Starting phenix.real_space_refine
on Tue Mar  3 14:29:19 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6pzt_20537/03_2026/6pzt_20537.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pzt_20537/03_2026/6pzt_20537.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.46
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pzt_20537/03_2026/6pzt_20537.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pzt_20537/03_2026/6pzt_20537.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6pzt_20537/03_2026/6pzt_20537.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pzt_20537/03_2026/6pzt_20537.map"
  }
  resolution = 3.46
  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=  -0.001 sd=   0.058
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      24      5.16       5
     C    3914      2.51       5
     N    1026      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 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6062
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 466, 3031
          Classifications: {'peptide': 466}
          Incomplete info: {'backbone_only': 21, 'truncation_to_alanine': 126}
          Link IDs: {'PTRANS': 15, 'TRANS': 450}
          Unresolved non-hydrogen bonds: 525
          Unresolved non-hydrogen angles: 683
          Unresolved non-hydrogen dihedrals: 401
          Unresolved non-hydrogen chiralities: 86
          Planarities with less than four sites: {'ASN:plan1': 10, 'PHE:plan': 8, 'ARG:plan': 4, 'TYR:plan': 6, 'GLU:plan': 12, 'ASP:plan': 8, 'GLN:plan1': 4}
          Unresolved non-hydrogen planarities: 233
  Restraints were copied for chains:
    A
  Time building chain proxies: 1.52, per 1000 atoms: 0.25
  Number of scatterers: 6062
  At special positions: 0
  Unit cell: (82.95, 101.85, 87.15, 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      24     16.00
     O    1098      8.00
     N    1026      7.00
     C    3914      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 563 " - pdb=" SG  CYS B 568 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 577 " - pdb=" SG  CYS B 582 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 563 " - pdb=" SG  CYS A 568 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 577 " - pdb=" SG  CYS A 582 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.41
  Conformation dependent library (CDL) restraints added in 376.5 milliseconds
  

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1624

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 0 sheets defined
      76.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'B' and resid 289 through 300
    Processing helix  chain 'B' and resid 301 through 315
      removed outlier: 4.364A  pdb=" N   PHE B 305 " --> pdb=" O   GLY B 301 " (cutoff:3.500A)
      removed outlier: 5.544A  pdb=" N   SER B 309 " --> pdb=" O   PHE B 305 " (cutoff:3.500A)
      removed outlier: 5.156A  pdb=" N   TRP B 310 " --> pdb=" O   ILE B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 342
      removed outlier: 3.789A  pdb=" N   VAL B 321 " --> pdb=" O   ILE B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 360
    Processing helix  chain 'B' and resid 361 through 398
      removed outlier: 3.702A  pdb=" N   ALA B 381 " --> pdb=" O   ALA B 377 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   HIS B 398 " --> pdb=" O   LEU B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 425
      removed outlier: 4.461A  pdb=" N   ARG B 410 " --> pdb=" O   ILE B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 430 through 454
      removed outlier: 4.104A  pdb=" N   ILE B 436 " --> pdb=" O   ALA B 432 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   VAL B 437 " --> pdb=" O   LYS B 433 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   PHE B 454 " --> pdb=" O   VAL B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 461
    Processing helix  chain 'B' and resid 469 through 475
    Processing helix  chain 'B' and resid 486 through 495
    Processing helix  chain 'B' and resid 496 through 499
    Processing helix  chain 'B' and resid 500 through 506
    Processing helix  chain 'B' and resid 514 through 516
      No H-bonds generated for 'chain 'B' and resid 514 through 516'
    Processing helix  chain 'B' and resid 517 through 542
      removed outlier: 3.699A  pdb=" N   GLY B 521 " --> pdb=" O   ALA B 517 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 565 through 571
      removed outlier: 3.790A  pdb=" N   LYS B 569 " --> pdb=" O   SER B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 591 through 597
      removed outlier: 3.528A  pdb=" N   SER B 597 " --> pdb=" O   MET B 593 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 599 through 632
      removed outlier: 4.069A  pdb=" N   ILE B 603 " --> pdb=" O   PHE B 599 " (cutoff:3.500A)
      Proline residue:  B 623  - end of helix
    Processing helix  chain 'B' and resid 635 through 639
    Processing helix  chain 'B' and resid 641 through 645
      removed outlier: 4.510A  pdb=" N   GLY B 644 " --> pdb=" O   PHE B 641 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 652 through 668
      removed outlier: 4.130A  pdb=" N   ILE B 668 " --> pdb=" O   GLY B 664 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 670 through 698
      Proline residue:  B 676  - end of helix
    Processing helix  chain 'B' and resid 712 through 730
      removed outlier: 3.901A  pdb=" N   SER B 716 " --> pdb=" O   ASN B 712 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 731 through 752
    Processing helix  chain 'A' and resid 289 through 300
    Processing helix  chain 'A' and resid 301 through 315
      removed outlier: 4.363A  pdb=" N   PHE A 305 " --> pdb=" O   GLY A 301 " (cutoff:3.500A)
      removed outlier: 5.543A  pdb=" N   SER A 309 " --> pdb=" O   PHE A 305 " (cutoff:3.500A)
      removed outlier: 5.156A  pdb=" N   TRP A 310 " --> pdb=" O   ILE A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 342
      removed outlier: 3.789A  pdb=" N   VAL A 321 " --> pdb=" O   ILE A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 360
    Processing helix  chain 'A' and resid 361 through 398
      removed outlier: 3.702A  pdb=" N   ALA A 381 " --> pdb=" O   ALA A 377 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   HIS A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 425
      removed outlier: 4.460A  pdb=" N   ARG A 410 " --> pdb=" O   ILE A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 454
      removed outlier: 4.104A  pdb=" N   ILE A 436 " --> pdb=" O   ALA A 432 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   VAL A 437 " --> pdb=" O   LYS A 433 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   PHE A 454 " --> pdb=" O   VAL A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 461
    Processing helix  chain 'A' and resid 469 through 475
    Processing helix  chain 'A' and resid 486 through 495
    Processing helix  chain 'A' and resid 496 through 499
    Processing helix  chain 'A' and resid 500 through 506
    Processing helix  chain 'A' and resid 514 through 516
      No H-bonds generated for 'chain 'A' and resid 514 through 516'
    Processing helix  chain 'A' and resid 517 through 542
      removed outlier: 3.698A  pdb=" N   GLY A 521 " --> pdb=" O   ALA A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 571
      removed outlier: 3.790A  pdb=" N   LYS A 569 " --> pdb=" O   SER A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 597
      removed outlier: 3.529A  pdb=" N   SER A 597 " --> pdb=" O   MET A 593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 632
      removed outlier: 4.069A  pdb=" N   ILE A 603 " --> pdb=" O   PHE A 599 " (cutoff:3.500A)
      Proline residue:  A 623  - end of helix
    Processing helix  chain 'A' and resid 635 through 639
    Processing helix  chain 'A' and resid 641 through 645
      removed outlier: 4.511A  pdb=" N   GLY A 644 " --> pdb=" O   PHE A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 668
      removed outlier: 4.130A  pdb=" N   ILE A 668 " --> pdb=" O   GLY A 664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 698
      Proline residue:  A 676  - end of helix
    Processing helix  chain 'A' and resid 712 through 730
      removed outlier: 3.901A  pdb=" N   SER A 716 " --> pdb=" O   ASN A 712 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 731 through 752

    492 hydrogen bonds defined for protein.
    1440 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: 1.00

  Time building geometry restraints manager: 0.57 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1990
        1.34 -     1.46: 1608
        1.46 -     1.58: 2564
        1.58 -     1.70: 0
        1.70 -     1.82: 32
  Bond restraints: 6194
  Sorted by residual:
  bond pdb=" CB  TRP A 310 "
       pdb=" CG  TRP A 310 "
    ideal  model  delta    sigma   weight residual
    1.498  1.453  0.045 3.10e-02 1.04e+03 2.09e+00
  bond pdb=" CB  TRP B 310 "
       pdb=" CG  TRP B 310 "
    ideal  model  delta    sigma   weight residual
    1.498  1.454  0.044 3.10e-02 1.04e+03 2.04e+00
  bond pdb=" CB  THR B 328 "
       pdb=" CG2 THR B 328 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.32e+00
  bond pdb=" CB  THR A 328 "
       pdb=" CG2 THR A 328 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.25e+00
  bond pdb=" CB  TYR A 468 "
       pdb=" CG  TYR A 468 "
    ideal  model  delta    sigma   weight residual
    1.512  1.487  0.025 2.20e-02 2.07e+03 1.24e+00
  ... (remaining 6189 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.35: 7957
        1.35 -     2.70: 435
        2.70 -     4.04: 65
        4.04 -     5.39: 31
        5.39 -     6.74: 6
  Bond angle restraints: 8494
  Sorted by residual:
  angle pdb=" C   PHE B 599 "
        pdb=" N   THR B 600 "
        pdb=" CA  THR B 600 "
      ideal   model   delta    sigma   weight residual
     120.58  125.14   -4.56 1.32e+00 5.74e-01 1.20e+01
  angle pdb=" N   VAL B 347 "
        pdb=" CA  VAL B 347 "
        pdb=" C   VAL B 347 "
      ideal   model   delta    sigma   weight residual
     112.50  108.27    4.23 1.39e+00 5.18e-01 9.25e+00
  angle pdb=" N   VAL A 347 "
        pdb=" CA  VAL A 347 "
        pdb=" C   VAL A 347 "
      ideal   model   delta    sigma   weight residual
     112.50  108.35    4.15 1.39e+00 5.18e-01 8.92e+00
  angle pdb=" C   GLY A 585 "
        pdb=" N   LEU A 586 "
        pdb=" CA  LEU A 586 "
      ideal   model   delta    sigma   weight residual
     121.54  126.52   -4.98 1.91e+00 2.74e-01 6.81e+00
  angle pdb=" C   GLY B 585 "
        pdb=" N   LEU B 586 "
        pdb=" CA  LEU B 586 "
      ideal   model   delta    sigma   weight residual
     121.54  126.52   -4.98 1.91e+00 2.74e-01 6.79e+00
  ... (remaining 8489 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.65: 2990
       10.65 -    21.31: 327
       21.31 -    31.96: 90
       31.96 -    42.61: 39
       42.61 -    53.27: 16
  Dihedral angle restraints: 3462
    sinusoidal: 888
      harmonic: 2574
  Sorted by residual:
  dihedral pdb=" CA  LEU B 698 "
           pdb=" C   LEU B 698 "
           pdb=" N   ALA B 699 "
           pdb=" CA  ALA B 699 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.96  -27.04     0      5.00e+00 4.00e-02 2.92e+01
  dihedral pdb=" CA  LEU A 698 "
           pdb=" C   LEU A 698 "
           pdb=" N   ALA A 699 "
           pdb=" CA  ALA A 699 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.01  -26.99     0      5.00e+00 4.00e-02 2.91e+01
  dihedral pdb=" CA  VAL A 557 "
           pdb=" C   VAL A 557 "
           pdb=" N   THR A 558 "
           pdb=" CA  THR A 558 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.71   20.29     0      5.00e+00 4.00e-02 1.65e+01
  ... (remaining 3459 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 444
       0.027 -    0.054: 319
       0.054 -    0.081: 165
       0.081 -    0.108: 51
       0.108 -    0.134: 37
  Chirality restraints: 1016
  Sorted by residual:
  chirality pdb=" CB  VAL A 673 "
            pdb=" CA  VAL A 673 "
            pdb=" CG1 VAL A 673 "
            pdb=" CG2 VAL A 673 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.13 2.00e-01 2.50e+01 4.52e-01
  chirality pdb=" CB  VAL B 673 "
            pdb=" CA  VAL B 673 "
            pdb=" CG1 VAL B 673 "
            pdb=" CG2 VAL B 673 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 4.48e-01
  chirality pdb=" CA  PRO B 601 "
            pdb=" N   PRO B 601 "
            pdb=" C   PRO B 601 "
            pdb=" CB  PRO B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.12e-01
  ... (remaining 1013 not shown)

  Planarity restraints: 1104
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 600 "    0.028 5.00e-02 4.00e+02   4.16e-02 2.77e+00
        pdb=" N   PRO A 601 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A 601 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 601 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 600 "   -0.027 5.00e-02 4.00e+02   4.12e-02 2.72e+00
        pdb=" N   PRO B 601 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO B 601 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 601 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 371 "   -0.007 2.00e-02 2.50e+03   1.32e-02 1.73e+00
        pdb=" C   ILE B 371 "    0.023 2.00e-02 2.50e+03
        pdb=" O   ILE B 371 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   PHE B 372 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1101 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 171
        2.68 -     3.23: 7210
        3.23 -     3.79: 10019
        3.79 -     4.34: 12017
        4.34 -     4.90: 19143
  Nonbonded interactions: 48560
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 448 "
            pdb=" OG  SER B 597 "
     model   vdw
     2.120 3.040
  nonbonded pdb=" OD2 ASP A 448 "
            pdb=" OG  SER A 597 "
     model   vdw
     2.121 3.040
  nonbonded pdb=" O   SER A 609 "
            pdb=" OG  SER A 613 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" O   SER B 609 "
            pdb=" OG  SER B 613 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" O   LEU B 336 "
            pdb=" OG  SER B 339 "
     model   vdw
     2.224 3.040
  ... (remaining 48555 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 'B'
  selection = chain 'A'
}

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:             2.670
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.570
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
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   0.045   6198  Z= 0.343
  Angle     :  0.747   6.741   8502  Z= 0.425
  Chirality :  0.047   0.134   1016
  Planarity :  0.004   0.042   1104
  Dihedral  : 11.587  50.244   1826
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 16.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.28 %
    Favored  : 87.72 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 10.30 %
    Favored  : 89.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.13 (0.25), residues: 928
  helix: -1.36 (0.17), residues: 628
  sheet:  None (None), residues: 0
  loop : -3.49 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 653 
 TYR   0.018   0.002   TYR A 751 
 PHE   0.016   0.002   PHE A 488 
 TRP   0.011   0.001   TRP A 733 
 HIS   0.001   0.000   HIS A 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00713 ( 6194)
  covalent geometry    : angle       0.74568 ( 8494)
  SS BOND              : bond        0.00337 (    4)
  SS BOND              : angle       1.69642 (    8)
  hydrogen bonds       : bond        0.13077 (  492)
  hydrogen bonds       : angle       6.62369 ( 1440)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 125
  time to evaluate  : 0.210 
Fit side-chains
REVERT: B  358 ARG cc_start: 0.8579 (ttm170) cc_final: 0.8173 (mtm180)
REVERT: B  433 LYS cc_start: 0.6335 (mmmt) cc_final: 0.5808 (tttt)
REVERT: B  436 ILE cc_start: 0.8072 (mm) cc_final: 0.7691 (mt)
REVERT: B  562 ASN cc_start: 0.7878 (p0) cc_final: 0.7305 (p0)
REVERT: A  358 ARG cc_start: 0.8591 (ttm170) cc_final: 0.8170 (mtm180)
REVERT: A  433 LYS cc_start: 0.6590 (mmmt) cc_final: 0.6211 (tttt)
REVERT: A  562 ASN cc_start: 0.7850 (p0) cc_final: 0.7338 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 125
  average time/residue: 0.0599
  time to fit residues: 10.2152
Evaluate side-chains
  89 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3761 r_free = 0.3761 target = 0.126199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.105495 restraints weight = 12662.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 2.77
r_work: 0.3350 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6198  Z= 0.150
  Angle     :  0.628   6.746   8502  Z= 0.340
  Chirality :  0.044   0.131   1016
  Planarity :  0.005   0.061   1104
  Dihedral  :  5.176  22.320    962
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.59 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 15.24 %
    Favored  : 80.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.28), residues: 928
  helix:  0.55 (0.20), residues: 626
  sheet:  None (None), residues: 0
  loop : -2.69 (0.38), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 294 
 TYR   0.009   0.001   TYR A 584 
 PHE   0.012   0.001   PHE B 465 
 TRP   0.010   0.001   TRP B 733 
 HIS   0.001   0.000   HIS A 695 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6194)
  covalent geometry    : angle       0.62529 ( 8494)
  SS BOND              : bond        0.00669 (    4)
  SS BOND              : angle       1.83770 (    8)
  hydrogen bonds       : bond        0.04129 (  492)
  hydrogen bonds       : angle       4.60557 ( 1440)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.211 
Fit side-chains
REVERT: B  358 ARG cc_start: 0.8291 (ttm170) cc_final: 0.7710 (mtm180)
REVERT: B  433 LYS cc_start: 0.6768 (mmmt) cc_final: 0.6191 (tttt)
REVERT: B  436 ILE cc_start: 0.8475 (mm) cc_final: 0.8055 (mt)
REVERT: B  562 ASN cc_start: 0.7655 (p0) cc_final: 0.7250 (p0)
REVERT: A  358 ARG cc_start: 0.8467 (ttm170) cc_final: 0.7938 (mtm180)
REVERT: A  433 LYS cc_start: 0.6901 (mmmt) cc_final: 0.6457 (tttt)
REVERT: A  435 GLN cc_start: 0.7541 (tt0) cc_final: 0.7327 (tt0)
REVERT: A  436 ILE cc_start: 0.8336 (mm) cc_final: 0.7919 (mt)
REVERT: A  562 ASN cc_start: 0.7663 (p0) cc_final: 0.7200 (p0)
  outliers start: 20
  outliers final: 8
  residues processed: 126
  average time/residue: 0.0681
  time to fit residues: 11.4973
Evaluate side-chains
  101 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  679 SER
Chi-restraints excluded: chain B residue  680 ASN
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  543 CYS
Chi-restraints excluded: chain A residue  679 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 73 optimal weight:   20.0000
   chunk 47 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 52 optimal weight:    7.9990
   chunk 33 optimal weight:    0.0000
   chunk 42 optimal weight:    0.7980
   chunk 91 optimal weight:    0.0980
   chunk 76 optimal weight:    0.0010
   chunk 71 optimal weight:    0.6980
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.2590

-------------------------------------------------------------------------------
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 = 0.3799 r_free = 0.3799 target = 0.129269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.108847 restraints weight = 12392.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 2.75
r_work: 0.3402 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6198  Z= 0.120
  Angle     :  0.581   7.875   8502  Z= 0.309
  Chirality :  0.042   0.121   1016
  Planarity :  0.005   0.065   1104
  Dihedral  :  4.690  19.213    962
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 17.38 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.28), residues: 928
  helix:  1.03 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -2.50 (0.38), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 294 
 TYR   0.005   0.001   TYR A 751 
 PHE   0.033   0.001   PHE B 659 
 TRP   0.008   0.001   TRP A 733 
 HIS   0.002   0.001   HIS A 695 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 6194)
  covalent geometry    : angle       0.57886 ( 8494)
  SS BOND              : bond        0.00133 (    4)
  SS BOND              : angle       1.66883 (    8)
  hydrogen bonds       : bond        0.03693 (  492)
  hydrogen bonds       : angle       4.15140 ( 1440)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.217 
Fit side-chains
REVERT: B  433 LYS cc_start: 0.6663 (mmmt) cc_final: 0.6080 (tttt)
REVERT: B  436 ILE cc_start: 0.8457 (mm) cc_final: 0.8025 (mt)
REVERT: B  562 ASN cc_start: 0.7645 (p0) cc_final: 0.7224 (m110)
REVERT: B  680 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8346 (t0)
REVERT: B  741 ILE cc_start: 0.8960 (mt) cc_final: 0.8753 (mp)
REVERT: A  433 LYS cc_start: 0.6900 (mmmt) cc_final: 0.6468 (tttt)
REVERT: A  436 ILE cc_start: 0.8264 (mm) cc_final: 0.7833 (mt)
REVERT: A  562 ASN cc_start: 0.7680 (p0) cc_final: 0.7379 (p0)
REVERT: A  751 TYR cc_start: 0.7300 (OUTLIER) cc_final: 0.6863 (p90)
  outliers start: 20
  outliers final: 6
  residues processed: 128
  average time/residue: 0.0645
  time to fit residues: 11.4611
Evaluate side-chains
  107 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  584 TYR
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  663 LEU
Chi-restraints excluded: chain B residue  680 ASN
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  543 CYS
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  751 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 73 optimal weight:    0.0870
   chunk 74 optimal weight:    6.9990
   chunk 41 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 5 optimal weight:    6.9990
   chunk 14 optimal weight:    0.6980
   chunk 13 optimal weight:    0.1980
   chunk 53 optimal weight:    6.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
B 298 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.128560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.108075 restraints weight = 12511.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 2.79
r_work: 0.3393 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.2815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6198  Z= 0.124
  Angle     :  0.579   6.134   8502  Z= 0.312
  Chirality :  0.042   0.121   1016
  Planarity :  0.004   0.065   1104
  Dihedral  :  4.518  18.677    962
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 18.88 %
    Favored  : 75.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.28), residues: 928
  helix:  1.14 (0.20), residues: 654
  sheet:  None (None), residues: 0
  loop : -2.42 (0.39), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 294 
 TYR   0.005   0.001   TYR B 751 
 PHE   0.033   0.001   PHE A 659 
 TRP   0.007   0.001   TRP A 733 
 HIS   0.001   0.001   HIS A 695 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 6194)
  covalent geometry    : angle       0.57690 ( 8494)
  SS BOND              : bond        0.00053 (    4)
  SS BOND              : angle       1.55776 (    8)
  hydrogen bonds       : bond        0.03594 (  492)
  hydrogen bonds       : angle       3.99613 ( 1440)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 0.196 
Fit side-chains
REVERT: B  433 LYS cc_start: 0.6708 (mmmt) cc_final: 0.6189 (tttt)
REVERT: B  436 ILE cc_start: 0.8377 (mm) cc_final: 0.7943 (mt)
REVERT: B  562 ASN cc_start: 0.7589 (p0) cc_final: 0.7015 (p0)
REVERT: B  679 SER cc_start: 0.9522 (OUTLIER) cc_final: 0.9132 (p)
REVERT: B  680 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.7965 (t0)
REVERT: A  358 ARG cc_start: 0.8564 (ptm160) cc_final: 0.8033 (ptm160)
REVERT: A  433 LYS cc_start: 0.6877 (mmmt) cc_final: 0.6421 (tttt)
REVERT: A  436 ILE cc_start: 0.8233 (mm) cc_final: 0.7802 (mt)
REVERT: A  562 ASN cc_start: 0.7594 (p0) cc_final: 0.7218 (p0)
REVERT: A  679 SER cc_start: 0.9519 (OUTLIER) cc_final: 0.9160 (p)
REVERT: A  751 TYR cc_start: 0.7257 (OUTLIER) cc_final: 0.6802 (p90)
  outliers start: 26
  outliers final: 8
  residues processed: 119
  average time/residue: 0.0564
  time to fit residues: 9.5001
Evaluate side-chains
  104 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  584 TYR
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  660 LEU
Chi-restraints excluded: chain B residue  663 LEU
Chi-restraints excluded: chain B residue  679 SER
Chi-restraints excluded: chain B residue  680 ASN
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  543 CYS
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  679 SER
Chi-restraints excluded: chain A residue  751 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0570
   chunk 35 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 50 optimal weight:    0.5980
   chunk 64 optimal weight:    0.7980
   chunk 69 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.6098

-------------------------------------------------------------------------------
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 = 0.3794 r_free = 0.3794 target = 0.128886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.108466 restraints weight = 12591.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 2.76
r_work: 0.3398 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.3007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6198  Z= 0.127
  Angle     :  0.589   8.773   8502  Z= 0.312
  Chirality :  0.043   0.179   1016
  Planarity :  0.004   0.064   1104
  Dihedral  :  4.430  17.669    962
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 19.10 %
    Favored  : 75.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.28), residues: 928
  helix:  1.28 (0.20), residues: 642
  sheet:  None (None), residues: 0
  loop : -2.31 (0.38), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 294 
 TYR   0.006   0.001   TYR B 751 
 PHE   0.030   0.001   PHE B 387 
 TRP   0.008   0.001   TRP A 733 
 HIS   0.001   0.001   HIS A 695 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6194)
  covalent geometry    : angle       0.58753 ( 8494)
  SS BOND              : bond        0.00105 (    4)
  SS BOND              : angle       1.58699 (    8)
  hydrogen bonds       : bond        0.03565 (  492)
  hydrogen bonds       : angle       3.99523 ( 1440)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 96
  time to evaluate  : 0.196 
Fit side-chains
REVERT: B  294 ARG cc_start: 0.8697 (ttm-80) cc_final: 0.8481 (tpp80)
REVERT: B  433 LYS cc_start: 0.6723 (mmmt) cc_final: 0.6177 (tttt)
REVERT: B  436 ILE cc_start: 0.8380 (mm) cc_final: 0.7949 (mt)
REVERT: B  562 ASN cc_start: 0.7604 (p0) cc_final: 0.7041 (p0)
REVERT: B  680 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8034 (t0)
REVERT: A  292 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7895 (tt)
REVERT: A  358 ARG cc_start: 0.8540 (ptm160) cc_final: 0.7976 (ptm160)
REVERT: A  433 LYS cc_start: 0.6883 (mmmt) cc_final: 0.6433 (tttt)
REVERT: A  436 ILE cc_start: 0.8243 (mm) cc_final: 0.7806 (mt)
REVERT: A  562 ASN cc_start: 0.7625 (p0) cc_final: 0.7226 (p0)
REVERT: A  626 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.6984 (t80)
REVERT: A  751 TYR cc_start: 0.7285 (OUTLIER) cc_final: 0.6839 (p90)
  outliers start: 27
  outliers final: 14
  residues processed: 115
  average time/residue: 0.0639
  time to fit residues: 10.1692
Evaluate side-chains
  110 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  543 CYS
Chi-restraints excluded: chain B residue  584 TYR
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  660 LEU
Chi-restraints excluded: chain B residue  680 ASN
Chi-restraints excluded: chain B residue  693 VAL
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  543 CYS
Chi-restraints excluded: chain A residue  584 TYR
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  626 PHE
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  751 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 71 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 57 optimal weight:    5.9990
   chunk 37 optimal weight:    0.3980
   chunk 33 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   chunk 76 optimal weight:    0.1980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3793 r_free = 0.3793 target = 0.128877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.108558 restraints weight = 12560.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 2.77
r_work: 0.3400 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.3175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6198  Z= 0.127
  Angle     :  0.584   6.783   8502  Z= 0.312
  Chirality :  0.043   0.172   1016
  Planarity :  0.004   0.064   1104
  Dihedral  :  4.376  17.614    962
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 18.88 %
    Favored  : 75.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.29), residues: 928
  helix:  1.24 (0.20), residues: 658
  sheet:  None (None), residues: 0
  loop : -2.37 (0.40), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 294 
 TYR   0.005   0.001   TYR B 751 
 PHE   0.027   0.001   PHE A 659 
 TRP   0.007   0.001   TRP A 733 
 HIS   0.001   0.001   HIS A 695 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6194)
  covalent geometry    : angle       0.58205 ( 8494)
  SS BOND              : bond        0.00047 (    4)
  SS BOND              : angle       1.58378 (    8)
  hydrogen bonds       : bond        0.03546 (  492)
  hydrogen bonds       : angle       3.94847 ( 1440)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 0.150 
Fit side-chains
REVERT: B  364 PHE cc_start: 0.8631 (m-80) cc_final: 0.8428 (m-80)
REVERT: B  433 LYS cc_start: 0.6718 (mmmt) cc_final: 0.6178 (tttt)
REVERT: B  436 ILE cc_start: 0.8361 (mm) cc_final: 0.7928 (mt)
REVERT: B  562 ASN cc_start: 0.7575 (p0) cc_final: 0.7065 (p0)
REVERT: B  679 SER cc_start: 0.9578 (OUTLIER) cc_final: 0.9110 (p)
REVERT: B  680 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8106 (t0)
REVERT: A  358 ARG cc_start: 0.8570 (ptm160) cc_final: 0.8113 (ptm160)
REVERT: A  433 LYS cc_start: 0.6864 (mmmt) cc_final: 0.6496 (tttt)
REVERT: A  436 ILE cc_start: 0.8277 (mm) cc_final: 0.7847 (mt)
REVERT: A  562 ASN cc_start: 0.7581 (p0) cc_final: 0.7167 (p0)
REVERT: A  626 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7099 (t80)
REVERT: A  679 SER cc_start: 0.9532 (OUTLIER) cc_final: 0.9101 (p)
REVERT: A  751 TYR cc_start: 0.7362 (OUTLIER) cc_final: 0.6806 (p90)
  outliers start: 26
  outliers final: 16
  residues processed: 122
  average time/residue: 0.0565
  time to fit residues: 9.6151
Evaluate side-chains
  114 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  543 CYS
Chi-restraints excluded: chain B residue  584 TYR
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  660 LEU
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  679 SER
Chi-restraints excluded: chain B residue  680 ASN
Chi-restraints excluded: chain B residue  693 VAL
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  543 CYS
Chi-restraints excluded: chain A residue  584 TYR
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  626 PHE
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  679 SER
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  751 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 81 optimal weight:    8.9990
   chunk 25 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 2 optimal weight:    0.3980
   chunk 36 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 91 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3781 r_free = 0.3781 target = 0.128051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.107653 restraints weight = 12592.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 2.75
r_work: 0.3387 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.3264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6198  Z= 0.142
  Angle     :  0.592   7.218   8502  Z= 0.316
  Chirality :  0.043   0.163   1016
  Planarity :  0.004   0.063   1104
  Dihedral  :  4.355  16.634    962
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.62 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  6.65 %
    Allowed  : 19.74 %
    Favored  : 73.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.29), residues: 928
  helix:  1.25 (0.20), residues: 658
  sheet:  None (None), residues: 0
  loop : -2.37 (0.40), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 294 
 TYR   0.006   0.001   TYR A 468 
 PHE   0.024   0.001   PHE A 659 
 TRP   0.009   0.001   TRP A 733 
 HIS   0.001   0.001   HIS A 695 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 6194)
  covalent geometry    : angle       0.59125 ( 8494)
  SS BOND              : bond        0.00064 (    4)
  SS BOND              : angle       1.33214 (    8)
  hydrogen bonds       : bond        0.03589 (  492)
  hydrogen bonds       : angle       3.97494 ( 1440)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 94
  time to evaluate  : 0.176 
Fit side-chains
REVERT: B  433 LYS cc_start: 0.6943 (mmmt) cc_final: 0.6344 (tttt)
REVERT: B  436 ILE cc_start: 0.8346 (mm) cc_final: 0.7907 (mt)
REVERT: B  562 ASN cc_start: 0.7569 (p0) cc_final: 0.7058 (p0)
REVERT: B  679 SER cc_start: 0.9595 (OUTLIER) cc_final: 0.9098 (p)
REVERT: B  680 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8215 (t0)
REVERT: A  296 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8276 (mtm)
REVERT: A  358 ARG cc_start: 0.8574 (ptm160) cc_final: 0.8041 (ptm160)
REVERT: A  433 LYS cc_start: 0.6788 (mmmt) cc_final: 0.6499 (tttt)
REVERT: A  436 ILE cc_start: 0.8316 (mm) cc_final: 0.7876 (mt)
REVERT: A  562 ASN cc_start: 0.7643 (p0) cc_final: 0.7259 (p0)
REVERT: A  626 PHE cc_start: 0.7774 (OUTLIER) cc_final: 0.7129 (t80)
REVERT: A  679 SER cc_start: 0.9548 (OUTLIER) cc_final: 0.9115 (p)
REVERT: A  751 TYR cc_start: 0.7395 (OUTLIER) cc_final: 0.6847 (p90)
  outliers start: 31
  outliers final: 17
  residues processed: 119
  average time/residue: 0.0622
  time to fit residues: 10.2808
Evaluate side-chains
  111 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  543 CYS
Chi-restraints excluded: chain B residue  584 TYR
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  660 LEU
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  679 SER
Chi-restraints excluded: chain B residue  680 ASN
Chi-restraints excluded: chain B residue  693 VAL
Chi-restraints excluded: chain B residue  751 TYR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  543 CYS
Chi-restraints excluded: chain A residue  584 TYR
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  626 PHE
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  679 SER
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  751 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 19 optimal weight:    0.2980
   chunk 22 optimal weight:    0.0270
   chunk 91 optimal weight:    0.7980
   chunk 6 optimal weight:    8.9990
   chunk 12 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0070
   chunk 75 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.3456

-------------------------------------------------------------------------------
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 = 0.3823 r_free = 0.3823 target = 0.131117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.110931 restraints weight = 12580.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 2.77
r_work: 0.3434 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.3556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6198  Z= 0.118
  Angle     :  0.600  12.887   8502  Z= 0.313
  Chirality :  0.043   0.172   1016
  Planarity :  0.004   0.064   1104
  Dihedral  :  4.241  17.736    962
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 22.53 %
    Favored  : 72.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.29), residues: 928
  helix:  1.28 (0.20), residues: 662
  sheet:  None (None), residues: 0
  loop : -2.48 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 294 
 TYR   0.004   0.001   TYR A 533 
 PHE   0.026   0.001   PHE A 659 
 TRP   0.011   0.001   TRP A 733 
 HIS   0.001   0.001   HIS B 695 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 6194)
  covalent geometry    : angle       0.59885 ( 8494)
  SS BOND              : bond        0.00033 (    4)
  SS BOND              : angle       1.28245 (    8)
  hydrogen bonds       : bond        0.03460 (  492)
  hydrogen bonds       : angle       3.86027 ( 1440)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.210 
Fit side-chains
REVERT: B  294 ARG cc_start: 0.8763 (ttm-80) cc_final: 0.8416 (tpp80)
REVERT: B  364 PHE cc_start: 0.8560 (m-80) cc_final: 0.8352 (m-80)
REVERT: B  433 LYS cc_start: 0.6895 (mmmt) cc_final: 0.6342 (tttt)
REVERT: B  436 ILE cc_start: 0.8319 (mm) cc_final: 0.7882 (mt)
REVERT: B  562 ASN cc_start: 0.7554 (p0) cc_final: 0.7051 (p0)
REVERT: B  680 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8259 (t0)
REVERT: A  294 ARG cc_start: 0.8780 (ttm170) cc_final: 0.8561 (ttm-80)
REVERT: A  296 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8193 (mtm)
REVERT: A  358 ARG cc_start: 0.8573 (ptm160) cc_final: 0.8056 (ptm160)
REVERT: A  433 LYS cc_start: 0.6808 (mmmt) cc_final: 0.6495 (tttt)
REVERT: A  436 ILE cc_start: 0.8241 (mm) cc_final: 0.7803 (mt)
REVERT: A  523 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8843 (mm)
REVERT: A  562 ASN cc_start: 0.7599 (p0) cc_final: 0.7221 (p0)
REVERT: A  626 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7131 (t80)
REVERT: A  751 TYR cc_start: 0.7422 (OUTLIER) cc_final: 0.6865 (p90)
  outliers start: 23
  outliers final: 15
  residues processed: 126
  average time/residue: 0.0620
  time to fit residues: 10.9561
Evaluate side-chains
  119 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  543 CYS
Chi-restraints excluded: chain B residue  584 TYR
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  660 LEU
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  680 ASN
Chi-restraints excluded: chain B residue  751 TYR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  543 CYS
Chi-restraints excluded: chain A residue  584 TYR
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  626 PHE
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  751 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 75 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0060
   chunk 62 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 76 optimal weight:    0.4980
   chunk 72 optimal weight:    0.0030
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.4006

-------------------------------------------------------------------------------
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 = 0.3821 r_free = 0.3821 target = 0.131127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.110920 restraints weight = 12658.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 2.78
r_work: 0.3436 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.3703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6198  Z= 0.119
  Angle     :  0.611  12.576   8502  Z= 0.317
  Chirality :  0.043   0.154   1016
  Planarity :  0.004   0.064   1104
  Dihedral  :  4.177  17.810    962
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 22.53 %
    Favored  : 72.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.29), residues: 928
  helix:  1.36 (0.20), residues: 664
  sheet:  None (None), residues: 0
  loop : -2.44 (0.39), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 294 
 TYR   0.012   0.001   TYR A 686 
 PHE   0.028   0.001   PHE A 659 
 TRP   0.009   0.001   TRP A 733 
 HIS   0.001   0.001   HIS B 695 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 6194)
  covalent geometry    : angle       0.60976 ( 8494)
  SS BOND              : bond        0.00218 (    4)
  SS BOND              : angle       1.61063 (    8)
  hydrogen bonds       : bond        0.03439 (  492)
  hydrogen bonds       : angle       3.84789 ( 1440)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 0.204 
Fit side-chains
REVERT: B  294 ARG cc_start: 0.8789 (ttm-80) cc_final: 0.8410 (tpp80)
REVERT: B  433 LYS cc_start: 0.6905 (mmmt) cc_final: 0.6362 (tttt)
REVERT: B  436 ILE cc_start: 0.8324 (mm) cc_final: 0.7899 (mt)
REVERT: B  562 ASN cc_start: 0.7581 (p0) cc_final: 0.7057 (p0)
REVERT: B  626 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.7119 (t80)
REVERT: B  680 ASN cc_start: 0.8776 (OUTLIER) cc_final: 0.8256 (t0)
REVERT: A  296 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8175 (mtm)
REVERT: A  358 ARG cc_start: 0.8584 (ptm160) cc_final: 0.8081 (ptm160)
REVERT: A  433 LYS cc_start: 0.6813 (mmmt) cc_final: 0.6511 (tttt)
REVERT: A  436 ILE cc_start: 0.8268 (mm) cc_final: 0.7852 (mt)
REVERT: A  523 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8848 (mm)
REVERT: A  562 ASN cc_start: 0.7601 (p0) cc_final: 0.7213 (p0)
REVERT: A  626 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7127 (t80)
REVERT: A  751 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.6735 (p90)
  outliers start: 25
  outliers final: 14
  residues processed: 118
  average time/residue: 0.0642
  time to fit residues: 10.4675
Evaluate side-chains
  118 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  543 CYS
Chi-restraints excluded: chain B residue  584 TYR
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  626 PHE
Chi-restraints excluded: chain B residue  660 LEU
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  680 ASN
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  543 CYS
Chi-restraints excluded: chain A residue  584 TYR
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  626 PHE
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  751 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0030
   chunk 2 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 26 optimal weight:   10.0000
   chunk 82 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    1.1396

-------------------------------------------------------------------------------
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 = 0.3770 r_free = 0.3770 target = 0.127318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.106900 restraints weight = 12612.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 2.75
r_work: 0.3377 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.3584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   6198  Z= 0.169
  Angle     :  0.657  11.900   8502  Z= 0.345
  Chirality :  0.044   0.148   1016
  Planarity :  0.004   0.063   1104
  Dihedral  :  4.372  16.501    962
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 24.03 %
    Favored  : 71.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.28), residues: 928
  helix:  1.22 (0.20), residues: 660
  sheet:  None (None), residues: 0
  loop : -2.34 (0.40), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 294 
 TYR   0.009   0.001   TYR A 686 
 PHE   0.013   0.001   PHE B 494 
 TRP   0.010   0.001   TRP A 733 
 HIS   0.001   0.000   HIS A 695 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 6194)
  covalent geometry    : angle       0.65571 ( 8494)
  SS BOND              : bond        0.00119 (    4)
  SS BOND              : angle       1.69134 (    8)
  hydrogen bonds       : bond        0.03753 (  492)
  hydrogen bonds       : angle       4.03240 ( 1440)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.201 
Fit side-chains
REVERT: B  294 ARG cc_start: 0.8829 (ttm-80) cc_final: 0.8490 (tpp80)
REVERT: B  433 LYS cc_start: 0.6976 (mmmt) cc_final: 0.6512 (tttt)
REVERT: B  436 ILE cc_start: 0.8344 (mm) cc_final: 0.7898 (mt)
REVERT: B  562 ASN cc_start: 0.7547 (p0) cc_final: 0.7063 (p0)
REVERT: B  680 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8200 (t0)
REVERT: A  294 ARG cc_start: 0.8753 (ttm-80) cc_final: 0.8381 (tpp80)
REVERT: A  358 ARG cc_start: 0.8604 (ptm160) cc_final: 0.8074 (ptm160)
REVERT: A  433 LYS cc_start: 0.6910 (mmmt) cc_final: 0.6589 (tttt)
REVERT: A  436 ILE cc_start: 0.8261 (mm) cc_final: 0.7809 (mt)
REVERT: A  523 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8902 (mm)
REVERT: A  562 ASN cc_start: 0.7619 (p0) cc_final: 0.7242 (p0)
REVERT: A  626 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7153 (t80)
REVERT: A  751 TYR cc_start: 0.7356 (OUTLIER) cc_final: 0.6696 (p90)
  outliers start: 22
  outliers final: 16
  residues processed: 107
  average time/residue: 0.0687
  time to fit residues: 10.0128
Evaluate side-chains
  110 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  543 CYS
Chi-restraints excluded: chain B residue  584 TYR
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  660 LEU
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  680 ASN
Chi-restraints excluded: chain B residue  751 TYR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  543 CYS
Chi-restraints excluded: chain A residue  584 TYR
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  626 PHE
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  751 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 3 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3793 r_free = 0.3793 target = 0.129024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.108476 restraints weight = 12625.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 2.78
r_work: 0.3403 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.3712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6198  Z= 0.139
  Angle     :  0.644  11.377   8502  Z= 0.334
  Chirality :  0.044   0.147   1016
  Planarity :  0.004   0.063   1104
  Dihedral  :  4.320  16.529    962
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 23.39 %
    Favored  : 71.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.28), residues: 928
  helix:  1.24 (0.20), residues: 658
  sheet:  None (None), residues: 0
  loop : -2.38 (0.39), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 294 
 TYR   0.010   0.001   TYR A 686 
 PHE   0.008   0.001   PHE B 488 
 TRP   0.011   0.001   TRP A 733 
 HIS   0.001   0.001   HIS B 695 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6194)
  covalent geometry    : angle       0.64250 ( 8494)
  SS BOND              : bond        0.00043 (    4)
  SS BOND              : angle       1.53694 (    8)
  hydrogen bonds       : bond        0.03626 (  492)
  hydrogen bonds       : angle       3.97479 ( 1440)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1124.83 seconds
wall clock time: 19 minutes 58.58 seconds (1198.58 seconds total)