Starting phenix.real_space_refine
on Tue Mar 11 14:30:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6pzt_20537/03_2025/6pzt_20537.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pzt_20537/03_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_20537/03_2025/6pzt_20537.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pzt_20537/03_2025/6pzt_20537.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pzt_20537/03_2025/6pzt_20537.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pzt_20537/03_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-5624/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: 5.61, per 1000 atoms: 0.93
  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: 1.82
  Conformation dependent library (CDL) restraints added in 873.6 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: 0.60
  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: 1.96

  Time building geometry restraints manager: 2.15 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:             1.070
  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:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     20.380
  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:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.990
-------------------------------------------------------------------------------
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  : 0.637 
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: 0.1567
  time to fit residues: 26.6829
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  : 0.659 
-------------------------------------------------------------------------------
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 = 0.105568 restraints weight = 12558.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 2.77
r_work: 0.3351 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
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   0.061   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  : 0.644 
Fit side-chains
REVERT: B  292 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7845 (tt)
REVERT: B  358 ARG cc_start: 0.8307 (ttm170) cc_final: 0.7725 (mtm180)
REVERT: B  433 LYS cc_start: 0.6727 (mmmt) cc_final: 0.6171 (tttt)
REVERT: B  436 ILE cc_start: 0.8447 (mm) cc_final: 0.8026 (mt)
REVERT: B  562 ASN cc_start: 0.7646 (p0) cc_final: 0.7087 (p0)
REVERT: A  358 ARG cc_start: 0.8485 (ttm170) cc_final: 0.7960 (mtm180)
REVERT: A  433 LYS cc_start: 0.6877 (mmmt) cc_final: 0.6483 (tttt)
REVERT: A  435 GLN cc_start: 0.7497 (tt0) cc_final: 0.7289 (tt0)
REVERT: A  436 ILE cc_start: 0.8308 (mm) cc_final: 0.7891 (mt)
REVERT: A  563 CYS cc_start: 0.6837 (t) cc_final: 0.6269 (t)
  outliers start: 20
  outliers final: 8
  residues processed: 128
  average time/residue: 0.1568
  time to fit residues: 27.3244
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  : 0.644 
-------------------------------------------------------------------------------
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:    0.0970
   chunk 49 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   chunk 41 optimal weight:    0.0050
   chunk 20 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.4992

-------------------------------------------------------------------------------
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 = 0.3776 r_free = 0.3776 target = 0.127339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.106852 restraints weight = 12687.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 2.80
r_work: 0.3373 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6194  Z= 0.173
  Angle     :  0.577   5.469   8494  Z= 0.312
  Chirality :  0.042   0.122   1016
  Planarity :  0.005   0.065   1104
  Dihedral  :  4.728  19.079    962
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  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: -0.19 (0.28), residues: 928
  helix:  0.85 (0.20), residues: 658
  sheet:  None (None), residues: 0
  loop : -2.61 (0.39), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 733 
 HIS   0.002   0.001   HIS A 695 
 PHE   0.026   0.001   PHE B 659 
 TYR   0.005   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
  127 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.664 
Fit side-chains
REVERT: B  433 LYS cc_start: 0.6726 (mmmt) cc_final: 0.6135 (tttt)
REVERT: B  436 ILE cc_start: 0.8439 (mm) cc_final: 0.8015 (mt)
REVERT: B  562 ASN cc_start: 0.7594 (p0) cc_final: 0.7177 (m110)
REVERT: B  680 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8270 (t0)
REVERT: A  358 ARG cc_start: 0.8505 (ttm170) cc_final: 0.8298 (ptm160)
REVERT: A  433 LYS cc_start: 0.6903 (mmmt) cc_final: 0.6450 (tttt)
REVERT: A  436 ILE cc_start: 0.8262 (mm) cc_final: 0.7831 (mt)
REVERT: A  562 ASN cc_start: 0.7423 (p0) cc_final: 0.6993 (p0)
REVERT: A  563 CYS cc_start: 0.6266 (t) cc_final: 0.5780 (t)
  outliers start: 22
  outliers final: 6
  residues processed: 120
  average time/residue: 0.1554
  time to fit residues: 25.4763
Evaluate side-chains
  103 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 30 optimal weight:    0.2980
   chunk 47 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 90 optimal weight:    0.0670
   chunk 21 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 73 optimal weight:   20.0000
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.5318

-------------------------------------------------------------------------------
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 = 0.3780 r_free = 0.3780 target = 0.127814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.107529 restraints weight = 12772.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 2.78
r_work: 0.3382 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6194  Z= 0.174
  Angle     :  0.574   6.370   8494  Z= 0.309
  Chirality :  0.042   0.122   1016
  Planarity :  0.005   0.065   1104
  Dihedral  :  4.545  18.653    962
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 19.31 %
    Favored  : 74.89 %
  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:  0.09 (0.28), residues: 928
  helix:  1.03 (0.20), residues: 658
  sheet:  None (None), residues: 0
  loop : -2.40 (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   0.008   0.001   TYR B 686 
 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
  133 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.662 
Fit side-chains
REVERT: B  433 LYS cc_start: 0.6732 (mmmt) cc_final: 0.6224 (tttt)
REVERT: B  436 ILE cc_start: 0.8417 (mm) cc_final: 0.7994 (mt)
REVERT: B  562 ASN cc_start: 0.7618 (p0) cc_final: 0.7020 (p0)
REVERT: B  679 SER cc_start: 0.9514 (OUTLIER) cc_final: 0.9129 (p)
REVERT: B  680 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.8004 (t0)
REVERT: A  358 ARG cc_start: 0.8509 (ttm170) cc_final: 0.8309 (ptm160)
REVERT: A  429 GLU cc_start: 0.8016 (pm20) cc_final: 0.7726 (pm20)
REVERT: A  433 LYS cc_start: 0.6872 (mmmt) cc_final: 0.6434 (tttt)
REVERT: A  436 ILE cc_start: 0.8258 (mm) cc_final: 0.7817 (mt)
REVERT: A  562 ASN cc_start: 0.7347 (p0) cc_final: 0.6815 (p0)
REVERT: A  563 CYS cc_start: 0.6315 (t) cc_final: 0.5924 (t)
REVERT: A  679 SER cc_start: 0.9513 (OUTLIER) cc_final: 0.9162 (p)
  outliers start: 27
  outliers final: 8
  residues processed: 125
  average time/residue: 0.1379
  time to fit residues: 24.3120
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  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  292 LEU
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 11 optimal weight:    0.4980
   chunk 37 optimal weight:    0.6980
   chunk 28 optimal weight:    7.9990
   chunk 12 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 53 optimal weight:    8.9990
   chunk 89 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.127715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.107354 restraints weight = 12717.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 2.79
r_work: 0.3379 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.2909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6194  Z= 0.184
  Angle     :  0.584   7.698   8494  Z= 0.311
  Chirality :  0.042   0.122   1016
  Planarity :  0.004   0.064   1104
  Dihedral  :  4.431  17.635    962
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.30 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 18.67 %
    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:  0.23 (0.28), residues: 928
  helix:  1.16 (0.20), residues: 650
  sheet:  None (None), residues: 0
  loop : -2.36 (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   0.007   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
  121 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 95
  time to evaluate  : 0.594 
Fit side-chains
REVERT: B  294 ARG cc_start: 0.8694 (ttm-80) cc_final: 0.8261 (tpp80)
REVERT: B  433 LYS cc_start: 0.6742 (mmmt) cc_final: 0.6201 (tttt)
REVERT: B  436 ILE cc_start: 0.8392 (mm) cc_final: 0.7962 (mt)
REVERT: B  562 ASN cc_start: 0.7608 (p0) cc_final: 0.7056 (p0)
REVERT: B  680 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8038 (t0)
REVERT: A  358 ARG cc_start: 0.8536 (ttm170) cc_final: 0.8038 (mtm180)
REVERT: A  433 LYS cc_start: 0.6882 (mmmt) cc_final: 0.6426 (tttt)
REVERT: A  436 ILE cc_start: 0.8251 (mm) cc_final: 0.7815 (mt)
REVERT: A  562 ASN cc_start: 0.7330 (p0) cc_final: 0.6819 (p0)
REVERT: A  563 CYS cc_start: 0.6356 (t) cc_final: 0.5936 (t)
REVERT: A  626 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.7014 (t80)
  outliers start: 26
  outliers final: 16
  residues processed: 115
  average time/residue: 0.1385
  time to fit residues: 22.1977
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  : 0.594 
-------------------------------------------------------------------------------
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  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  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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 6 optimal weight:   10.0000
   chunk 15 optimal weight:    0.6980
   chunk 5 optimal weight:    8.9990
   chunk 8 optimal weight:    1.9990
   chunk 29 optimal weight:    0.4980
   chunk 13 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 54 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 = 0.3781 r_free = 0.3781 target = 0.127932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.107685 restraints weight = 12462.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 2.82
r_work: 0.3384 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.3063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6194  Z= 0.187
  Angle     :  0.583   7.531   8494  Z= 0.311
  Chirality :  0.042   0.136   1016
  Planarity :  0.004   0.064   1104
  Dihedral  :  4.361  17.674    962
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  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 (0.28), residues: 928
  helix:  1.22 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -2.22 (0.39), residues: 280

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   0.026   0.001   PHE B 659 
 TYR   0.007   0.001   TYR B 686 
 ARG   0.007   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
  130 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 101
  time to evaluate  : 0.653 
Fit side-chains
REVERT: B  294 ARG cc_start: 0.8750 (ttm-80) cc_final: 0.8323 (tpp80)
REVERT: B  429 GLU cc_start: 0.8095 (pm20) cc_final: 0.7817 (pm20)
REVERT: B  433 LYS cc_start: 0.6772 (mmmt) cc_final: 0.6229 (tttt)
REVERT: B  436 ILE cc_start: 0.8381 (mm) cc_final: 0.7953 (mt)
REVERT: B  562 ASN cc_start: 0.7558 (p0) cc_final: 0.7018 (p0)
REVERT: B  626 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.7032 (t80)
REVERT: B  679 SER cc_start: 0.9558 (OUTLIER) cc_final: 0.9093 (p)
REVERT: B  680 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8090 (t0)
REVERT: A  358 ARG cc_start: 0.8580 (ttm170) cc_final: 0.8105 (mtm180)
REVERT: A  433 LYS cc_start: 0.6838 (mmmt) cc_final: 0.6457 (tttt)
REVERT: A  436 ILE cc_start: 0.8278 (mm) cc_final: 0.7847 (mt)
REVERT: A  562 ASN cc_start: 0.7283 (p0) cc_final: 0.6830 (p0)
REVERT: A  679 SER cc_start: 0.9542 (OUTLIER) cc_final: 0.9092 (p)
  outliers start: 29
  outliers final: 18
  residues processed: 123
  average time/residue: 0.1365
  time to fit residues: 23.7975
Evaluate side-chains
  111 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
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  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  679 SER
Chi-restraints excluded: chain B residue  680 ASN
Chi-restraints excluded: chain B residue  693 VAL
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   chunk 57 optimal weight:    6.9990
   chunk 70 optimal weight:    0.6980
   chunk 61 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3775 r_free = 0.3775 target = 0.127615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.107163 restraints weight = 12679.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 2.86
r_work: 0.3373 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.3187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6194  Z= 0.202
  Angle     :  0.591   8.694   8494  Z= 0.314
  Chirality :  0.043   0.186   1016
  Planarity :  0.004   0.063   1104
  Dihedral  :  4.358  17.627    962
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  6.22 %
    Allowed  : 19.74 %
    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:  0.27 (0.28), residues: 928
  helix:  1.16 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -2.20 (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   0.025   0.001   PHE B 659 
 TYR   0.006   0.001   TYR B 686 
 ARG   0.007   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
  121 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 92
  time to evaluate  : 0.584 
Fit side-chains
REVERT: B  296 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8227 (mtm)
REVERT: B  429 GLU cc_start: 0.8129 (pm20) cc_final: 0.7829 (pm20)
REVERT: B  433 LYS cc_start: 0.6890 (mmmt) cc_final: 0.6370 (tttt)
REVERT: B  436 ILE cc_start: 0.8386 (mm) cc_final: 0.7959 (mt)
REVERT: B  562 ASN cc_start: 0.7563 (p0) cc_final: 0.7057 (p0)
REVERT: B  679 SER cc_start: 0.9548 (OUTLIER) cc_final: 0.9023 (p)
REVERT: B  680 ASN cc_start: 0.8761 (OUTLIER) cc_final: 0.8219 (t0)
REVERT: A  358 ARG cc_start: 0.8602 (ttm170) cc_final: 0.8106 (mtm180)
REVERT: A  433 LYS cc_start: 0.6783 (mmmt) cc_final: 0.6479 (tttt)
REVERT: A  436 ILE cc_start: 0.8313 (mm) cc_final: 0.7869 (mt)
REVERT: A  562 ASN cc_start: 0.7173 (p0) cc_final: 0.6844 (p0)
REVERT: A  626 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7139 (t80)
  outliers start: 29
  outliers final: 19
  residues processed: 114
  average time/residue: 0.1353
  time to fit residues: 21.8713
Evaluate side-chains
  110 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  292 LEU
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  660 LEU
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  679 SER
Chi-restraints excluded: chain B residue  680 ASN
Chi-restraints excluded: chain B residue  693 VAL
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  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  693 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 85 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 48 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 84 optimal weight:    0.0970
   chunk 55 optimal weight:    0.2980
   chunk 14 optimal weight:    0.2980
   chunk 57 optimal weight:    1.9990
   chunk 41 optimal weight:    0.3980
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.3378

-------------------------------------------------------------------------------
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 = 0.3809 r_free = 0.3809 target = 0.130095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.109996 restraints weight = 12653.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 2.78
r_work: 0.3422 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.3456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6194  Z= 0.162
  Angle     :  0.586  10.662   8494  Z= 0.306
  Chirality :  0.042   0.184   1016
  Planarity :  0.004   0.064   1104
  Dihedral  :  4.205  16.466    962
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 21.24 %
    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:  0.30 (0.28), residues: 928
  helix:  1.18 (0.20), residues: 662
  sheet:  None (None), residues: 0
  loop : -2.36 (0.40), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 733 
 HIS   0.001   0.001   HIS B 695 
 PHE   0.026   0.001   PHE A 659 
 TYR   0.011   0.001   TYR A 686 
 ARG   0.001   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
  128 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 103
  time to evaluate  : 0.615 
Fit side-chains
REVERT: B  429 GLU cc_start: 0.8163 (pm20) cc_final: 0.7828 (pm20)
REVERT: B  433 LYS cc_start: 0.6950 (mmmt) cc_final: 0.6409 (tttt)
REVERT: B  436 ILE cc_start: 0.8354 (mm) cc_final: 0.7922 (mt)
REVERT: B  562 ASN cc_start: 0.7559 (p0) cc_final: 0.7059 (p0)
REVERT: B  626 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.7111 (t80)
REVERT: B  679 SER cc_start: 0.9565 (OUTLIER) cc_final: 0.9019 (p)
REVERT: B  680 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8237 (t0)
REVERT: A  294 ARG cc_start: 0.8804 (ttm170) cc_final: 0.8587 (ttm-80)
REVERT: A  358 ARG cc_start: 0.8601 (ttm170) cc_final: 0.8063 (mtm180)
REVERT: A  433 LYS cc_start: 0.6794 (mmmt) cc_final: 0.6479 (tttt)
REVERT: A  436 ILE cc_start: 0.8225 (mm) cc_final: 0.7788 (mt)
REVERT: A  626 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7099 (t80)
REVERT: A  679 SER cc_start: 0.9523 (OUTLIER) cc_final: 0.9013 (p)
  outliers start: 25
  outliers final: 15
  residues processed: 121
  average time/residue: 0.1418
  time to fit residues: 24.0615
Evaluate side-chains
  118 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  292 LEU
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  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  679 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 72 optimal weight:    0.0370
   chunk 32 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 4 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 29 optimal weight:    8.9990
   overall best weight:    0.7058

-------------------------------------------------------------------------------
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 = 0.3791 r_free = 0.3791 target = 0.128839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.108589 restraints weight = 12791.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 2.80
r_work: 0.3399 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.3486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6194  Z= 0.194
  Angle     :  0.612  11.595   8494  Z= 0.318
  Chirality :  0.043   0.176   1016
  Planarity :  0.004   0.064   1104
  Dihedral  :  4.197  16.523    962
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 22.32 %
    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:  0.37 (0.28), residues: 928
  helix:  1.23 (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   0.010   0.001   TRP A 733 
 HIS   0.001   0.001   HIS A 695 
 PHE   0.030   0.001   PHE A 659 
 TYR   0.008   0.001   TYR A 686 
 ARG   0.005   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
  119 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 0.599 
Fit side-chains
REVERT: B  294 ARG cc_start: 0.8833 (tpp80) cc_final: 0.8332 (tpp80)
REVERT: B  429 GLU cc_start: 0.8139 (pm20) cc_final: 0.7806 (pm20)
REVERT: B  433 LYS cc_start: 0.6957 (mmmt) cc_final: 0.6357 (tttt)
REVERT: B  436 ILE cc_start: 0.8324 (mm) cc_final: 0.7893 (mt)
REVERT: B  562 ASN cc_start: 0.7579 (p0) cc_final: 0.7073 (p0)
REVERT: B  626 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.7119 (t80)
REVERT: B  679 SER cc_start: 0.9562 (OUTLIER) cc_final: 0.9027 (p)
REVERT: B  680 ASN cc_start: 0.8761 (OUTLIER) cc_final: 0.8211 (t0)
REVERT: A  294 ARG cc_start: 0.8799 (ttm170) cc_final: 0.8579 (ttm-80)
REVERT: A  358 ARG cc_start: 0.8594 (ttm170) cc_final: 0.8061 (mtm180)
REVERT: A  433 LYS cc_start: 0.6773 (mmmt) cc_final: 0.6499 (tttt)
REVERT: A  436 ILE cc_start: 0.8251 (mm) cc_final: 0.7821 (mt)
REVERT: A  626 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.7131 (t80)
REVERT: A  679 SER cc_start: 0.9519 (OUTLIER) cc_final: 0.9025 (p)
  outliers start: 24
  outliers final: 15
  residues processed: 112
  average time/residue: 0.1399
  time to fit residues: 21.8495
Evaluate side-chains
  114 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  292 LEU
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 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 87 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   chunk 72 optimal weight:    8.9990
   chunk 71 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 91 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 398 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.124877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.104515 restraints weight = 12979.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 2.80
r_work: 0.3341 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.3376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   6194  Z= 0.288
  Angle     :  0.660  11.775   8494  Z= 0.348
  Chirality :  0.045   0.165   1016
  Planarity :  0.005   0.063   1104
  Dihedral  :  4.503  16.571    962
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.62 %
    Favored  : 91.38 %
  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:  0.11 (0.28), residues: 928
  helix:  1.01 (0.20), residues: 656
  sheet:  None (None), residues: 0
  loop : -2.28 (0.41), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 430 
 HIS   0.001   0.000   HIS B 695 
 PHE   0.032   0.002   PHE A 659 
 TYR   0.007   0.001   TYR A 686 
 ARG   0.005   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
  117 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 91
  time to evaluate  : 0.678 
Fit side-chains
REVERT: B  294 ARG cc_start: 0.8924 (tpp80) cc_final: 0.8550 (tpp80)
REVERT: B  358 ARG cc_start: 0.8590 (ptm160) cc_final: 0.8268 (ptm160)
REVERT: B  429 GLU cc_start: 0.8128 (pm20) cc_final: 0.7798 (pm20)
REVERT: B  433 LYS cc_start: 0.6979 (mmmt) cc_final: 0.6474 (tttt)
REVERT: B  436 ILE cc_start: 0.8397 (mm) cc_final: 0.7954 (mt)
REVERT: B  562 ASN cc_start: 0.7562 (p0) cc_final: 0.7100 (p0)
REVERT: B  679 SER cc_start: 0.9583 (OUTLIER) cc_final: 0.9013 (p)
REVERT: A  358 ARG cc_start: 0.8582 (ttm170) cc_final: 0.8055 (mtm180)
REVERT: A  433 LYS cc_start: 0.6992 (mmmt) cc_final: 0.6683 (tttt)
REVERT: A  436 ILE cc_start: 0.8315 (mm) cc_final: 0.7861 (mt)
REVERT: A  562 ASN cc_start: 0.7271 (p0) cc_final: 0.6922 (p0)
REVERT: A  626 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.7177 (t80)
  outliers start: 26
  outliers final: 18
  residues processed: 112
  average time/residue: 0.1566
  time to fit residues: 24.0813
Evaluate side-chains
  112 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  543 CYS
Chi-restraints excluded: chain B residue  584 TYR
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  660 LEU
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  679 SER
Chi-restraints excluded: chain B residue  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  679 SER
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:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   chunk 87 optimal weight:    0.0060
   chunk 58 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 74 optimal weight:   10.0000
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.7198

-------------------------------------------------------------------------------
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 = 0.3775 r_free = 0.3775 target = 0.127573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.107320 restraints weight = 12982.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 2.83
r_work: 0.3382 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.3605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6194  Z= 0.201
  Angle     :  0.637  10.919   8494  Z= 0.329
  Chirality :  0.044   0.177   1016
  Planarity :  0.005   0.064   1104
  Dihedral  :  4.356  16.689    962
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 22.32 %
    Favored  : 72.75 %
  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:  0.18 (0.28), residues: 928
  helix:  1.07 (0.20), residues: 658
  sheet:  None (None), residues: 0
  loop : -2.29 (0.40), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 733 
 HIS   0.002   0.001   HIS B 695 
 PHE   0.028   0.001   PHE A 659 
 TYR   0.008   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: 2570.61 seconds
wall clock time: 44 minutes 45.47 seconds (2685.47 seconds total)