Starting phenix.real_space_refine
on Fri Aug 22 18:02:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6nf6_9361/08_2025/6nf6_9361.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nf6_9361/08_2025/6nf6_9361.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.32
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nf6_9361/08_2025/6nf6_9361.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nf6_9361/08_2025/6nf6_9361.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6nf6_9361/08_2025/6nf6_9361.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nf6_9361/08_2025/6nf6_9361.cif"
  }
  resolution = 3.32
  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=   1.000
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      48      5.16       5
     C    4428      2.51       5
     N    1024      2.21       5
     O    1098      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s

  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: 6598
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 411, 3264
          Classifications: {'peptide': 411}
          Link IDs: {'PTRANS': 12, 'TRANS': 398}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 3264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 411, 3264
          Classifications: {'peptide': 411}
          Link IDs: {'PTRANS': 12, 'TRANS': 398}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'Y01': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'Y01': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.52, per 1000 atoms: 0.23
  Number of scatterers: 6598
  At special positions: 0
  Unit cell: (91.67, 75.19, 75.19, 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      48     16.00
     O    1098      8.00
     N    1024      7.00
     C    4428      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: 0.38
  Conformation dependent library (CDL) restraints added in 250.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1548

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 0 sheets defined
      83.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 49 through 78
      removed outlier: 3.964A  pdb=" N   GLY A  53 " --> pdb=" O   ALA A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 109
    Processing helix  chain 'A' and resid 127 through 152
    Processing helix  chain 'A' and resid 162 through 182
      removed outlier: 3.724A  pdb=" N   HIS A 181 " --> pdb=" O   PHE A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 215
    Processing helix  chain 'A' and resid 216 through 226
      removed outlier: 3.820A  pdb=" N   GLU A 223 " --> pdb=" O   HIS A 219 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   GLN A 225 " --> pdb=" O   GLU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 280
      Proline residue:  A 261  - end of helix
      removed outlier: 3.824A  pdb=" N   THR A 264 " --> pdb=" O   TYR A 260 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU A 268 " --> pdb=" O   THR A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 328
    Processing helix  chain 'A' and resid 334 through 365
      removed outlier: 3.812A  pdb=" N   VAL A 338 " --> pdb=" O   TYR A 334 " (cutoff:3.500A)
      Proline residue:  A 349  - end of helix
    Processing helix  chain 'A' and resid 376 through 405
      removed outlier: 4.212A  pdb=" N   GLY A 390 " --> pdb=" O   GLY A 386 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   GLN A 391 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   THR A 405 " --> pdb=" O   ALA A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 437
      removed outlier: 3.589A  pdb=" N   LEU A 416 " --> pdb=" O   ASN A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 509
    Processing helix  chain 'A' and resid 510 through 512
      No H-bonds generated for 'chain 'A' and resid 510 through 512'
    Processing helix  chain 'A' and resid 528 through 559
      Proline residue:  A 541  - end of helix
      removed outlier: 3.525A  pdb=" N   VAL A 559 " --> pdb=" O   LEU A 555 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 78
    Processing helix  chain 'B' and resid 83 through 109
    Processing helix  chain 'B' and resid 127 through 152
    Processing helix  chain 'B' and resid 162 through 182
      removed outlier: 3.724A  pdb=" N   HIS B 181 " --> pdb=" O   PHE B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 215
    Processing helix  chain 'B' and resid 216 through 226
      removed outlier: 3.820A  pdb=" N   GLU B 223 " --> pdb=" O   HIS B 219 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   GLN B 225 " --> pdb=" O   GLU B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 280
      Proline residue:  B 261  - end of helix
      removed outlier: 3.824A  pdb=" N   THR B 264 " --> pdb=" O   TYR B 260 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU B 268 " --> pdb=" O   THR B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 305 through 328
    Processing helix  chain 'B' and resid 334 through 365
      removed outlier: 3.812A  pdb=" N   VAL B 338 " --> pdb=" O   TYR B 334 " (cutoff:3.500A)
      Proline residue:  B 349  - end of helix
    Processing helix  chain 'B' and resid 376 through 405
      removed outlier: 4.212A  pdb=" N   GLY B 390 " --> pdb=" O   GLY B 386 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   GLN B 391 " --> pdb=" O   ALA B 387 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   THR B 405 " --> pdb=" O   ALA B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 437
      removed outlier: 3.589A  pdb=" N   LEU B 416 " --> pdb=" O   ASN B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 488 through 509
    Processing helix  chain 'B' and resid 510 through 512
      No H-bonds generated for 'chain 'B' and resid 510 through 512'
    Processing helix  chain 'B' and resid 528 through 559
      Proline residue:  B 541  - end of helix
      removed outlier: 3.525A  pdb=" N   VAL B 559 " --> pdb=" O   LEU B 555 " (cutoff:3.500A)

    536 hydrogen bonds defined for protein.
    1608 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: 0.96

  Time building geometry restraints manager: 0.50 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: 1136
        1.33 -     1.45: 1756
        1.45 -     1.57: 3800
        1.57 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 6764
  Sorted by residual:
  bond pdb=" CAX Y01 A 601 "
       pdb=" OAH Y01 A 601 "
    ideal  model  delta    sigma   weight residual
    1.248  1.342 -0.094 2.00e-02 2.50e+03 2.21e+01
  bond pdb=" CAX Y01 B 601 "
       pdb=" OAH Y01 B 601 "
    ideal  model  delta    sigma   weight residual
    1.248  1.341 -0.093 2.00e-02 2.50e+03 2.18e+01
  bond pdb=" C   GLN A 112 "
       pdb=" N   PRO A 113 "
    ideal  model  delta    sigma   weight residual
    1.332  1.361 -0.029 1.12e-02 7.97e+03 6.52e+00
  bond pdb=" C   GLN B 112 "
       pdb=" N   PRO B 113 "
    ideal  model  delta    sigma   weight residual
    1.332  1.361 -0.029 1.12e-02 7.97e+03 6.52e+00
  bond pdb=" C   ASN A 280 "
       pdb=" N   VAL A 281 "
    ideal  model  delta    sigma   weight residual
    1.335  1.306  0.029 1.16e-02 7.43e+03 6.31e+00
  ... (remaining 6759 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 8779
        1.99 -     3.97: 337
        3.97 -     5.96: 68
        5.96 -     7.95: 20
        7.95 -     9.93: 6
  Bond angle restraints: 9210
  Sorted by residual:
  angle pdb=" CA  GLY B 528 "
        pdb=" C   GLY B 528 "
        pdb=" O   GLY B 528 "
      ideal   model   delta    sigma   weight residual
     122.22  119.74    2.48 6.50e-01 2.37e+00 1.46e+01
  angle pdb=" CA  GLY A 528 "
        pdb=" C   GLY A 528 "
        pdb=" O   GLY A 528 "
      ideal   model   delta    sigma   weight residual
     122.22  119.74    2.48 6.50e-01 2.37e+00 1.46e+01
  angle pdb=" C   MET B 277 "
        pdb=" N   TRP B 278 "
        pdb=" CA  TRP B 278 "
      ideal   model   delta    sigma   weight residual
     122.11  116.69    5.42 1.64e+00 3.72e-01 1.09e+01
  angle pdb=" C   MET A 277 "
        pdb=" N   TRP A 278 "
        pdb=" CA  TRP A 278 "
      ideal   model   delta    sigma   weight residual
     122.11  116.69    5.42 1.64e+00 3.72e-01 1.09e+01
  angle pdb=" CA  TRP A 101 "
        pdb=" CB  TRP A 101 "
        pdb=" CG  TRP A 101 "
      ideal   model   delta    sigma   weight residual
     113.60  107.43    6.17 1.90e+00 2.77e-01 1.06e+01
  ... (remaining 9205 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.85: 3446
       16.85 -    33.70: 434
       33.70 -    50.55: 90
       50.55 -    67.39: 18
       67.39 -    84.24: 10
  Dihedral angle restraints: 3998
    sinusoidal: 1600
      harmonic: 2398
  Sorted by residual:
  dihedral pdb=" CA  ALA B 331 "
           pdb=" C   ALA B 331 "
           pdb=" N   PRO B 332 "
           pdb=" CA  PRO B 332 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.60  -29.40     0      5.00e+00 4.00e-02 3.46e+01
  dihedral pdb=" CA  ALA A 331 "
           pdb=" C   ALA A 331 "
           pdb=" N   PRO A 332 "
           pdb=" CA  PRO A 332 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.60  -29.40     0      5.00e+00 4.00e-02 3.46e+01
  dihedral pdb=" CA  ASN B 280 "
           pdb=" C   ASN B 280 "
           pdb=" N   VAL B 281 "
           pdb=" CA  VAL B 281 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.48   24.52     0      5.00e+00 4.00e-02 2.41e+01
  ... (remaining 3995 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.093: 1002
       0.093 -    0.185: 98
       0.185 -    0.278: 6
       0.278 -    0.370: 2
       0.370 -    0.463: 2
  Chirality restraints: 1110
  Sorted by residual:
  chirality pdb=" CBG Y01 A 601 "
            pdb=" CAQ Y01 A 601 "
            pdb=" CBD Y01 A 601 "
            pdb=" CBI Y01 A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.80    0.46 2.00e-01 2.50e+01 5.36e+00
  chirality pdb=" CBG Y01 B 601 "
            pdb=" CAQ Y01 B 601 "
            pdb=" CBD Y01 B 601 "
            pdb=" CBI Y01 B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.79    0.46 2.00e-01 2.50e+01 5.35e+00
  chirality pdb=" CBH Y01 B 601 "
            pdb=" CAT Y01 B 601 "
            pdb=" CAZ Y01 B 601 "
            pdb=" CBF Y01 B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.57   -0.29 2.00e-01 2.50e+01 2.05e+00
  ... (remaining 1107 not shown)

  Planarity restraints: 1082
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 305 "   -0.044 5.00e-02 4.00e+02   6.68e-02 7.14e+00
        pdb=" N   PRO A 306 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A 306 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 306 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 305 "    0.044 5.00e-02 4.00e+02   6.68e-02 7.14e+00
        pdb=" N   PRO B 306 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO B 306 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 306 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 260 "    0.039 5.00e-02 4.00e+02   5.77e-02 5.33e+00
        pdb=" N   PRO B 261 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO B 261 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 261 "    0.033 5.00e-02 4.00e+02
  ... (remaining 1079 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2049
        2.83 -     3.35: 6386
        3.35 -     3.86: 11322
        3.86 -     4.38: 12375
        4.38 -     4.90: 22258
  Nonbonded interactions: 54390
  Sorted by model distance:
  nonbonded pdb=" O   VAL B 338 "
            pdb=" OG  SER B 342 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   VAL A 338 "
            pdb=" OG  SER A 342 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   VAL B  65 "
            pdb=" OG  SER B  69 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" O   VAL A  65 "
            pdb=" OG  SER A  69 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" O   GLN A 190 "
            pdb=" OG1 THR A 194 "
     model   vdw
     2.328 3.040
  ... (remaining 54385 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: 0.01
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=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:             0.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.200
  Find NCS groups from input model:        0.030
  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:             0.010
  Load rotamer database and sin/cos tables:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
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      :  0.007   0.094   6764  Z= 0.303
  Angle     :  0.976   9.934   9210  Z= 0.513
  Chirality :  0.060   0.463   1110
  Planarity :  0.008   0.067   1082
  Dihedral  : 15.515  84.243   2450
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.51 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.84 %
    Favored  : 91.16 %
  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: -2.74 (0.24), residues: 798
  helix: -1.19 (0.15), residues: 660
  sheet:  None (None), residues: 0
  loop : -4.17 (0.48), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 377 
 TYR   0.016   0.002   TYR A 275 
 PHE   0.016   0.002   PHE A  71 
 TRP   0.030   0.003   TRP A 101 
 HIS   0.008   0.001   HIS A 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00695 ( 6764)
  covalent geometry    : angle       0.97642 ( 9210)
  hydrogen bonds       : bond        0.10775 (  536)
  hydrogen bonds       : angle       6.03087 ( 1608)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 LYS cc_start: 0.6887 (tttt) cc_final: 0.6623 (tmtt)
REVERT: A  254 LYS cc_start: 0.6552 (mtpt) cc_final: 0.5822 (mmtm)
REVERT: A  260 TYR cc_start: 0.8620 (t80) cc_final: 0.8217 (t80)
REVERT: A  335 GLN cc_start: 0.8292 (mp10) cc_final: 0.8081 (mp10)
REVERT: A  424 PHE cc_start: 0.7969 (t80) cc_final: 0.7662 (t80)
REVERT: B  184 LYS cc_start: 0.6878 (tttt) cc_final: 0.6624 (tmtt)
REVERT: B  254 LYS cc_start: 0.6525 (mtpt) cc_final: 0.5792 (mmtm)
REVERT: B  260 TYR cc_start: 0.8626 (t80) cc_final: 0.8219 (t80)
REVERT: B  335 GLN cc_start: 0.8297 (mp10) cc_final: 0.8083 (mp10)
REVERT: B  424 PHE cc_start: 0.7974 (t80) cc_final: 0.7669 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.0624
  time to fit residues: 17.8488
Evaluate side-chains
  162 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 515 HIS
B 515 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.155168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.129005 restraints weight = 8028.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 1.73
r_work: 0.3337 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6764  Z= 0.136
  Angle     :  0.579   6.434   9210  Z= 0.307
  Chirality :  0.040   0.133   1110
  Planarity :  0.005   0.058   1082
  Dihedral  :  6.536  50.780   1010
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 12.98 %
    Favored  : 85.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.29), residues: 798
  helix:  1.03 (0.18), residues: 680
  sheet:  None (None), residues: 0
  loop : -4.43 (0.53), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 489 
 TYR   0.013   0.002   TYR A 340 
 PHE   0.012   0.001   PHE A 178 
 TRP   0.022   0.002   TRP B 101 
 HIS   0.006   0.001   HIS B 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6764)
  covalent geometry    : angle       0.57929 ( 9210)
  hydrogen bonds       : bond        0.04302 (  536)
  hydrogen bonds       : angle       4.34366 ( 1608)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 200
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  254 LYS cc_start: 0.6871 (mtpt) cc_final: 0.6013 (mmtm)
REVERT: A  260 TYR cc_start: 0.8666 (t80) cc_final: 0.8430 (t80)
REVERT: A  424 PHE cc_start: 0.8222 (t80) cc_final: 0.8006 (t80)
REVERT: A  546 TYR cc_start: 0.8307 (t80) cc_final: 0.8057 (t80)
REVERT: B  254 LYS cc_start: 0.6867 (mtpt) cc_final: 0.6020 (mmtm)
REVERT: B  260 TYR cc_start: 0.8661 (t80) cc_final: 0.8426 (t80)
REVERT: B  424 PHE cc_start: 0.8193 (t80) cc_final: 0.7975 (t80)
REVERT: B  546 TYR cc_start: 0.8303 (t80) cc_final: 0.8052 (t80)
  outliers start: 10
  outliers final: 6
  residues processed: 202
  average time/residue: 0.0616
  time to fit residues: 17.3179
Evaluate side-chains
  184 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 178
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 TRP
Chi-restraints excluded: chain A residue  487 TRP
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain B residue  278 TRP
Chi-restraints excluded: chain B residue  487 TRP
Chi-restraints excluded: chain B residue  559 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 58 optimal weight:    9.9990
   chunk 9 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 71 optimal weight:    0.0170
   chunk 4 optimal weight:    2.9990
   overall best weight:    1.3624

-------------------------------------------------------------------------------
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 = 0.3736 r_free = 0.3736 target = 0.151916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.125736 restraints weight = 7955.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.71
r_work: 0.3309 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3177 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.1911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6764  Z= 0.155
  Angle     :  0.591   6.834   9210  Z= 0.309
  Chirality :  0.042   0.215   1110
  Planarity :  0.005   0.054   1082
  Dihedral  :  6.374  48.439   1010
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.26 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 15.88 %
    Favored  : 82.04 %
  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:  1.24 (0.30), residues: 798
  helix:  1.70 (0.19), residues: 682
  sheet:  None (None), residues: 0
  loop : -4.76 (0.53), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 408 
 TYR   0.015   0.002   TYR B 340 
 PHE   0.018   0.002   PHE A 320 
 TRP   0.019   0.002   TRP B 101 
 HIS   0.004   0.001   HIS B 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 6764)
  covalent geometry    : angle       0.59089 ( 9210)
  hydrogen bonds       : bond        0.04273 (  536)
  hydrogen bonds       : angle       4.24726 ( 1608)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 186
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  254 LYS cc_start: 0.6897 (mtpt) cc_final: 0.6229 (mmtm)
REVERT: A  326 GLN cc_start: 0.8194 (tp40) cc_final: 0.7990 (tp40)
REVERT: A  546 TYR cc_start: 0.8317 (t80) cc_final: 0.8057 (t80)
REVERT: B  254 LYS cc_start: 0.6920 (mtpt) cc_final: 0.6232 (mmtm)
REVERT: B  326 GLN cc_start: 0.8192 (tp40) cc_final: 0.7984 (tp40)
REVERT: B  546 TYR cc_start: 0.8315 (t80) cc_final: 0.8052 (t80)
  outliers start: 15
  outliers final: 11
  residues processed: 188
  average time/residue: 0.0637
  time to fit residues: 16.7508
Evaluate side-chains
  182 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 171
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  278 TRP
Chi-restraints excluded: chain A residue  487 TRP
Chi-restraints excluded: chain A residue  548 MET
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  278 TRP
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  487 TRP
Chi-restraints excluded: chain B residue  548 MET
Chi-restraints excluded: chain B residue  559 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 17 optimal weight:    9.9990
   chunk 25 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   chunk 58 optimal weight:    8.9990
   chunk 11 optimal weight:    0.6980
   chunk 54 optimal weight:    8.9990
   chunk 14 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   chunk 81 optimal weight:    3.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3754 r_free = 0.3754 target = 0.153561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.127234 restraints weight = 8053.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 1.75
r_work: 0.3320 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.2190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6764  Z= 0.140
  Angle     :  0.573   6.409   9210  Z= 0.301
  Chirality :  0.042   0.201   1110
  Planarity :  0.004   0.051   1082
  Dihedral  :  6.173  50.516   1010
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 16.30 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.31), residues: 798
  helix:  1.99 (0.19), residues: 684
  sheet:  None (None), residues: 0
  loop : -4.79 (0.52), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 377 
 TYR   0.009   0.001   TYR A 418 
 PHE   0.011   0.001   PHE A 178 
 TRP   0.016   0.002   TRP A 101 
 HIS   0.003   0.001   HIS B 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 6764)
  covalent geometry    : angle       0.57312 ( 9210)
  hydrogen bonds       : bond        0.04093 (  536)
  hydrogen bonds       : angle       4.22351 ( 1608)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 187
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 ILE cc_start: 0.8838 (mp) cc_final: 0.8396 (pt)
REVERT: A  254 LYS cc_start: 0.6875 (mtpt) cc_final: 0.6161 (mmtm)
REVERT: A  546 TYR cc_start: 0.8379 (t80) cc_final: 0.8096 (t80)
REVERT: B  162 ILE cc_start: 0.8901 (mp) cc_final: 0.8434 (pt)
REVERT: B  254 LYS cc_start: 0.6886 (mtpt) cc_final: 0.6154 (mmtm)
REVERT: B  546 TYR cc_start: 0.8360 (t80) cc_final: 0.8074 (t80)
  outliers start: 17
  outliers final: 13
  residues processed: 192
  average time/residue: 0.0617
  time to fit residues: 16.2966
Evaluate side-chains
  185 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 172
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  278 TRP
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  487 TRP
Chi-restraints excluded: chain A residue  548 MET
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  278 TRP
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  487 TRP
Chi-restraints excluded: chain B residue  548 MET
Chi-restraints excluded: chain B residue  559 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 78 optimal weight:    0.7980
   chunk 37 optimal weight:    6.9990
   chunk 75 optimal weight:    0.6980
   chunk 50 optimal weight:    8.9990
   chunk 70 optimal weight:    0.8980
   chunk 76 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3759 r_free = 0.3759 target = 0.154020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.127944 restraints weight = 8151.908|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 1.74
r_work: 0.3325 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.2340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6764  Z= 0.141
  Angle     :  0.578   6.561   9210  Z= 0.306
  Chirality :  0.041   0.177   1110
  Planarity :  0.004   0.050   1082
  Dihedral  :  6.120  52.298   1010
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 17.54 %
    Favored  : 79.97 %
  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 (0.31), residues: 798
  helix:  2.11 (0.19), residues: 684
  sheet:  None (None), residues: 0
  loop : -4.76 (0.50), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 377 
 TYR   0.018   0.002   TYR A 340 
 PHE   0.021   0.001   PHE A 320 
 TRP   0.016   0.002   TRP A 127 
 HIS   0.003   0.001   HIS A 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 6764)
  covalent geometry    : angle       0.57795 ( 9210)
  hydrogen bonds       : bond        0.04097 (  536)
  hydrogen bonds       : angle       4.23526 ( 1608)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 184
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 ILE cc_start: 0.8866 (mp) cc_final: 0.8412 (pt)
REVERT: A  199 MET cc_start: 0.7795 (mmt) cc_final: 0.7265 (mmt)
REVERT: A  254 LYS cc_start: 0.6953 (mtpt) cc_final: 0.6198 (mmtp)
REVERT: A  546 TYR cc_start: 0.8324 (t80) cc_final: 0.8024 (t80)
REVERT: B  162 ILE cc_start: 0.8884 (mp) cc_final: 0.8428 (pt)
REVERT: B  199 MET cc_start: 0.7761 (mmt) cc_final: 0.7218 (mmt)
REVERT: B  254 LYS cc_start: 0.6977 (mtpt) cc_final: 0.6216 (mmtp)
REVERT: B  546 TYR cc_start: 0.8309 (t80) cc_final: 0.8006 (t80)
  outliers start: 18
  outliers final: 16
  residues processed: 192
  average time/residue: 0.0580
  time to fit residues: 15.7380
Evaluate side-chains
  191 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 175
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  278 TRP
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  487 TRP
Chi-restraints excluded: chain A residue  548 MET
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  110 SER
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  278 TRP
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  487 TRP
Chi-restraints excluded: chain B residue  548 MET
Chi-restraints excluded: chain B residue  559 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 27 optimal weight:    7.9990
   chunk 73 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0060
   chunk 13 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.6796

-------------------------------------------------------------------------------
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 = 0.3786 r_free = 0.3786 target = 0.156411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.130265 restraints weight = 8073.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 1.75
r_work: 0.3364 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6764  Z= 0.124
  Angle     :  0.577   7.627   9210  Z= 0.298
  Chirality :  0.041   0.196   1110
  Planarity :  0.004   0.049   1082
  Dihedral  :  5.958  53.003   1010
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 17.96 %
    Favored  : 79.70 %
  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:  2.08 (0.31), residues: 798
  helix:  2.28 (0.19), residues: 684
  sheet:  None (None), residues: 0
  loop : -4.68 (0.51), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 377 
 TYR   0.015   0.001   TYR B 340 
 PHE   0.008   0.001   PHE A 512 
 TRP   0.014   0.002   TRP B 101 
 HIS   0.002   0.000   HIS B 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6764)
  covalent geometry    : angle       0.57683 ( 9210)
  hydrogen bonds       : bond        0.03925 (  536)
  hydrogen bonds       : angle       4.18696 ( 1608)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 183
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 ILE cc_start: 0.8810 (mp) cc_final: 0.8346 (pt)
REVERT: A  223 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7512 (mp0)
REVERT: A  254 LYS cc_start: 0.6807 (mtpt) cc_final: 0.6233 (mmtm)
REVERT: B  162 ILE cc_start: 0.8842 (mp) cc_final: 0.8369 (pt)
REVERT: B  223 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7492 (mp0)
REVERT: B  254 LYS cc_start: 0.6797 (mtpt) cc_final: 0.6225 (mmtm)
  outliers start: 17
  outliers final: 13
  residues processed: 188
  average time/residue: 0.0685
  time to fit residues: 17.8915
Evaluate side-chains
  188 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 173
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  223 GLU
Chi-restraints excluded: chain A residue  278 TRP
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  487 TRP
Chi-restraints excluded: chain A residue  548 MET
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  223 GLU
Chi-restraints excluded: chain B residue  278 TRP
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  487 TRP
Chi-restraints excluded: chain B residue  548 MET
Chi-restraints excluded: chain B residue  559 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0060
   chunk 11 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 16 optimal weight:    0.3980
   chunk 30 optimal weight:    0.2980
   chunk 40 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.5196

-------------------------------------------------------------------------------
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 = 0.3814 r_free = 0.3814 target = 0.158894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.133079 restraints weight = 8010.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 1.73
r_work: 0.3404 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6764  Z= 0.123
  Angle     :  0.582   6.608   9210  Z= 0.303
  Chirality :  0.040   0.161   1110
  Planarity :  0.004   0.048   1082
  Dihedral  :  5.861  53.370   1010
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 18.92 %
    Favored  : 78.45 %
  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:  2.11 (0.31), residues: 798
  helix:  2.30 (0.19), residues: 684
  sheet:  None (None), residues: 0
  loop : -4.71 (0.53), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 547 
 TYR   0.027   0.002   TYR B 546 
 PHE   0.023   0.001   PHE B 320 
 TRP   0.012   0.002   TRP B 127 
 HIS   0.002   0.000   HIS A 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 6764)
  covalent geometry    : angle       0.58162 ( 9210)
  hydrogen bonds       : bond        0.03805 (  536)
  hydrogen bonds       : angle       4.17607 ( 1608)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 183
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 ILE cc_start: 0.8823 (mp) cc_final: 0.8372 (pt)
REVERT: A  223 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7492 (mp0)
REVERT: A  254 LYS cc_start: 0.6748 (mtpt) cc_final: 0.6171 (mmtp)
REVERT: A  279 LYS cc_start: 0.7622 (tptt) cc_final: 0.7324 (tttp)
REVERT: B  162 ILE cc_start: 0.8854 (mp) cc_final: 0.8397 (pt)
REVERT: B  223 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7472 (mp0)
REVERT: B  254 LYS cc_start: 0.6741 (mtpt) cc_final: 0.6181 (mmtp)
REVERT: B  279 LYS cc_start: 0.7607 (tptt) cc_final: 0.7309 (tttp)
  outliers start: 19
  outliers final: 15
  residues processed: 191
  average time/residue: 0.0719
  time to fit residues: 18.8465
Evaluate side-chains
  188 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 171
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  223 GLU
Chi-restraints excluded: chain A residue  278 TRP
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  487 TRP
Chi-restraints excluded: chain A residue  548 MET
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain B residue  110 SER
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  223 GLU
Chi-restraints excluded: chain B residue  278 TRP
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  487 TRP
Chi-restraints excluded: chain B residue  548 MET
Chi-restraints excluded: chain B residue  559 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 38 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   chunk 81 optimal weight:    0.7980
   chunk 55 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 503 ASN ** 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 = 0.3791 r_free = 0.3791 target = 0.156810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.131085 restraints weight = 8119.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 1.72
r_work: 0.3382 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.2703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6764  Z= 0.138
  Angle     :  0.598   6.529   9210  Z= 0.317
  Chirality :  0.041   0.173   1110
  Planarity :  0.004   0.048   1082
  Dihedral  :  5.927  54.474   1010
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 19.48 %
    Favored  : 77.62 %
  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:  2.11 (0.31), residues: 798
  helix:  2.30 (0.19), residues: 684
  sheet:  None (None), residues: 0
  loop : -4.68 (0.51), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 129 
 TYR   0.022   0.002   TYR B 546 
 PHE   0.009   0.001   PHE B 178 
 TRP   0.012   0.002   TRP A 127 
 HIS   0.002   0.000   HIS A 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6764)
  covalent geometry    : angle       0.59788 ( 9210)
  hydrogen bonds       : bond        0.03960 (  536)
  hydrogen bonds       : angle       4.26059 ( 1608)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 173
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 ILE cc_start: 0.8872 (mp) cc_final: 0.8442 (pt)
REVERT: A  223 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7442 (mp0)
REVERT: A  254 LYS cc_start: 0.6820 (mtpt) cc_final: 0.6271 (mmtp)
REVERT: B  162 ILE cc_start: 0.8908 (mp) cc_final: 0.8447 (pt)
REVERT: B  223 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7426 (mp0)
REVERT: B  254 LYS cc_start: 0.6826 (mtpt) cc_final: 0.6312 (mmtm)
  outliers start: 21
  outliers final: 19
  residues processed: 180
  average time/residue: 0.0672
  time to fit residues: 16.8991
Evaluate side-chains
  181 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 160
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  223 GLU
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  278 TRP
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  487 TRP
Chi-restraints excluded: chain A residue  548 MET
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain B residue  110 SER
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  223 GLU
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  278 TRP
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  487 TRP
Chi-restraints excluded: chain B residue  548 MET
Chi-restraints excluded: chain B residue  559 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 78 optimal weight:    7.9990
   chunk 39 optimal weight:    0.6980
   chunk 34 optimal weight:    6.9990
   chunk 68 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.3812 r_free = 0.3812 target = 0.158837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.133449 restraints weight = 8085.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 1.70
r_work: 0.3419 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.2802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   6764  Z= 0.132
  Angle     :  0.604   9.334   9210  Z= 0.318
  Chirality :  0.041   0.209   1110
  Planarity :  0.004   0.048   1082
  Dihedral  :  5.863  54.217   1010
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 19.34 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.13 (0.31), residues: 798
  helix:  2.30 (0.19), residues: 682
  sheet:  None (None), residues: 0
  loop : -4.49 (0.53), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 129 
 TYR   0.020   0.002   TYR B 546 
 PHE   0.021   0.001   PHE B 320 
 TRP   0.012   0.002   TRP A 101 
 HIS   0.002   0.000   HIS B 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 6764)
  covalent geometry    : angle       0.60407 ( 9210)
  hydrogen bonds       : bond        0.03921 (  536)
  hydrogen bonds       : angle       4.25962 ( 1608)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 167
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 ILE cc_start: 0.8816 (mp) cc_final: 0.8388 (pt)
REVERT: A  223 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7471 (mp0)
REVERT: A  254 LYS cc_start: 0.6783 (mtpt) cc_final: 0.6249 (mmtm)
REVERT: B  162 ILE cc_start: 0.8850 (mp) cc_final: 0.8407 (pt)
REVERT: B  223 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7433 (mp0)
REVERT: B  254 LYS cc_start: 0.6735 (mtpt) cc_final: 0.6280 (mmtm)
  outliers start: 24
  outliers final: 18
  residues processed: 178
  average time/residue: 0.0716
  time to fit residues: 17.8020
Evaluate side-chains
  178 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 158
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  223 GLU
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  278 TRP
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  487 TRP
Chi-restraints excluded: chain A residue  548 MET
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain B residue  110 SER
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  223 GLU
Chi-restraints excluded: chain B residue  278 TRP
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  487 TRP
Chi-restraints excluded: chain B residue  548 MET
Chi-restraints excluded: chain B residue  559 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 10 optimal weight:    0.0470
   chunk 65 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   chunk 42 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   chunk 43 optimal weight:    0.8980
   chunk 48 optimal weight:    5.9990
   overall best weight:    0.6478

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

Flipped N/Q/H residues before XYZ refinement:
B 114 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.160660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.135317 restraints weight = 7941.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 1.69
r_work: 0.3456 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3326 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.2987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   6764  Z= 0.133
  Angle     :  0.613   8.829   9210  Z= 0.325
  Chirality :  0.041   0.180   1110
  Planarity :  0.004   0.048   1082
  Dihedral  :  5.789  53.710   1010
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 20.03 %
    Favored  : 77.07 %
  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:  2.17 (0.31), residues: 798
  helix:  2.32 (0.19), residues: 682
  sheet:  None (None), residues: 0
  loop : -4.39 (0.54), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 129 
 TYR   0.019   0.002   TYR A 546 
 PHE   0.009   0.001   PHE A 138 
 TRP   0.029   0.002   TRP B 180 
 HIS   0.002   0.000   HIS B 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6764)
  covalent geometry    : angle       0.61295 ( 9210)
  hydrogen bonds       : bond        0.03897 (  536)
  hydrogen bonds       : angle       4.29182 ( 1608)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 160
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 ILE cc_start: 0.8785 (mp) cc_final: 0.8398 (pt)
REVERT: A  223 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7452 (mp0)
REVERT: A  254 LYS cc_start: 0.6728 (mtpt) cc_final: 0.6298 (mmtp)
REVERT: B  162 ILE cc_start: 0.8817 (mp) cc_final: 0.8411 (pt)
REVERT: B  223 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7407 (mp0)
REVERT: B  254 LYS cc_start: 0.6801 (mtpt) cc_final: 0.6456 (mmtm)
  outliers start: 21
  outliers final: 19
  residues processed: 167
  average time/residue: 0.0635
  time to fit residues: 14.9137
Evaluate side-chains
  179 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 158
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  223 GLU
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  278 TRP
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  487 TRP
Chi-restraints excluded: chain A residue  548 MET
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain B residue  110 SER
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  223 GLU
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  278 TRP
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  487 TRP
Chi-restraints excluded: chain B residue  548 MET
Chi-restraints excluded: chain B residue  559 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 74 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0040
   chunk 23 optimal weight:    0.2980
   chunk 34 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0970
   chunk 29 optimal weight:    4.9990
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.3590

-------------------------------------------------------------------------------
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 = 0.3860 r_free = 0.3860 target = 0.162853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.137934 restraints weight = 8005.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 1.68
r_work: 0.3467 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.3173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   6764  Z= 0.122
  Angle     :  0.598   8.858   9210  Z= 0.314
  Chirality :  0.040   0.169   1110
  Planarity :  0.004   0.047   1082
  Dihedral  :  5.552  51.131   1010
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 21.41 %
    Favored  : 75.83 %
  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:  2.46 (0.31), residues: 798
  helix:  2.49 (0.19), residues: 684
  sheet:  None (None), residues: 0
  loop : -4.24 (0.57), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 129 
 TYR   0.017   0.001   TYR A 546 
 PHE   0.025   0.001   PHE A 320 
 TRP   0.017   0.002   TRP A 180 
 HIS   0.002   0.000   HIS B 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 6764)
  covalent geometry    : angle       0.59797 ( 9210)
  hydrogen bonds       : bond        0.03744 (  536)
  hydrogen bonds       : angle       4.18197 ( 1608)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1548.80 seconds
wall clock time: 27 minutes 12.71 seconds (1632.71 seconds total)