Starting phenix.real_space_refine
on Tue Feb 11 15:16:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6pzt_20537/02_2025/6pzt_20537.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pzt_20537/02_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_20537/02_2025/6pzt_20537.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pzt_20537/02_2025/6pzt_20537.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pzt_20537/02_2025/6pzt_20537.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pzt_20537/02_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-5592/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: 5.23, per 1000 atoms: 0.86
  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 878.7 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: 0.63
  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: 1.85

  Time building geometry restraints manager: 1.89 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.290
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.450
-------------------------------------------------------------------------------
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   6194  Z= 0.473
  Angle     :  0.746   6.741   8494  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 

*********************** 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  : 1.296 
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: 0.1591
  time to fit residues: 27.0987
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  : 0.615 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 53 optimal weight:    8.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.6596

-------------------------------------------------------------------------------
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 = 0.3760 r_free = 0.3760 target = 0.126114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.105569 restraints weight = 12558.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 2.77
r_work: 0.3350 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.1823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6194  Z= 0.200
  Angle     :  0.623   6.764   8494  Z= 0.338
  Chirality :  0.043   0.133   1016
  Planarity :  0.005   0.062   1104
  Dihedral  :  5.135  22.415    962
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.59 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 14.81 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.70 (0.28), residues: 928
  helix:  0.56 (0.20), residues: 626
  sheet:  None (None), residues: 0
  loop : -2.68 (0.38), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 733 
 HIS   0.001   0.000   HIS A 695 
 PHE   0.011   0.001   PHE B 465 
 TYR   0.011   0.001   TYR A 584 
 ARG   0.006   0.001   ARG B 294 

*********************** 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
  132 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 0.626 
Fit side-chains
REVERT: B  292 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7821 (tt)
REVERT: B  358 ARG cc_start: 0.8298 (ttm170) cc_final: 0.7720 (mtm180)
REVERT: B  433 LYS cc_start: 0.6705 (mmmt) cc_final: 0.6160 (tttt)
REVERT: B  436 ILE cc_start: 0.8441 (mm) cc_final: 0.8019 (mt)
REVERT: B  562 ASN cc_start: 0.7656 (p0) cc_final: 0.7094 (p0)
REVERT: A  358 ARG cc_start: 0.8478 (ttm170) cc_final: 0.7957 (mtm180)
REVERT: A  433 LYS cc_start: 0.6864 (mmmt) cc_final: 0.6475 (tttt)
REVERT: A  435 GLN cc_start: 0.7511 (tt0) cc_final: 0.7300 (tt0)
REVERT: A  436 ILE cc_start: 0.8304 (mm) cc_final: 0.7886 (mt)
REVERT: A  563 CYS cc_start: 0.6856 (t) cc_final: 0.6287 (t)
  outliers start: 20
  outliers final: 8
  residues processed: 128
  average time/residue: 0.1622
  time to fit residues: 28.0101
Evaluate side-chains
  99 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  292 LEU
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:    0.0670
   chunk 49 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0670
   chunk 20 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.4456

-------------------------------------------------------------------------------
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 = 0.3783 r_free = 0.3783 target = 0.127901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.107581 restraints weight = 12607.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 2.78
r_work: 0.3385 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.2443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6194  Z= 0.169
  Angle     :  0.572   5.590   8494  Z= 0.309
  Chirality :  0.043   0.122   1016
  Planarity :  0.005   0.065   1104
  Dihedral  :  4.671  18.964    962
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 17.81 %
    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: -0.08 (0.28), residues: 928
  helix:  0.93 (0.20), residues: 656
  sheet:  None (None), residues: 0
  loop : -2.53 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 704 
 HIS   0.002   0.001   HIS A 695 
 PHE   0.027   0.001   PHE B 659 
 TYR   0.004   0.001   TYR A 751 
 ARG   0.007   0.001   ARG A 294 

*********************** 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
  132 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.563 
Fit side-chains
REVERT: B  433 LYS cc_start: 0.6729 (mmmt) cc_final: 0.6146 (tttt)
REVERT: B  436 ILE cc_start: 0.8473 (mm) cc_final: 0.8053 (mt)
REVERT: B  562 ASN cc_start: 0.7585 (p0) cc_final: 0.7177 (m110)
REVERT: B  680 ASN cc_start: 0.8639 (OUTLIER) cc_final: 0.8318 (t0)
REVERT: A  433 LYS cc_start: 0.6881 (mmmt) cc_final: 0.6444 (tttt)
REVERT: A  436 ILE cc_start: 0.8272 (mm) cc_final: 0.7847 (mt)
REVERT: A  562 ASN cc_start: 0.7409 (p0) cc_final: 0.6973 (p0)
REVERT: A  563 CYS cc_start: 0.6263 (t) cc_final: 0.5768 (t)
REVERT: A  751 TYR cc_start: 0.7323 (OUTLIER) cc_final: 0.6901 (p90)
  outliers start: 22
  outliers final: 6
  residues processed: 123
  average time/residue: 0.1513
  time to fit residues: 25.3523
Evaluate side-chains
  103 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
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
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 50 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 90 optimal weight:    0.0470
   chunk 21 optimal weight:    0.6980
   chunk 49 optimal weight:    0.7980
   chunk 73 optimal weight:   20.0000
   chunk 91 optimal weight:    0.7980
   overall best weight:    0.6478

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.127537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.107143 restraints weight = 12791.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 2.80
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:          0.2773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6194  Z= 0.183
  Angle     :  0.573   6.137   8494  Z= 0.310
  Chirality :  0.042   0.122   1016
  Planarity :  0.004   0.065   1104
  Dihedral  :  4.521  18.679    962
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  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 (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:  0.15 (0.28), residues: 928
  helix:  1.06 (0.20), residues: 658
  sheet:  None (None), residues: 0
  loop : -2.36 (0.40), residues: 270

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   0.035   0.001   PHE A 659 
 TYR   0.006   0.001   TYR B 751 
 ARG   0.007   0.001   ARG A 294 

*********************** 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
  125 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 99
  time to evaluate  : 0.659 
Fit side-chains
REVERT: B  433 LYS cc_start: 0.6731 (mmmt) cc_final: 0.6219 (tttt)
REVERT: B  436 ILE cc_start: 0.8422 (mm) cc_final: 0.8001 (mt)
REVERT: B  562 ASN cc_start: 0.7590 (p0) cc_final: 0.7010 (p0)
REVERT: B  679 SER cc_start: 0.9517 (OUTLIER) cc_final: 0.9129 (p)
REVERT: B  680 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.7959 (t0)
REVERT: A  358 ARG cc_start: 0.8588 (ptm160) cc_final: 0.8075 (ptm160)
REVERT: A  433 LYS cc_start: 0.6884 (mmmt) cc_final: 0.6436 (tttt)
REVERT: A  436 ILE cc_start: 0.8262 (mm) cc_final: 0.7825 (mt)
REVERT: A  562 ASN cc_start: 0.7402 (p0) cc_final: 0.6873 (p0)
REVERT: A  563 CYS cc_start: 0.6356 (t) cc_final: 0.5977 (t)
REVERT: A  679 SER cc_start: 0.9522 (OUTLIER) cc_final: 0.9164 (p)
REVERT: A  751 TYR cc_start: 0.7292 (OUTLIER) cc_final: 0.6844 (p90)
  outliers start: 26
  outliers final: 7
  residues processed: 118
  average time/residue: 0.1442
  time to fit residues: 23.9546
Evaluate side-chains
  103 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
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  679 SER
Chi-restraints excluded: chain B residue  680 ASN
Chi-restraints excluded: chain A residue  292 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
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 23 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0470
   chunk 53 optimal weight:    4.9990
   chunk 89 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.6878

-------------------------------------------------------------------------------
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 = 0.3777 r_free = 0.3777 target = 0.127723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.107416 restraints weight = 12707.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 2.78
r_work: 0.3380 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.2973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6194  Z= 0.183
  Angle     :  0.588   9.581   8494  Z= 0.311
  Chirality :  0.043   0.177   1016
  Planarity :  0.004   0.064   1104
  Dihedral  :  4.427  17.519    962
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  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 (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:  0.29 (0.28), residues: 928
  helix:  1.22 (0.20), residues: 642
  sheet:  None (None), residues: 0
  loop : -2.25 (0.38), residues: 286

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   0.007   0.001   TYR B 751 
 ARG   0.007   0.001   ARG A 294 

*********************** 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: 26
    poor density    : 97
  time to evaluate  : 0.651 
Fit side-chains
REVERT: B  294 ARG cc_start: 0.8716 (ttm-80) cc_final: 0.8273 (tpp80)
REVERT: B  429 GLU cc_start: 0.8085 (pm20) cc_final: 0.7811 (pm20)
REVERT: B  433 LYS cc_start: 0.6757 (mmmt) cc_final: 0.6219 (tttt)
REVERT: B  436 ILE cc_start: 0.8411 (mm) cc_final: 0.7983 (mt)
REVERT: B  562 ASN cc_start: 0.7594 (p0) cc_final: 0.7046 (p0)
REVERT: B  626 PHE cc_start: 0.7702 (OUTLIER) cc_final: 0.7029 (t80)
REVERT: B  680 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8007 (t0)
REVERT: A  292 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7879 (tt)
REVERT: A  358 ARG cc_start: 0.8573 (ptm160) cc_final: 0.8100 (ptm160)
REVERT: A  433 LYS cc_start: 0.6870 (mmmt) cc_final: 0.6428 (tttt)
REVERT: A  436 ILE cc_start: 0.8254 (mm) cc_final: 0.7812 (mt)
REVERT: A  562 ASN cc_start: 0.7362 (p0) cc_final: 0.6852 (p0)
REVERT: A  563 CYS cc_start: 0.6338 (t) cc_final: 0.5911 (t)
REVERT: A  626 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7028 (t80)
REVERT: A  751 TYR cc_start: 0.7286 (OUTLIER) cc_final: 0.6830 (p90)
  outliers start: 26
  outliers final: 13
  residues processed: 115
  average time/residue: 0.1675
  time to fit residues: 26.7511
Evaluate side-chains
  108 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
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  444 LEU
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  543 CYS
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 38 optimal weight:    0.3980
   chunk 6 optimal weight:    8.9990
   chunk 15 optimal weight:    0.6980
   chunk 5 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 13 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9990
   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 = 0.3781 r_free = 0.3781 target = 0.128046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.107798 restraints weight = 12466.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 2.84
r_work: 0.3384 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.3166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6194  Z= 0.179
  Angle     :  0.575   8.038   8494  Z= 0.307
  Chirality :  0.043   0.178   1016
  Planarity :  0.004   0.064   1104
  Dihedral  :  4.339  17.819    962
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  6.22 %
    Allowed  : 17.38 %
    Favored  : 76.39 %
  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:  0.33 (0.29), residues: 928
  helix:  1.22 (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   0.008   0.001   TRP A 733 
 HIS   0.001   0.001   HIS A 695 
 PHE   0.027   0.001   PHE A 659 
 TYR   0.005   0.001   TYR A 533 
 ARG   0.006   0.001   ARG A 294 

*********************** 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: 29
    poor density    : 100
  time to evaluate  : 0.633 
Fit side-chains
REVERT: B  294 ARG cc_start: 0.8729 (ttm-80) cc_final: 0.8299 (tpp80)
REVERT: B  429 GLU cc_start: 0.8109 (pm20) cc_final: 0.7821 (pm20)
REVERT: B  433 LYS cc_start: 0.6775 (mmmt) cc_final: 0.6242 (tttt)
REVERT: B  436 ILE cc_start: 0.8392 (mm) cc_final: 0.7962 (mt)
REVERT: B  562 ASN cc_start: 0.7519 (p0) cc_final: 0.6974 (p0)
REVERT: B  626 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7051 (t80)
REVERT: B  679 SER cc_start: 0.9584 (OUTLIER) cc_final: 0.9112 (p)
REVERT: B  680 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8078 (t0)
REVERT: A  358 ARG cc_start: 0.8580 (ptm160) cc_final: 0.8109 (ptm160)
REVERT: A  433 LYS cc_start: 0.6833 (mmmt) cc_final: 0.6461 (tttt)
REVERT: A  436 ILE cc_start: 0.8275 (mm) cc_final: 0.7841 (mt)
REVERT: A  562 ASN cc_start: 0.7274 (p0) cc_final: 0.6821 (p0)
REVERT: A  626 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7098 (t80)
REVERT: A  679 SER cc_start: 0.9546 (OUTLIER) cc_final: 0.9100 (p)
REVERT: A  751 TYR cc_start: 0.7395 (OUTLIER) cc_final: 0.6849 (p90)
  outliers start: 29
  outliers final: 14
  residues processed: 120
  average time/residue: 0.1391
  time to fit residues: 23.3805
Evaluate side-chains
  109 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
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  679 SER
Chi-restraints excluded: chain B residue  680 ASN
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 16 optimal weight:    0.7980
   chunk 36 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   chunk 57 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9990
   chunk 61 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3779 r_free = 0.3779 target = 0.127924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.107717 restraints weight = 12678.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 2.78
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: 0.7875
moved from start:          0.3291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6194  Z= 0.193
  Angle     :  0.593   9.806   8494  Z= 0.312
  Chirality :  0.043   0.166   1016
  Planarity :  0.004   0.063   1104
  Dihedral  :  4.286  16.800    962
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  6.44 %
    Allowed  : 19.10 %
    Favored  : 74.46 %
  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:  0.35 (0.28), residues: 928
  helix:  1.23 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -2.19 (0.39), residues: 280

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   0.006   0.001   TYR A 468 
 ARG   0.006   0.001   ARG A 294 

*********************** 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
  127 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 97
  time to evaluate  : 0.712 
Fit side-chains
REVERT: B  294 ARG cc_start: 0.8773 (ttm-80) cc_final: 0.8286 (tpp80)
REVERT: B  429 GLU cc_start: 0.8116 (pm20) cc_final: 0.7816 (pm20)
REVERT: B  433 LYS cc_start: 0.6898 (mmmt) cc_final: 0.6389 (tttt)
REVERT: B  436 ILE cc_start: 0.8388 (mm) cc_final: 0.7965 (mt)
REVERT: B  562 ASN cc_start: 0.7549 (p0) cc_final: 0.7045 (p0)
REVERT: B  626 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7123 (t80)
REVERT: B  679 SER cc_start: 0.9591 (OUTLIER) cc_final: 0.9101 (p)
REVERT: B  680 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8217 (t0)
REVERT: A  296 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8295 (mtm)
REVERT: A  358 ARG cc_start: 0.8611 (ptm160) cc_final: 0.8152 (ptm160)
REVERT: A  433 LYS cc_start: 0.6800 (mmmt) cc_final: 0.6494 (tttt)
REVERT: A  436 ILE cc_start: 0.8310 (mm) cc_final: 0.7867 (mt)
REVERT: A  562 ASN cc_start: 0.7160 (p0) cc_final: 0.6836 (p0)
REVERT: A  626 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.7141 (t80)
REVERT: A  679 SER cc_start: 0.9513 (OUTLIER) cc_final: 0.9032 (p)
REVERT: A  751 TYR cc_start: 0.7352 (OUTLIER) cc_final: 0.6839 (p90)
  outliers start: 30
  outliers final: 17
  residues processed: 118
  average time/residue: 0.1549
  time to fit residues: 25.6126
Evaluate side-chains
  113 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
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  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 9 optimal weight:    0.6980
   chunk 85 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 84 optimal weight:    1.9990
   chunk 55 optimal weight:    0.1980
   chunk 14 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   chunk 41 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.128411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.108278 restraints weight = 12662.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 2.76
r_work: 0.3394 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.3420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6194  Z= 0.193
  Angle     :  0.597   9.620   8494  Z= 0.314
  Chirality :  0.043   0.160   1016
  Planarity :  0.004   0.063   1104
  Dihedral  :  4.288  17.979    962
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.30 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 20.82 %
    Favored  : 74.03 %
  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:  0.35 (0.28), residues: 928
  helix:  1.21 (0.20), residues: 650
  sheet:  None (None), residues: 0
  loop : -2.18 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 733 
 HIS   0.001   0.001   HIS B 695 
 PHE   0.029   0.001   PHE A 659 
 TYR   0.011   0.001   TYR A 686 
 ARG   0.003   0.000   ARG B 294 

*********************** 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
  116 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 0.677 
Fit side-chains
REVERT: B  429 GLU cc_start: 0.8126 (pm20) cc_final: 0.7801 (pm20)
REVERT: B  433 LYS cc_start: 0.6922 (mmmt) cc_final: 0.6443 (tttt)
REVERT: B  436 ILE cc_start: 0.8386 (mm) cc_final: 0.7964 (mt)
REVERT: B  562 ASN cc_start: 0.7620 (p0) cc_final: 0.7111 (p0)
REVERT: B  626 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7143 (t80)
REVERT: B  680 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8239 (t0)
REVERT: A  294 ARG cc_start: 0.8831 (ttm170) cc_final: 0.8608 (ttm-80)
REVERT: A  296 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8262 (mtm)
REVERT: A  358 ARG cc_start: 0.8603 (ptm160) cc_final: 0.8121 (ptm160)
REVERT: A  433 LYS cc_start: 0.6773 (mmmt) cc_final: 0.6501 (tttt)
REVERT: A  436 ILE cc_start: 0.8258 (mm) cc_final: 0.7812 (mt)
REVERT: A  562 ASN cc_start: 0.7345 (p0) cc_final: 0.6949 (p0)
REVERT: A  626 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.7133 (t80)
REVERT: A  679 SER cc_start: 0.9529 (OUTLIER) cc_final: 0.9036 (p)
REVERT: A  751 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.6908 (p90)
  outliers start: 24
  outliers final: 15
  residues processed: 110
  average time/residue: 0.1498
  time to fit residues: 22.7881
Evaluate side-chains
  111 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.4980
   chunk 25 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 4 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3788 r_free = 0.3788 target = 0.128674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.108552 restraints weight = 12690.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 2.79
r_work: 0.3399 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.3525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6194  Z= 0.189
  Angle     :  0.606  12.188   8494  Z= 0.316
  Chirality :  0.043   0.158   1016
  Planarity :  0.004   0.063   1104
  Dihedral  :  4.236  16.363    962
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 21.46 %
    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:  0.36 (0.28), residues: 928
  helix:  1.22 (0.20), residues: 650
  sheet:  None (None), residues: 0
  loop : -2.18 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 733 
 HIS   0.001   0.001   HIS B 695 
 PHE   0.028   0.001   PHE A 659 
 TYR   0.009   0.001   TYR A 686 
 ARG   0.008   0.001   ARG B 294 

*********************** 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
  114 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.771 
Fit side-chains
REVERT: B  294 ARG cc_start: 0.8652 (ttm-80) cc_final: 0.8401 (tpp80)
REVERT: B  429 GLU cc_start: 0.8164 (pm20) cc_final: 0.7819 (pm20)
REVERT: B  433 LYS cc_start: 0.6943 (mmmt) cc_final: 0.6396 (tttt)
REVERT: B  436 ILE cc_start: 0.8383 (mm) cc_final: 0.7984 (mt)
REVERT: B  562 ASN cc_start: 0.7572 (p0) cc_final: 0.7070 (p0)
REVERT: B  626 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.7131 (t80)
REVERT: B  680 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8258 (t0)
REVERT: A  294 ARG cc_start: 0.8776 (ttm170) cc_final: 0.8563 (ttm-80)
REVERT: A  296 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8236 (mtm)
REVERT: A  358 ARG cc_start: 0.8608 (ptm160) cc_final: 0.8130 (ptm160)
REVERT: A  433 LYS cc_start: 0.6743 (mmmt) cc_final: 0.6464 (tttt)
REVERT: A  436 ILE cc_start: 0.8245 (mm) cc_final: 0.7810 (mt)
REVERT: A  626 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7143 (t80)
REVERT: A  679 SER cc_start: 0.9520 (OUTLIER) cc_final: 0.9017 (p)
REVERT: A  751 TYR cc_start: 0.7393 (OUTLIER) cc_final: 0.6887 (p90)
  outliers start: 24
  outliers final: 15
  residues processed: 108
  average time/residue: 0.1572
  time to fit residues: 23.6012
Evaluate side-chains
  111 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 B residue  693 VAL
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 72 optimal weight:    8.9990
   chunk 71 optimal weight:    3.9990
   chunk 52 optimal weight:    9.9990
   chunk 26 optimal weight:   10.0000
   chunk 91 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.3774 r_free = 0.3774 target = 0.127696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.107427 restraints weight = 12860.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 2.84
r_work: 0.3378 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.3552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6194  Z= 0.209
  Angle     :  0.616  12.800   8494  Z= 0.322
  Chirality :  0.044   0.155   1016
  Planarity :  0.004   0.063   1104
  Dihedral  :  4.276  16.303    962
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 21.89 %
    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:  0.32 (0.28), residues: 928
  helix:  1.18 (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   0.029   0.001   PHE A 659 
 TYR   0.008   0.001   TYR A 686 
 ARG   0.004   0.001   ARG B 294 

********************** 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
  120 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 94
  time to evaluate  : 0.565 
Fit side-chains
REVERT: B  294 ARG cc_start: 0.8717 (ttm-80) cc_final: 0.8327 (tpp80)
REVERT: B  429 GLU cc_start: 0.8094 (pm20) cc_final: 0.7773 (pm20)
REVERT: B  433 LYS cc_start: 0.6889 (mmmt) cc_final: 0.6434 (tttt)
REVERT: B  435 GLN cc_start: 0.7457 (pt0) cc_final: 0.7110 (tt0)
REVERT: B  436 ILE cc_start: 0.8397 (mm) cc_final: 0.7955 (mt)
REVERT: B  562 ASN cc_start: 0.7516 (p0) cc_final: 0.7026 (p0)
REVERT: B  626 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.7134 (t80)
REVERT: B  680 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8199 (t0)
REVERT: A  296 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8280 (mtm)
REVERT: A  358 ARG cc_start: 0.8597 (ptm160) cc_final: 0.8075 (ptm160)
REVERT: A  433 LYS cc_start: 0.6893 (mmmt) cc_final: 0.6605 (tttt)
REVERT: A  436 ILE cc_start: 0.8271 (mm) cc_final: 0.7830 (mt)
REVERT: A  562 ASN cc_start: 0.7296 (p0) cc_final: 0.6937 (p0)
REVERT: A  626 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.7159 (t80)
REVERT: A  679 SER cc_start: 0.9550 (OUTLIER) cc_final: 0.9057 (p)
REVERT: A  751 TYR cc_start: 0.7354 (OUTLIER) cc_final: 0.6769 (p90)
  outliers start: 26
  outliers final: 16
  residues processed: 112
  average time/residue: 0.1500
  time to fit residues: 23.2629
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  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 87 optimal weight:    0.2980
   chunk 58 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 26 optimal weight:    8.9990
   chunk 70 optimal weight:    0.6980
   chunk 74 optimal weight:   10.0000
   chunk 8 optimal weight:    0.9990
   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 = 0.3754 r_free = 0.3754 target = 0.126201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.105885 restraints weight = 13014.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 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: 0.7897
moved from start:          0.3523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   6194  Z= 0.251
  Angle     :  0.639  13.393   8494  Z= 0.336
  Chirality :  0.044   0.151   1016
  Planarity :  0.004   0.063   1104
  Dihedral  :  4.418  17.254    962
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.94 %
    Favored  : 91.06 %
  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 (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:  0.18 (0.28), residues: 928
  helix:  1.03 (0.20), residues: 664
  sheet:  None (None), residues: 0
  loop : -2.24 (0.41), residues: 264

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 A 686 
 ARG   0.007   0.001   ARG A 294 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2451.55 seconds
wall clock time: 44 minutes 13.59 seconds (2653.59 seconds total)