t80) cc_final: 0.7895 (t80)
REVERT: A  260 LYS cc_start: 0.7386 (mptt) cc_final: 0.6460 (mmmt)
REVERT: A  261 GLN cc_start: 0.7239 (mm-40) cc_final: 0.6977 (mm-40)
REVERT: A  430 ARG cc_start: 0.8382 (ptt90) cc_final: 0.7793 (ptt180)
REVERT: B  181 PHE cc_start: 0.8121 (t80) cc_final: 0.7889 (t80)
REVERT: B  554 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8479 (tt)
  outliers start: 9
  outliers final: 4
  residues processed: 100
  average time/residue: 0.0935
  time to fit residues: 12.8422
Evaluate side-chains
  100 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 95
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain B residue  554 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 30 optimal weight:    7.9990
   chunk 65 optimal weight:    4.9990
   chunk 56 optimal weight:   10.0000
   chunk 21 optimal weight:    9.9990
   chunk 83 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 26 optimal weight:   20.0000
   chunk 13 optimal weight:    0.8980
   chunk 8 optimal weight:   10.0000
   chunk 53 optimal weight:    3.9990
   overall best weight:    2.9788

-------------------------------------------------------------------------------
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 = 0.3640 r_free = 0.3640 target = 0.136341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.089752 restraints weight = 22522.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.2980 rms_B_bonded: 2.91
r_work: 0.2838 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2817
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2817 r_free = 0.2817    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2817 r_free = 0.2817    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2817
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.1813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   7998  Z= 0.254
  Angle     :  0.532   4.864  10818  Z= 0.297
  Chirality :  0.042   0.160   1252
  Planarity :  0.004   0.035   1294
  Dihedral  :  3.768  17.072   1058
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 10.69 %
    Favored  : 88.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.10 (0.26), residues: 962
  helix:  2.16 (0.18), residues: 740
  sheet:  None (None), residues: 0
  loop : -1.32 (0.38), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  90 
 TYR   0.023   0.002   TYR A 453 
 PHE   0.015   0.002   PHE A  63 
 TRP   0.007   0.002   TRP B  89 
 HIS   0.004   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00598 ( 7998)
  covalent geometry    : angle       0.53176 (10818)
  hydrogen bonds       : bond        0.05212 (  614)
  hydrogen bonds       : angle       3.72042 ( 1820)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.271 
Fit side-chains
REVERT: A  179 GLU cc_start: 0.8164 (tp30) cc_final: 0.7734 (mm-30)
REVERT: A  260 LYS cc_start: 0.7343 (mptt) cc_final: 0.6386 (mmmt)
REVERT: B   91 THR cc_start: 0.8622 (p) cc_final: 0.8418 (p)
REVERT: B  179 GLU cc_start: 0.8160 (tp30) cc_final: 0.7728 (mm-30)
REVERT: B  181 PHE cc_start: 0.8158 (t80) cc_final: 0.7939 (t80)
REVERT: B  261 GLN cc_start: 0.7413 (mm-40) cc_final: 0.7139 (mm-40)
REVERT: B  554 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8524 (tt)
  outliers start: 8
  outliers final: 3
  residues processed: 95
  average time/residue: 0.0882
  time to fit residues: 11.4034
Evaluate side-chains
  94 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 90
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain B residue  554 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 88 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 63 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 26 optimal weight:    9.9990
   chunk 8 optimal weight:    4.9990
   chunk 21 optimal weight:    9.9990
   chunk 75 optimal weight:    5.9990
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN
A 311 HIS
B 311 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.138008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.093419 restraints weight = 21959.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.2982 rms_B_bonded: 2.82
r_work: 0.2838 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2805
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2805 r_free = 0.2805    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2805 r_free = 0.2805    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2805
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.1781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   7998  Z= 0.120
  Angle     :  0.433   5.475  10818  Z= 0.246
  Chirality :  0.037   0.131   1252
  Planarity :  0.003   0.035   1294
  Dihedral  :  3.499  18.062   1058
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 11.52 %
    Favored  : 88.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.76 (0.26), residues: 962
  helix:  2.71 (0.18), residues: 722
  sheet:  None (None), residues: 0
  loop : -1.06 (0.37), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 430 
 TYR   0.015   0.001   TYR A 101 
 PHE   0.009   0.001   PHE B  63 
 TRP   0.007   0.001   TRP A 338 
 HIS   0.002   0.001   HIS A 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 7998)
  covalent geometry    : angle       0.43336 (10818)
  hydrogen bonds       : bond        0.04358 (  614)
  hydrogen bonds       : angle       3.57248 ( 1820)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 89
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.8123 (t80) cc_final: 0.7910 (t80)
REVERT: A  260 LYS cc_start: 0.7341 (mptt) cc_final: 0.6464 (mmmt)
REVERT: A  261 GLN cc_start: 0.7273 (mm-40) cc_final: 0.7020 (mm-40)
REVERT: A  430 ARG cc_start: 0.8387 (ptt90) cc_final: 0.7772 (ptt180)
REVERT: B  181 PHE cc_start: 0.8108 (t80) cc_final: 0.7895 (t80)
REVERT: B  261 GLN cc_start: 0.7414 (mm-40) cc_final: 0.7122 (mm-40)
REVERT: B  554 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8448 (tt)
  outliers start: 4
  outliers final: 2
  residues processed: 90
  average time/residue: 0.1007
  time to fit residues: 12.3606
Evaluate side-chains
  92 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 89
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain B residue  554 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 34 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9980
   chunk 88 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 70 optimal weight:    8.9990
   chunk 87 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.3670 r_free = 0.3670 target = 0.138120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.093269 restraints weight = 24878.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 2.95
r_work: 0.2821 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2894
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2894 r_free = 0.2894    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2894 r_free = 0.2894    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2894
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   7998  Z= 0.134
  Angle     :  0.438   5.110  10818  Z= 0.248
  Chirality :  0.037   0.126   1252
  Planarity :  0.003   0.035   1294
  Dihedral  :  3.466  17.822   1058
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 10.93 %
    Favored  : 88.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.77 (0.26), residues: 962
  helix:  2.72 (0.18), residues: 722
  sheet:  None (None), residues: 0
  loop : -1.07 (0.37), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 430 
 TYR   0.017   0.001   TYR B 101 
 PHE   0.012   0.001   PHE B 389 
 TRP   0.007   0.001   TRP A 239 
 HIS   0.002   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 7998)
  covalent geometry    : angle       0.43818 (10818)
  hydrogen bonds       : bond        0.04411 (  614)
  hydrogen bonds       : angle       3.53212 ( 1820)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2015.97 seconds
wall clock time: 35 minutes 21.36 seconds (2121.36 seconds total)