Starting phenix.real_space_refine
on Thu Jul 24 11:53:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6pzt_20537/07_2025/6pzt_20537.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pzt_20537/07_2025/6pzt_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6pzt_20537/07_2025/6pzt_20537.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pzt_20537/07_2025/6pzt_20537.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pzt_20537/07_2025/6pzt_20537.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pzt_20537/07_2025/6pzt_20537.cif"
  }
  resolution = 3.46
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6062
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      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: {'GLN:plan1': 4, 'TYR:plan': 6, 'ASN:plan1': 10, 'ASP:plan': 8, 'PHE:plan': 8, 'GLU:plan': 12, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 233
  Restraints were copied for chains:
    B
  Time building chain proxies: 5.25, per 1000 atoms: 0.87
  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=2, 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

  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: 1.63
  Conformation dependent library (CDL) restraints added in 797.4 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: 0.64
  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: 1.90

  Time building geometry restraints manager: 1.91 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: 2988
       10.65 -    21.30: 326
       21.30 -    31.96: 89
       31.96 -    42.61: 39
       42.61 -    53.26: 14
  Dihedral angle restraints: 3456
    sinusoidal: 882
      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 3453 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:
        2.03 -     2.60: 80
        2.60 -     3.18: 6456
        3.18 -     3.75: 9862
        3.75 -     4.33: 12445
        4.33 -     4.90: 19723
  Nonbonded interactions: 48566
  Sorted by model distance:
  nonbonded pdb=" SG  CYS A 563 "
            pdb=" SG  CYS A 568 "
     model   vdw
     2.026 3.760
  nonbonded pdb=" SG  CYS A 577 "
            pdb=" SG  CYS A 582 "
     model   vdw
     2.031 3.760
  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
  ... (remaining 48561 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: 0.04
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:             1.880
  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:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     19.600
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.900
-------------------------------------------------------------------------------
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   6196  Z= 0.343
  Angle     :  0.746   6.741   8498  Z= 0.425
  Chirality :  0.047   0.134   1016
  Planarity :  0.004   0.042   1104
  Dihedral  : 11.587  50.244   1826
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 16.50
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.011   0.001   TRP A 733 
 HIS   0.001   0.000   HIS A 398 
 PHE   0.016   0.002   PHE A 488 
 TYR   0.018   0.002   TYR A 751 
 ARG   0.004   0.001   ARG A 653 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13077 (  492)
  hydrogen bonds       : angle       6.62369 ( 1440)
  SS BOND              : bond        0.00351 (    2)
  SS BOND              : angle       1.70820 (    4)
  covalent geometry    : bond        0.00713 ( 6194)
  covalent geometry    : angle       0.74568 ( 8494)

*********************** 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  : 0.680 
Fit side-chains
REVERT: B  358 ARG cc_start: 0.8579 (ttm170) cc_final: 0.8174 (mtm180)
REVERT: B  433 LYS cc_start: 0.6335 (mmmt) cc_final: 0.5809 (tttt)
REVERT: B  436 ILE cc_start: 0.8072 (mm) cc_final: 0.7690 (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: 0.8171 (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: 0.2137
  time to fit residues: 36.5768
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  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    9.9990
   chunk 69 optimal weight:    0.0060
   chunk 38 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 72 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   chunk 43 optimal weight:    0.9980
   chunk 53 optimal weight:    8.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.6996

-------------------------------------------------------------------------------
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 = 0.125647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.105106 restraints weight = 12580.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 2.76
r_work: 0.3343 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.1736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6196  Z= 0.151
  Angle     :  0.628   6.812   8498  Z= 0.341
  Chirality :  0.043   0.128   1016
  Planarity :  0.005   0.061   1104
  Dihedral  :  5.153  22.771    962
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.91 %
    Favored  : 90.09 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 15.45 %
    Favored  : 80.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.28), residues: 928
  helix:  0.49 (0.20), residues: 626
  sheet:  None (None), residues: 0
  loop : -2.70 (0.38), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 733 
 HIS   0.001   0.000   HIS A 695 
 PHE   0.011   0.001   PHE B 465 
 TYR   0.012   0.001   TYR A 584 
 ARG   0.006   0.001   ARG B 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04270 (  492)
  hydrogen bonds       : angle       4.67369 ( 1440)
  SS BOND              : bond        0.00470 (    2)
  SS BOND              : angle       1.75364 (    4)
  covalent geometry    : bond        0.00312 ( 6194)
  covalent geometry    : angle       0.62744 ( 8494)

*********************** 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
  127 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.664 
Fit side-chains
REVERT: B  358 ARG cc_start: 0.8303 (ttm170) cc_final: 0.7731 (mtm180)
REVERT: B  433 LYS cc_start: 0.6759 (mmmt) cc_final: 0.6174 (tttt)
REVERT: B  436 ILE cc_start: 0.8455 (mm) cc_final: 0.8037 (mt)
REVERT: B  562 ASN cc_start: 0.7667 (p0) cc_final: 0.7102 (p0)
REVERT: B  680 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8351 (t0)
REVERT: A  358 ARG cc_start: 0.8483 (ttm170) cc_final: 0.7964 (mtm180)
REVERT: A  433 LYS cc_start: 0.6870 (mmmt) cc_final: 0.6480 (tttt)
REVERT: A  436 ILE cc_start: 0.8306 (mm) cc_final: 0.7883 (mt)
REVERT: A  563 CYS cc_start: 0.6893 (t) cc_final: 0.6345 (t)
  outliers start: 20
  outliers final: 7
  residues processed: 122
  average time/residue: 0.1611
  time to fit residues: 26.5808
Evaluate side-chains
  97 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
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 27 optimal weight:   20.0000
   chunk 49 optimal weight:    0.9990
   chunk 35 optimal weight:    0.2980
   chunk 41 optimal weight:    0.0040
   chunk 20 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.6192

-------------------------------------------------------------------------------
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 = 0.3762 r_free = 0.3762 target = 0.126334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.106094 restraints weight = 12680.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 2.77
r_work: 0.3361 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6196  Z= 0.132
  Angle     :  0.590   7.110   8498  Z= 0.318
  Chirality :  0.043   0.128   1016
  Planarity :  0.005   0.065   1104
  Dihedral  :  4.814  19.823    962
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.94 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 18.03 %
    Favored  : 77.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.28), residues: 928
  helix:  0.93 (0.20), residues: 640
  sheet:  None (None), residues: 0
  loop : -2.47 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 733 
 HIS   0.001   0.001   HIS A 695 
 PHE   0.024   0.001   PHE B 659 
 TYR   0.005   0.001   TYR A 751 
 ARG   0.007   0.001   ARG A 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03862 (  492)
  hydrogen bonds       : angle       4.30986 ( 1440)
  SS BOND              : bond        0.00615 (    2)
  SS BOND              : angle       1.97263 (    4)
  covalent geometry    : bond        0.00273 ( 6194)
  covalent geometry    : angle       0.58870 ( 8494)

*********************** 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
  123 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.617 
Fit side-chains
REVERT: B  358 ARG cc_start: 0.8295 (ttm170) cc_final: 0.7738 (mtm180)
REVERT: B  433 LYS cc_start: 0.6738 (mmmt) cc_final: 0.6161 (tttt)
REVERT: B  436 ILE cc_start: 0.8487 (mm) cc_final: 0.8073 (mt)
REVERT: B  562 ASN cc_start: 0.7622 (p0) cc_final: 0.7240 (p0)
REVERT: B  680 ASN cc_start: 0.8639 (OUTLIER) cc_final: 0.8249 (t0)
REVERT: A  433 LYS cc_start: 0.6900 (mmmt) cc_final: 0.6464 (tttt)
REVERT: A  436 ILE cc_start: 0.8304 (mm) cc_final: 0.7877 (mt)
REVERT: A  562 ASN cc_start: 0.7468 (p0) cc_final: 0.7040 (p0)
REVERT: A  563 CYS cc_start: 0.6368 (t) cc_final: 0.5880 (t)
  outliers start: 21
  outliers final: 6
  residues processed: 117
  average time/residue: 0.1602
  time to fit residues: 25.3691
Evaluate side-chains
  99 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 90 optimal weight:    2.9990
   chunk 21 optimal weight:    0.4980
   chunk 49 optimal weight:    0.9990
   chunk 73 optimal weight:   30.0000
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3763 r_free = 0.3763 target = 0.126559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.106045 restraints weight = 12859.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 2.80
r_work: 0.3359 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6196  Z= 0.134
  Angle     :  0.583   6.037   8498  Z= 0.315
  Chirality :  0.043   0.124   1016
  Planarity :  0.005   0.065   1104
  Dihedral  :  4.633  18.900    962
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.05 %
    Favored  : 90.95 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 19.74 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.28), residues: 928
  helix:  1.04 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop : -2.28 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 704 
 HIS   0.001   0.001   HIS A 695 
 PHE   0.034   0.001   PHE A 659 
 TYR   0.009   0.001   TYR B 686 
 ARG   0.007   0.001   ARG A 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03700 (  492)
  hydrogen bonds       : angle       4.15583 ( 1440)
  SS BOND              : bond        0.00064 (    2)
  SS BOND              : angle       1.63325 (    4)
  covalent geometry    : bond        0.00287 ( 6194)
  covalent geometry    : angle       0.58163 ( 8494)

*********************** 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
  131 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 107
  time to evaluate  : 0.644 
Fit side-chains
REVERT: B  433 LYS cc_start: 0.6762 (mmmt) cc_final: 0.6231 (tttt)
REVERT: B  436 ILE cc_start: 0.8392 (mm) cc_final: 0.7966 (mt)
REVERT: B  562 ASN cc_start: 0.7612 (p0) cc_final: 0.7026 (p0)
REVERT: B  680 ASN cc_start: 0.8809 (OUTLIER) cc_final: 0.8211 (t0)
REVERT: A  358 ARG cc_start: 0.8611 (ptm160) cc_final: 0.8169 (ptm160)
REVERT: A  429 GLU cc_start: 0.8004 (pm20) cc_final: 0.7699 (pm20)
REVERT: A  433 LYS cc_start: 0.6886 (mmmt) cc_final: 0.6452 (tttt)
REVERT: A  436 ILE cc_start: 0.8297 (mm) cc_final: 0.7840 (mt)
REVERT: A  562 ASN cc_start: 0.7407 (p0) cc_final: 0.6976 (p0)
REVERT: A  563 CYS cc_start: 0.6358 (t) cc_final: 0.5837 (t)
REVERT: A  679 SER cc_start: 0.9526 (OUTLIER) cc_final: 0.9147 (p)
  outliers start: 24
  outliers final: 10
  residues processed: 124
  average time/residue: 0.1830
  time to fit residues: 31.1025
Evaluate side-chains
  110 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  320 SER
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 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  693 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0170
   chunk 11 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 28 optimal weight:    4.9990
   chunk 12 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 53 optimal weight:    4.9990
   chunk 89 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.6620

-------------------------------------------------------------------------------
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 = 0.3771 r_free = 0.3771 target = 0.127320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.107072 restraints weight = 12717.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 2.79
r_work: 0.3375 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.2917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6196  Z= 0.129
  Angle     :  0.582   7.131   8498  Z= 0.312
  Chirality :  0.043   0.122   1016
  Planarity :  0.005   0.064   1104
  Dihedral  :  4.475  17.682    962
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.30 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 18.45 %
    Favored  : 75.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.28), residues: 928
  helix:  1.23 (0.20), residues: 640
  sheet:  None (None), residues: 0
  loop : -2.19 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 733 
 HIS   0.001   0.001   HIS A 695 
 PHE   0.028   0.001   PHE A 659 
 TYR   0.008   0.001   TYR B 686 
 ARG   0.007   0.001   ARG B 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03596 (  492)
  hydrogen bonds       : angle       4.04366 ( 1440)
  SS BOND              : bond        0.00095 (    2)
  SS BOND              : angle       1.69568 (    4)
  covalent geometry    : bond        0.00278 ( 6194)
  covalent geometry    : angle       0.58085 ( 8494)

*********************** 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
  130 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 103
  time to evaluate  : 0.616 
Fit side-chains
REVERT: B  358 ARG cc_start: 0.8515 (ptm160) cc_final: 0.8086 (ptm160)
REVERT: B  433 LYS cc_start: 0.6766 (mmmt) cc_final: 0.6205 (tttt)
REVERT: B  436 ILE cc_start: 0.8396 (mm) cc_final: 0.7964 (mt)
REVERT: B  562 ASN cc_start: 0.7628 (p0) cc_final: 0.7065 (p0)
REVERT: B  680 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8197 (t0)
REVERT: A  358 ARG cc_start: 0.8572 (ptm160) cc_final: 0.8011 (ptm160)
REVERT: A  433 LYS cc_start: 0.6873 (mmmt) cc_final: 0.6444 (tttt)
REVERT: A  436 ILE cc_start: 0.8298 (mm) cc_final: 0.7858 (mt)
REVERT: A  562 ASN cc_start: 0.7426 (p0) cc_final: 0.6890 (p0)
REVERT: A  563 CYS cc_start: 0.6339 (t) cc_final: 0.5928 (t)
  outliers start: 27
  outliers final: 15
  residues processed: 124
  average time/residue: 0.1442
  time to fit residues: 25.0249
Evaluate side-chains
  108 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
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 A residue  292 LEU
Chi-restraints excluded: chain A residue  320 SER
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  660 LEU
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  693 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 38 optimal weight:    0.0970
   chunk 6 optimal weight:    5.9990
   chunk 15 optimal weight:    0.5980
   chunk 5 optimal weight:    5.9990
   chunk 8 optimal weight:    0.7980
   chunk 29 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.5978

-------------------------------------------------------------------------------
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 = 0.3778 r_free = 0.3778 target = 0.127825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.107651 restraints weight = 12579.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 2.78
r_work: 0.3383 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.3119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6196  Z= 0.125
  Angle     :  0.585   9.502   8498  Z= 0.310
  Chirality :  0.043   0.124   1016
  Planarity :  0.005   0.064   1104
  Dihedral  :  4.382  17.733    962
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 19.10 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.28), residues: 928
  helix:  1.23 (0.20), residues: 650
  sheet:  None (None), residues: 0
  loop : -2.33 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 733 
 HIS   0.001   0.001   HIS A 695 
 PHE   0.027   0.001   PHE A 659 
 TYR   0.008   0.001   TYR B 686 
 ARG   0.006   0.000   ARG A 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03569 (  492)
  hydrogen bonds       : angle       4.01418 ( 1440)
  SS BOND              : bond        0.00036 (    2)
  SS BOND              : angle       1.59181 (    4)
  covalent geometry    : bond        0.00270 ( 6194)
  covalent geometry    : angle       0.58375 ( 8494)

*********************** 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
  126 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 101
  time to evaluate  : 0.641 
Fit side-chains
REVERT: B  358 ARG cc_start: 0.8454 (ptm160) cc_final: 0.8093 (ptm160)
REVERT: B  433 LYS cc_start: 0.6761 (mmmt) cc_final: 0.6129 (tttt)
REVERT: B  436 ILE cc_start: 0.8312 (mm) cc_final: 0.7869 (mt)
REVERT: B  562 ASN cc_start: 0.7527 (p0) cc_final: 0.6993 (p0)
REVERT: B  626 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7033 (t80)
REVERT: B  680 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8512 (t0)
REVERT: A  358 ARG cc_start: 0.8581 (ptm160) cc_final: 0.8124 (ptm160)
REVERT: A  433 LYS cc_start: 0.6843 (mmmt) cc_final: 0.6476 (tttt)
REVERT: A  436 ILE cc_start: 0.8285 (mm) cc_final: 0.7844 (mt)
REVERT: A  562 ASN cc_start: 0.7353 (p0) cc_final: 0.6849 (p0)
REVERT: A  563 CYS cc_start: 0.6314 (t) cc_final: 0.5869 (t)
  outliers start: 25
  outliers final: 17
  residues processed: 117
  average time/residue: 0.1582
  time to fit residues: 25.4241
Evaluate side-chains
  114 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  320 SER
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  444 LEU
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  526 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  660 LEU
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  693 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3763 r_free = 0.3763 target = 0.126845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.106660 restraints weight = 12756.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.82
r_work: 0.3365 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
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   0.054   6196  Z= 0.147
  Angle     :  0.600  10.202   8498  Z= 0.320
  Chirality :  0.043   0.156   1016
  Planarity :  0.004   0.063   1104
  Dihedral  :  4.390  17.180    962
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.94 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  6.44 %
    Allowed  : 18.88 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.28), residues: 928
  helix:  1.09 (0.20), residues: 656
  sheet:  None (None), residues: 0
  loop : -2.32 (0.40), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 733 
 HIS   0.001   0.001   HIS A 695 
 PHE   0.024   0.001   PHE A 659 
 TYR   0.006   0.001   TYR B 739 
 ARG   0.001   0.000   ARG A 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03686 (  492)
  hydrogen bonds       : angle       4.08266 ( 1440)
  SS BOND              : bond        0.00064 (    2)
  SS BOND              : angle       1.39597 (    4)
  covalent geometry    : bond        0.00326 ( 6194)
  covalent geometry    : angle       0.59966 ( 8494)

*********************** 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
  124 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 94
  time to evaluate  : 0.671 
Fit side-chains
REVERT: B  296 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8254 (mtm)
REVERT: B  358 ARG cc_start: 0.8473 (ptm160) cc_final: 0.8140 (ptm160)
REVERT: B  433 LYS cc_start: 0.6957 (mmmt) cc_final: 0.6309 (tttt)
REVERT: B  436 ILE cc_start: 0.8312 (mm) cc_final: 0.7861 (mt)
REVERT: B  562 ASN cc_start: 0.7512 (p0) cc_final: 0.6967 (p0)
REVERT: B  626 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7115 (t80)
REVERT: A  358 ARG cc_start: 0.8615 (ptm160) cc_final: 0.8178 (ptm160)
REVERT: A  433 LYS cc_start: 0.6816 (mmmt) cc_final: 0.6523 (tttt)
REVERT: A  436 ILE cc_start: 0.8305 (mm) cc_final: 0.7861 (mt)
REVERT: A  562 ASN cc_start: 0.7350 (p0) cc_final: 0.6861 (p0)
REVERT: A  563 CYS cc_start: 0.6479 (t) cc_final: 0.6275 (t)
REVERT: A  626 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7132 (t80)
REVERT: A  679 SER cc_start: 0.9539 (OUTLIER) cc_final: 0.9060 (p)
  outliers start: 30
  outliers final: 18
  residues processed: 118
  average time/residue: 0.1648
  time to fit residues: 27.4731
Evaluate side-chains
  114 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  296 MET
Chi-restraints excluded: chain B residue  320 SER
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  693 VAL
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  320 SER
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 85 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.3749 r_free = 0.3749 target = 0.125686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.105424 restraints weight = 12802.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 2.78
r_work: 0.3351 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.3222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   6196  Z= 0.164
  Angle     :  0.616  10.467   8498  Z= 0.330
  Chirality :  0.044   0.184   1016
  Planarity :  0.005   0.063   1104
  Dihedral  :  4.489  17.728    962
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.94 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 19.31 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.28), residues: 928
  helix:  1.05 (0.20), residues: 656
  sheet:  None (None), residues: 0
  loop : -2.34 (0.40), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 733 
 HIS   0.001   0.001   HIS A 695 
 PHE   0.027   0.001   PHE A 659 
 TYR   0.010   0.001   TYR B 686 
 ARG   0.007   0.001   ARG A 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03782 (  492)
  hydrogen bonds       : angle       4.14728 ( 1440)
  SS BOND              : bond        0.00297 (    2)
  SS BOND              : angle       1.70831 (    4)
  covalent geometry    : bond        0.00371 ( 6194)
  covalent geometry    : angle       0.61514 ( 8494)

*********************** 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
  124 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 0.615 
Fit side-chains
REVERT: B  296 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8176 (mtm)
REVERT: B  358 ARG cc_start: 0.8517 (ptm160) cc_final: 0.8199 (ptm160)
REVERT: B  433 LYS cc_start: 0.6942 (mmmt) cc_final: 0.6400 (tttt)
REVERT: B  436 ILE cc_start: 0.8373 (mm) cc_final: 0.7928 (mt)
REVERT: B  562 ASN cc_start: 0.7596 (p0) cc_final: 0.7110 (p0)
REVERT: B  626 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7129 (t80)
REVERT: B  680 ASN cc_start: 0.8821 (t0) cc_final: 0.8306 (t0)
REVERT: A  358 ARG cc_start: 0.8648 (ptm160) cc_final: 0.8220 (ptm160)
REVERT: A  433 LYS cc_start: 0.6835 (mmmt) cc_final: 0.6547 (tttt)
REVERT: A  436 ILE cc_start: 0.8355 (mm) cc_final: 0.7905 (mt)
REVERT: A  562 ASN cc_start: 0.7424 (p0) cc_final: 0.6926 (p0)
REVERT: A  563 CYS cc_start: 0.6762 (t) cc_final: 0.6505 (t)
REVERT: A  626 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7168 (t80)
REVERT: A  679 SER cc_start: 0.9555 (OUTLIER) cc_final: 0.9064 (p)
  outliers start: 28
  outliers final: 19
  residues processed: 118
  average time/residue: 0.1563
  time to fit residues: 25.0969
Evaluate side-chains
  116 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  296 MET
Chi-restraints excluded: chain B residue  320 SER
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  693 VAL
Chi-restraints excluded: chain B residue  751 TYR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  320 SER
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 72 optimal weight:    0.0570
   chunk 32 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 29 optimal weight:    7.9990
   overall best weight:    0.5698

-------------------------------------------------------------------------------
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 = 0.3782 r_free = 0.3782 target = 0.128061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.108028 restraints weight = 12769.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 2.81
r_work: 0.3391 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.3418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6196  Z= 0.128
  Angle     :  0.656  18.110   8498  Z= 0.329
  Chirality :  0.043   0.181   1016
  Planarity :  0.005   0.064   1104
  Dihedral  :  4.345  16.687    962
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 21.67 %
    Favored  : 73.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.28), residues: 928
  helix:  1.14 (0.20), residues: 652
  sheet:  None (None), residues: 0
  loop : -2.32 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 733 
 HIS   0.001   0.001   HIS B 695 
 PHE   0.029   0.001   PHE A 659 
 TYR   0.009   0.001   TYR B 686 
 ARG   0.004   0.000   ARG B 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03620 (  492)
  hydrogen bonds       : angle       4.06514 ( 1440)
  SS BOND              : bond        0.00066 (    2)
  SS BOND              : angle       1.75644 (    4)
  covalent geometry    : bond        0.00274 ( 6194)
  covalent geometry    : angle       0.65504 ( 8494)

*********************** 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: 23
    poor density    : 104
  time to evaluate  : 0.653 
Fit side-chains
REVERT: B  296 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8153 (mtm)
REVERT: B  358 ARG cc_start: 0.8531 (ptm160) cc_final: 0.8219 (ptm160)
REVERT: B  433 LYS cc_start: 0.6825 (mmmt) cc_final: 0.6332 (tttt)
REVERT: B  436 ILE cc_start: 0.8340 (mm) cc_final: 0.7898 (mt)
REVERT: B  562 ASN cc_start: 0.7556 (p0) cc_final: 0.7054 (p0)
REVERT: B  626 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.7128 (t80)
REVERT: B  680 ASN cc_start: 0.8779 (t0) cc_final: 0.8272 (t0)
REVERT: A  294 ARG cc_start: 0.8780 (ttm170) cc_final: 0.8556 (ttm-80)
REVERT: A  358 ARG cc_start: 0.8636 (ptm160) cc_final: 0.8159 (ptm160)
REVERT: A  433 LYS cc_start: 0.6800 (mmmt) cc_final: 0.6529 (tttt)
REVERT: A  436 ILE cc_start: 0.8283 (mm) cc_final: 0.7832 (mt)
REVERT: A  562 ASN cc_start: 0.7422 (p0) cc_final: 0.6954 (p0)
REVERT: A  563 CYS cc_start: 0.6767 (t) cc_final: 0.6476 (t)
REVERT: A  626 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.7160 (t80)
  outliers start: 23
  outliers final: 16
  residues processed: 119
  average time/residue: 0.1811
  time to fit residues: 29.6651
Evaluate side-chains
  117 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  296 MET
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  693 VAL
Chi-restraints excluded: chain B residue  751 TYR
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 87 optimal weight:    0.0970
   chunk 11 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 52 optimal weight:    8.9990
   chunk 26 optimal weight:   10.0000
   chunk 91 optimal weight:    0.0980
   chunk 18 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.5782

-------------------------------------------------------------------------------
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 = 0.3782 r_free = 0.3782 target = 0.128179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.108216 restraints weight = 12913.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 2.84
r_work: 0.3398 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.3583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6196  Z= 0.129
  Angle     :  0.651  17.196   8498  Z= 0.330
  Chirality :  0.043   0.180   1016
  Planarity :  0.005   0.064   1104
  Dihedral  :  4.258  16.366    962
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 22.53 %
    Favored  : 72.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.28), residues: 928
  helix:  1.23 (0.20), residues: 652
  sheet:  None (None), residues: 0
  loop : -2.27 (0.40), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 733 
 HIS   0.001   0.001   HIS B 695 
 PHE   0.029   0.001   PHE A 659 
 TYR   0.014   0.001   TYR A 686 
 ARG   0.004   0.000   ARG B 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03596 (  492)
  hydrogen bonds       : angle       4.00734 ( 1440)
  SS BOND              : bond        0.00051 (    2)
  SS BOND              : angle       1.57394 (    4)
  covalent geometry    : bond        0.00280 ( 6194)
  covalent geometry    : angle       0.65054 ( 8494)

********************** 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
  122 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.706 
Fit side-chains
REVERT: B  364 PHE cc_start: 0.8635 (m-80) cc_final: 0.8425 (m-80)
REVERT: B  433 LYS cc_start: 0.6797 (mmmt) cc_final: 0.6357 (tttt)
REVERT: B  436 ILE cc_start: 0.8351 (mm) cc_final: 0.7902 (mt)
REVERT: B  562 ASN cc_start: 0.7500 (p0) cc_final: 0.6982 (p0)
REVERT: B  626 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.7137 (t80)
REVERT: B  680 ASN cc_start: 0.8796 (t0) cc_final: 0.8335 (t0)
REVERT: A  358 ARG cc_start: 0.8627 (ptm160) cc_final: 0.8171 (ptm160)
REVERT: A  433 LYS cc_start: 0.6947 (mmmt) cc_final: 0.6660 (tttt)
REVERT: A  436 ILE cc_start: 0.8249 (mm) cc_final: 0.7815 (mt)
REVERT: A  562 ASN cc_start: 0.7386 (p0) cc_final: 0.6921 (p0)
REVERT: A  563 CYS cc_start: 0.7104 (t) cc_final: 0.6737 (t)
REVERT: A  626 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7162 (t80)
  outliers start: 21
  outliers final: 17
  residues processed: 115
  average time/residue: 0.1529
  time to fit residues: 24.4690
Evaluate side-chains
  117 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  320 SER
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  693 VAL
Chi-restraints excluded: chain B residue  751 TYR
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0970
   chunk 58 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   chunk 26 optimal weight:   10.0000
   chunk 70 optimal weight:    0.5980
   chunk 74 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3784 r_free = 0.3784 target = 0.128213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.108202 restraints weight = 13010.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 2.81
r_work: 0.3397 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.3633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6196  Z= 0.135
  Angle     :  0.657  18.174   8498  Z= 0.331
  Chirality :  0.043   0.174   1016
  Planarity :  0.005   0.063   1104
  Dihedral  :  4.258  15.801    962
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 22.75 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.28), residues: 928
  helix:  1.17 (0.20), residues: 658
  sheet:  None (None), residues: 0
  loop : -2.26 (0.40), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 733 
 HIS   0.001   0.000   HIS B 695 
 PHE   0.030   0.001   PHE A 659 
 TYR   0.009   0.001   TYR B 686 
 ARG   0.006   0.001   ARG A 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03601 (  492)
  hydrogen bonds       : angle       3.99380 ( 1440)
  SS BOND              : bond        0.00049 (    2)
  SS BOND              : angle       1.48504 (    4)
  covalent geometry    : bond        0.00296 ( 6194)
  covalent geometry    : angle       0.65600 ( 8494)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2711.77 seconds
wall clock time: 48 minutes 28.65 seconds (2908.65 seconds total)