Starting phenix.real_space_refine
on Wed Sep 17 07:26:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zyn_60573/09_2025/8zyn_60573.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zyn_60573/09_2025/8zyn_60573.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zyn_60573/09_2025/8zyn_60573.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zyn_60573/09_2025/8zyn_60573.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zyn_60573/09_2025/8zyn_60573.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zyn_60573/09_2025/8zyn_60573.map"
  }
  resolution = 3.27
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.051
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      32      5.16       5
     C    4462      2.51       5
     N    1066      2.21       5
     O    1080      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6640
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1658
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1658
          Classifications: {'peptide': 210}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 6, 'TRANS': 203}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 6
    Chain: "B"
      Number of atoms: 1662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1662
          Classifications: {'peptide': 210}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 6, 'TRANS': 203}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 6
    Chain: "C"
      Number of atoms: 1662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1662
          Classifications: {'peptide': 210}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 6, 'TRANS': 203}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 6
    Chain: "D"
      Number of atoms: 1658
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1658
          Classifications: {'peptide': 210}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 6, 'TRANS': 203}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 6
  Time building chain proxies: 2.05, per 1000 atoms: 0.31
  Number of scatterers: 6640
  At special positions: 0
  Unit cell: (92.13, 92.13, 73.87, 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      32     16.00
     O    1080      8.00
     N    1066      7.00
     C    4462      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.59
  Conformation dependent library (CDL) restraints added in 378.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1568

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 0 sheets defined
      82.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 409 through 431
      Proline residue:  A 426  - end of helix
    Processing helix  chain 'A' and resid 453 through 471
      removed outlier: 3.851A  pdb=" N   PHE A 471 " --> pdb=" O   ILE A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 495
      removed outlier: 4.329A  pdb=" N   HIS A 492 " --> pdb=" O   ARG A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 506
    Processing helix  chain 'A' and resid 520 through 531
      removed outlier: 3.576A  pdb=" N   LEU A 523 " --> pdb=" O   LEU A 520 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LEU A 524 " --> pdb=" O   ILE A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 538
      removed outlier: 3.645A  pdb=" N   ALA A 536 " --> pdb=" O   LEU A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 543
      removed outlier: 3.645A  pdb=" N   TYR A 542 " --> pdb=" O   LYS A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 576
    Processing helix  chain 'A' and resid 584 through 593
    Processing helix  chain 'A' and resid 606 through 623
    Processing helix  chain 'A' and resid 634 through 665
      removed outlier: 3.802A  pdb=" N   ALA A 653 " --> pdb=" O   SER A 649 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 408 through 431
      Proline residue:  B 426  - end of helix
    Processing helix  chain 'B' and resid 453 through 471
      removed outlier: 4.045A  pdb=" N   PHE B 471 " --> pdb=" O   ILE B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 488 through 495
      removed outlier: 3.931A  pdb=" N   HIS B 492 " --> pdb=" O   ARG B 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 497 through 506
      removed outlier: 4.345A  pdb=" N   VAL B 503 " --> pdb=" O   LEU B 499 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 521 through 525
    Processing helix  chain 'B' and resid 526 through 531
    Processing helix  chain 'B' and resid 532 through 537
    Processing helix  chain 'B' and resid 546 through 574
      removed outlier: 3.679A  pdb=" N   LEU B 550 " --> pdb=" O   GLY B 546 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 584 through 594
    Processing helix  chain 'B' and resid 606 through 623
    Processing helix  chain 'B' and resid 634 through 664
      removed outlier: 3.822A  pdb=" N   GLN B 664 " --> pdb=" O   SER B 660 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 408 through 432
      removed outlier: 3.791A  pdb=" N   TRP C 412 " --> pdb=" O   ALA C 408 " (cutoff:3.500A)
      Proline residue:  C 426  - end of helix
    Processing helix  chain 'C' and resid 453 through 470
    Processing helix  chain 'C' and resid 488 through 496
      removed outlier: 4.103A  pdb=" N   HIS C 492 " --> pdb=" O   ARG C 488 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 497 through 506
      removed outlier: 4.012A  pdb=" N   VAL C 503 " --> pdb=" O   LEU C 499 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 520 through 537
      removed outlier: 3.697A  pdb=" N   THR C 526 " --> pdb=" O   LEU C 523 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   VAL C 533 " --> pdb=" O   LEU C 530 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ARG C 537 " --> pdb=" O   ARG C 534 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 538 through 543
    Processing helix  chain 'C' and resid 545 through 575
      removed outlier: 3.679A  pdb=" N   GLU C 575 " --> pdb=" O   ILE C 571 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 584 through 593
    Processing helix  chain 'C' and resid 606 through 624
    Processing helix  chain 'C' and resid 634 through 665
      removed outlier: 3.809A  pdb=" N   GLN C 664 " --> pdb=" O   SER C 660 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 408 through 431
      Proline residue:  D 426  - end of helix
    Processing helix  chain 'D' and resid 453 through 470
    Processing helix  chain 'D' and resid 488 through 495
      removed outlier: 4.174A  pdb=" N   HIS D 492 " --> pdb=" O   ARG D 488 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 497 through 504
      removed outlier: 3.513A  pdb=" N   ASP D 501 " --> pdb=" O   TRP D 497 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 521 through 531
      removed outlier: 3.745A  pdb=" N   LEU D 524 " --> pdb=" O   ILE D 521 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   LYS D 525 " --> pdb=" O   GLY D 522 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 532 through 537
      removed outlier: 3.533A  pdb=" N   ALA D 536 " --> pdb=" O   LEU D 532 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 538 through 543
    Processing helix  chain 'D' and resid 545 through 576
    Processing helix  chain 'D' and resid 584 through 593
      removed outlier: 3.549A  pdb=" N   ASN D 588 " --> pdb=" O   GLY D 584 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 606 through 624
    Processing helix  chain 'D' and resid 634 through 664
      removed outlier: 4.500A  pdb=" N   GLN D 664 " --> pdb=" O   SER D 660 " (cutoff:3.500A)

    487 hydrogen bonds defined for protein.
    1377 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: 1.04

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1939
        1.34 -     1.46: 1274
        1.46 -     1.57: 3535
        1.57 -     1.69: 0
        1.69 -     1.81: 52
  Bond restraints: 6800
  Sorted by residual:
  bond pdb=" N   PHE C 508 "
       pdb=" CA  PHE C 508 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.16e-02 7.43e+03 7.07e+00
  bond pdb=" N   ASP C 509 "
       pdb=" CA  ASP C 509 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.23e-02 6.61e+03 6.59e+00
  bond pdb=" N   LEU C 510 "
       pdb=" CA  LEU C 510 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 1.90e-02 2.77e+03 2.39e+00
  bond pdb=" C   ASP C 509 "
       pdb=" O   ASP C 509 "
    ideal  model  delta    sigma   weight residual
    1.234  1.252 -0.018 1.19e-02 7.06e+03 2.23e+00
  bond pdb=" CB  ARG C 582 "
       pdb=" CG  ARG C 582 "
    ideal  model  delta    sigma   weight residual
    1.520  1.557 -0.037 3.00e-02 1.11e+03 1.49e+00
  ... (remaining 6795 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 9056
        1.57 -     3.14: 118
        3.14 -     4.71: 34
        4.71 -     6.28: 14
        6.28 -     7.85: 6
  Bond angle restraints: 9228
  Sorted by residual:
  angle pdb=" N   PHE C 508 "
        pdb=" CA  PHE C 508 "
        pdb=" C   PHE C 508 "
      ideal   model   delta    sigma   weight residual
     112.59  107.75    4.84 1.22e+00 6.72e-01 1.57e+01
  angle pdb=" CA  ARG C 582 "
        pdb=" CB  ARG C 582 "
        pdb=" CG  ARG C 582 "
      ideal   model   delta    sigma   weight residual
     114.10  120.36   -6.26 2.00e+00 2.50e-01 9.79e+00
  angle pdb=" CB  ARG D 665 "
        pdb=" CG  ARG D 665 "
        pdb=" CD  ARG D 665 "
      ideal   model   delta    sigma   weight residual
     111.30  118.48   -7.18 2.30e+00 1.89e-01 9.73e+00
  angle pdb=" CB  ARG C 582 "
        pdb=" CG  ARG C 582 "
        pdb=" CD  ARG C 582 "
      ideal   model   delta    sigma   weight residual
     111.30  118.04   -6.74 2.30e+00 1.89e-01 8.59e+00
  angle pdb=" CG  ARG C 582 "
        pdb=" CD  ARG C 582 "
        pdb=" NE  ARG C 582 "
      ideal   model   delta    sigma   weight residual
     112.00  118.24   -6.24 2.20e+00 2.07e-01 8.04e+00
  ... (remaining 9223 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.51: 3255
       14.51 -    29.01: 439
       29.01 -    43.52: 153
       43.52 -    58.03: 32
       58.03 -    72.53: 5
  Dihedral angle restraints: 3884
    sinusoidal: 1460
      harmonic: 2424
  Sorted by residual:
  dihedral pdb=" CB  MET A 645 "
           pdb=" CG  MET A 645 "
           pdb=" SD  MET A 645 "
           pdb=" CE  MET A 645 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -120.73  -59.27     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CB  LYS D 538 "
           pdb=" CG  LYS D 538 "
           pdb=" CD  LYS D 538 "
           pdb=" CE  LYS D 538 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  121.19   58.81     3      1.50e+01 4.44e-03 9.47e+00
  dihedral pdb=" N   LEU C 550 "
           pdb=" CA  LEU C 550 "
           pdb=" CB  LEU C 550 "
           pdb=" CG  LEU C 550 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.67   58.67     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 3881 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 723
       0.032 -    0.064: 264
       0.064 -    0.096: 85
       0.096 -    0.129: 17
       0.129 -    0.161: 3
  Chirality restraints: 1092
  Sorted by residual:
  chirality pdb=" CA  THR B 425 "
            pdb=" N   THR B 425 "
            pdb=" C   THR B 425 "
            pdb=" CB  THR B 425 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.37    0.16 2.00e-01 2.50e+01 6.46e-01
  chirality pdb=" CA  PHE A 656 "
            pdb=" N   PHE A 656 "
            pdb=" C   PHE A 656 "
            pdb=" CB  PHE A 656 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.83e-01
  chirality pdb=" CA  PHE B 656 "
            pdb=" N   PHE B 656 "
            pdb=" C   PHE B 656 "
            pdb=" CB  PHE B 656 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.62e-01
  ... (remaining 1089 not shown)

  Planarity restraints: 1088
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 595 "    0.028 5.00e-02 4.00e+02   4.26e-02 2.91e+00
        pdb=" N   PRO B 596 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B 596 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 596 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 425 "    0.018 5.00e-02 4.00e+02   2.75e-02 1.21e+00
        pdb=" N   PRO B 426 "   -0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO B 426 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B 426 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 656 "   -0.005 2.00e-02 2.50e+03   1.03e-02 1.07e+00
        pdb=" C   PHE B 656 "    0.018 2.00e-02 2.50e+03
        pdb=" O   PHE B 656 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   GLY B 657 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1085 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1627
        2.79 -     3.31: 6515
        3.31 -     3.84: 10995
        3.84 -     4.37: 12103
        4.37 -     4.90: 21322
  Nonbonded interactions: 52562
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 466 "
            pdb=" NH1 ARG A 534 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" OH  TYR C 420 "
            pdb=" OD1 ASP C 456 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OE1 GLN D 576 "
            pdb=" NE2 HIS D 587 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" OD2 ASP C 466 "
            pdb=" NH2 ARG C 534 "
     model   vdw
     2.309 3.120
  nonbonded pdb=" O   LEU B 523 "
            pdb=" OG1 THR B 526 "
     model   vdw
     2.310 3.040
  ... (remaining 52557 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 407 through 494 or (resid 495 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 496 through 665))
  selection = (chain 'C' and (resid 407 through 494 or (resid 495 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 496 through 665))
  selection = chain 'D'
}

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:             3.800
  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:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.820
  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:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
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      :  0.003   0.037   6800  Z= 0.134
  Angle     :  0.555   7.853   9228  Z= 0.283
  Chirality :  0.037   0.161   1092
  Planarity :  0.003   0.043   1088
  Dihedral  : 15.249  72.533   2316
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 24.78 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.30), residues: 792
  helix:  0.93 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.54 (0.61), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 665 
 TYR   0.013   0.001   TYR C 616 
 PHE   0.017   0.001   PHE C 656 
 TRP   0.014   0.001   TRP D 568 
 HIS   0.004   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6800)
  covalent geometry    : angle       0.55504 ( 9228)
  hydrogen bonds       : bond        0.13423 (  487)
  hydrogen bonds       : angle       4.32624 ( 1377)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 0.234 
Fit side-chains
REVERT: B  591 ASP cc_start: 0.8543 (t0) cc_final: 0.8188 (t0)
REVERT: B  596 PRO cc_start: 0.7915 (Cg_exo) cc_final: 0.7613 (Cg_endo)
REVERT: C  461 ILE cc_start: 0.8507 (mm) cc_final: 0.8170 (mt)
REVERT: C  462 MET cc_start: 0.8597 (mpp) cc_final: 0.7738 (mpp)
REVERT: C  493 TYR cc_start: 0.7474 (t80) cc_final: 0.6855 (t80)
REVERT: C  624 SER cc_start: 0.8265 (p) cc_final: 0.7798 (m)
REVERT: D  582 ARG cc_start: 0.6070 (mmp80) cc_final: 0.5421 (mmp80)
  outliers start: 6
  outliers final: 3
  residues processed: 112
  average time/residue: 0.1050
  time to fit residues: 14.7174
Evaluate side-chains
  109 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 106
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain D residue  650 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
D 573 ASN
D 576 GLN
D 588 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.184706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.125067 restraints weight = 8274.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 1.86
r_work: 0.3211 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.0943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6800  Z= 0.176
  Angle     :  0.554   7.030   9228  Z= 0.291
  Chirality :  0.040   0.172   1092
  Planarity :  0.004   0.039   1088
  Dihedral  :  4.082  34.052    893
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 22.62 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.31), residues: 792
  helix:  0.95 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.13 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 528 
 TYR   0.017   0.002   TYR C 616 
 PHE   0.021   0.001   PHE B 656 
 TRP   0.013   0.001   TRP A 568 
 HIS   0.003   0.001   HIS B 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 6800)
  covalent geometry    : angle       0.55432 ( 9228)
  hydrogen bonds       : bond        0.04412 (  487)
  hydrogen bonds       : angle       4.02171 ( 1377)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 114
  time to evaluate  : 0.248 
Fit side-chains
REVERT: B  552 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8381 (mt)
REVERT: B  591 ASP cc_start: 0.8593 (t0) cc_final: 0.8156 (t0)
REVERT: B  596 PRO cc_start: 0.8045 (Cg_exo) cc_final: 0.7775 (Cg_endo)
REVERT: C  461 ILE cc_start: 0.8522 (mm) cc_final: 0.8252 (mt)
REVERT: C  462 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8039 (mpp)
REVERT: C  493 TYR cc_start: 0.7578 (t80) cc_final: 0.6840 (t80)
REVERT: C  624 SER cc_start: 0.8397 (p) cc_final: 0.7919 (m)
  outliers start: 25
  outliers final: 11
  residues processed: 133
  average time/residue: 0.1025
  time to fit residues: 17.3502
Evaluate side-chains
  122 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  665 ARG
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  552 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  462 MET
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  591 ASP
Chi-restraints excluded: chain C residue  606 SER
Chi-restraints excluded: chain C residue  636 SER
Chi-restraints excluded: chain D residue  499 LEU
Chi-restraints excluded: chain D residue  535 VAL
Chi-restraints excluded: chain D residue  655 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    6.9990
   chunk 69 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 26 optimal weight:    8.9990
   chunk 33 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 633 ASN
B 587 HIS
C 633 ASN
D 573 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.182874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.122265 restraints weight = 8294.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 2.06
r_work: 0.3230 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.1436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   6800  Z= 0.217
  Angle     :  0.582   7.147   9228  Z= 0.309
  Chirality :  0.042   0.184   1092
  Planarity :  0.004   0.039   1088
  Dihedral  :  3.951  16.652    888
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 22.05 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.30), residues: 792
  helix:  0.74 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -0.07 (0.60), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 528 
 TYR   0.019   0.002   TYR C 616 
 PHE   0.022   0.002   PHE C 656 
 TRP   0.014   0.001   TRP A 568 
 HIS   0.004   0.001   HIS C 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 ( 6800)
  covalent geometry    : angle       0.58241 ( 9228)
  hydrogen bonds       : bond        0.04476 (  487)
  hydrogen bonds       : angle       4.16056 ( 1377)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 114
  time to evaluate  : 0.241 
Fit side-chains
REVERT: B  428 SER cc_start: 0.8919 (t) cc_final: 0.8379 (p)
REVERT: B  552 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8197 (mp)
REVERT: B  596 PRO cc_start: 0.8049 (Cg_exo) cc_final: 0.7813 (Cg_endo)
REVERT: C  434 LYS cc_start: 0.6387 (mmtm) cc_final: 0.5878 (ptpt)
REVERT: C  461 ILE cc_start: 0.8550 (mm) cc_final: 0.8295 (mt)
REVERT: C  462 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.7932 (mpp)
REVERT: C  493 TYR cc_start: 0.7489 (t80) cc_final: 0.6751 (t80)
REVERT: C  534 ARG cc_start: 0.7707 (ttm170) cc_final: 0.7351 (mmm-85)
  outliers start: 31
  outliers final: 17
  residues processed: 138
  average time/residue: 0.1068
  time to fit residues: 18.5661
Evaluate side-chains
  128 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  606 SER
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  665 ARG
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  521 ILE
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  552 LEU
Chi-restraints excluded: chain B residue  663 ILE
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  462 MET
Chi-restraints excluded: chain C residue  591 ASP
Chi-restraints excluded: chain C residue  606 SER
Chi-restraints excluded: chain C residue  636 SER
Chi-restraints excluded: chain D residue  456 ASP
Chi-restraints excluded: chain D residue  499 LEU
Chi-restraints excluded: chain D residue  535 VAL
Chi-restraints excluded: chain D residue  655 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 55 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 492 HIS
A 633 ASN
C 633 ASN
D 573 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.185727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.127140 restraints weight = 8297.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 2.05
r_work: 0.3301 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3150 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.1378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6800  Z= 0.131
  Angle     :  0.502   6.814   9228  Z= 0.266
  Chirality :  0.038   0.167   1092
  Planarity :  0.004   0.033   1088
  Dihedral  :  3.733  15.819    888
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 22.33 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.31), residues: 792
  helix:  0.93 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.09 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 665 
 TYR   0.015   0.001   TYR C 616 
 PHE   0.020   0.001   PHE B 656 
 TRP   0.014   0.001   TRP D 568 
 HIS   0.003   0.001   HIS C 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6800)
  covalent geometry    : angle       0.50200 ( 9228)
  hydrogen bonds       : bond        0.03987 (  487)
  hydrogen bonds       : angle       3.90115 ( 1377)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 114
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A  528 ARG cc_start: 0.8675 (mtp85) cc_final: 0.8230 (mtt180)
REVERT: B  428 SER cc_start: 0.9025 (t) cc_final: 0.8429 (p)
REVERT: B  534 ARG cc_start: 0.8202 (ttm170) cc_final: 0.7870 (mtt180)
REVERT: B  596 PRO cc_start: 0.8231 (Cg_exo) cc_final: 0.8011 (Cg_endo)
REVERT: C  434 LYS cc_start: 0.6352 (mmtm) cc_final: 0.5807 (ptpt)
REVERT: C  461 ILE cc_start: 0.8542 (mm) cc_final: 0.8300 (mt)
REVERT: C  462 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8104 (mpp)
REVERT: C  493 TYR cc_start: 0.7463 (t80) cc_final: 0.6958 (t80)
REVERT: C  534 ARG cc_start: 0.7659 (ttm170) cc_final: 0.7299 (mmm-85)
REVERT: C  624 SER cc_start: 0.8302 (p) cc_final: 0.7812 (m)
REVERT: D  633 ASN cc_start: 0.9007 (t0) cc_final: 0.8524 (t0)
REVERT: D  650 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7975 (tt)
  outliers start: 25
  outliers final: 12
  residues processed: 130
  average time/residue: 0.1235
  time to fit residues: 20.0101
Evaluate side-chains
  123 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  665 ARG
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  462 MET
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  591 ASP
Chi-restraints excluded: chain C residue  606 SER
Chi-restraints excluded: chain C residue  636 SER
Chi-restraints excluded: chain D residue  497 TRP
Chi-restraints excluded: chain D residue  499 LEU
Chi-restraints excluded: chain D residue  650 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 77 optimal weight:    0.0030
   chunk 13 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   chunk 82 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 27 optimal weight:    0.0980
   chunk 38 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 30 optimal weight:    8.9990
   overall best weight:    0.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 492 HIS
** C 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.187084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.128581 restraints weight = 8344.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 2.10
r_work: 0.3313 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.1397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6800  Z= 0.117
  Angle     :  0.504   7.565   9228  Z= 0.261
  Chirality :  0.037   0.161   1092
  Planarity :  0.003   0.030   1088
  Dihedral  :  3.628  15.545    888
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 23.92 %
    Favored  : 73.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.29 (0.31), residues: 792
  helix:  1.05 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.27 (0.63), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 582 
 TYR   0.014   0.001   TYR C 616 
 PHE   0.019   0.001   PHE B 656 
 TRP   0.013   0.001   TRP D 568 
 HIS   0.003   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 6800)
  covalent geometry    : angle       0.50425 ( 9228)
  hydrogen bonds       : bond        0.03810 (  487)
  hydrogen bonds       : angle       3.81979 ( 1377)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  528 ARG cc_start: 0.8647 (mtp85) cc_final: 0.8236 (mtt180)
REVERT: B  428 SER cc_start: 0.9035 (t) cc_final: 0.8442 (p)
REVERT: B  534 ARG cc_start: 0.8186 (ttm170) cc_final: 0.7854 (mtt180)
REVERT: C  434 LYS cc_start: 0.6311 (mmtm) cc_final: 0.5743 (ptpt)
REVERT: C  461 ILE cc_start: 0.8569 (mm) cc_final: 0.8341 (mt)
REVERT: C  462 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8102 (mpp)
REVERT: C  493 TYR cc_start: 0.7487 (t80) cc_final: 0.6940 (t80)
REVERT: C  624 SER cc_start: 0.8300 (p) cc_final: 0.7799 (m)
REVERT: D  529 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8080 (mp)
REVERT: D  633 ASN cc_start: 0.8991 (t0) cc_final: 0.8552 (t0)
  outliers start: 20
  outliers final: 12
  residues processed: 126
  average time/residue: 0.1102
  time to fit residues: 17.4406
Evaluate side-chains
  125 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  665 ARG
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  591 ASP
Chi-restraints excluded: chain C residue  462 MET
Chi-restraints excluded: chain C residue  591 ASP
Chi-restraints excluded: chain C residue  606 SER
Chi-restraints excluded: chain C residue  636 SER
Chi-restraints excluded: chain D residue  497 TRP
Chi-restraints excluded: chain D residue  499 LEU
Chi-restraints excluded: chain D residue  521 ILE
Chi-restraints excluded: chain D residue  529 LEU
Chi-restraints excluded: chain D residue  650 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 70 optimal weight:    9.9990
   chunk 18 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 57 optimal weight:    0.0770
   overall best weight:    0.7940

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

Flipped N/Q/H residues before XYZ refinement:
A 492 HIS
** C 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 573 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.186468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.126511 restraints weight = 8331.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 1.91
r_work: 0.3312 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3172 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.1503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6800  Z= 0.128
  Angle     :  0.508   6.784   9228  Z= 0.265
  Chirality :  0.038   0.167   1092
  Planarity :  0.003   0.029   1088
  Dihedral  :  3.644  15.664    888
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 23.49 %
    Favored  : 73.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (0.31), residues: 792
  helix:  1.05 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.20 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 537 
 TYR   0.015   0.001   TYR C 616 
 PHE   0.019   0.001   PHE B 656 
 TRP   0.013   0.001   TRP A 568 
 HIS   0.004   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6800)
  covalent geometry    : angle       0.50827 ( 9228)
  hydrogen bonds       : bond        0.03854 (  487)
  hydrogen bonds       : angle       3.81187 ( 1377)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 0.267 
Fit side-chains
REVERT: B  428 SER cc_start: 0.9019 (t) cc_final: 0.8492 (p)
REVERT: B  534 ARG cc_start: 0.8251 (ttm170) cc_final: 0.7883 (mtt180)
REVERT: C  434 LYS cc_start: 0.6302 (mmtm) cc_final: 0.5753 (ptpt)
REVERT: C  461 ILE cc_start: 0.8580 (mm) cc_final: 0.8355 (mt)
REVERT: C  462 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8183 (mpp)
REVERT: C  493 TYR cc_start: 0.7451 (t80) cc_final: 0.6915 (t80)
REVERT: C  624 SER cc_start: 0.8368 (p) cc_final: 0.7841 (m)
  outliers start: 23
  outliers final: 16
  residues processed: 124
  average time/residue: 0.1169
  time to fit residues: 18.0870
Evaluate side-chains
  127 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  665 ARG
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  591 ASP
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  462 MET
Chi-restraints excluded: chain C residue  467 ILE
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  591 ASP
Chi-restraints excluded: chain C residue  606 SER
Chi-restraints excluded: chain C residue  636 SER
Chi-restraints excluded: chain D residue  497 TRP
Chi-restraints excluded: chain D residue  521 ILE
Chi-restraints excluded: chain D residue  573 ASN
Chi-restraints excluded: chain D residue  631 SER
Chi-restraints excluded: chain D residue  650 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 26 optimal weight:   10.0000
   chunk 83 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0050
   chunk 23 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 5 optimal weight:    7.9990
   overall best weight:    0.6996

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

Flipped N/Q/H residues before XYZ refinement:
A 492 HIS
** C 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.186716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.129163 restraints weight = 8198.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 2.23
r_work: 0.3267 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.1553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6800  Z= 0.122
  Angle     :  0.506   6.737   9228  Z= 0.262
  Chirality :  0.038   0.162   1092
  Planarity :  0.003   0.028   1088
  Dihedral  :  3.610  15.618    888
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 22.91 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.31), residues: 792
  helix:  1.08 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.24 (0.63), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 537 
 TYR   0.014   0.001   TYR C 616 
 PHE   0.019   0.001   PHE B 656 
 TRP   0.012   0.001   TRP A 568 
 HIS   0.004   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 6800)
  covalent geometry    : angle       0.50640 ( 9228)
  hydrogen bonds       : bond        0.03797 (  487)
  hydrogen bonds       : angle       3.78292 ( 1377)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.200 
Fit side-chains
REVERT: B  428 SER cc_start: 0.8919 (t) cc_final: 0.8281 (p)
REVERT: B  534 ARG cc_start: 0.8094 (ttm170) cc_final: 0.7712 (mtt180)
REVERT: C  461 ILE cc_start: 0.8571 (mm) cc_final: 0.8344 (mt)
REVERT: C  462 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8042 (mpp)
REVERT: C  493 TYR cc_start: 0.7408 (t80) cc_final: 0.6855 (t80)
REVERT: C  624 SER cc_start: 0.8210 (p) cc_final: 0.7687 (m)
REVERT: D  541 ARG cc_start: 0.8158 (ptm160) cc_final: 0.7934 (ptm160)
  outliers start: 23
  outliers final: 16
  residues processed: 122
  average time/residue: 0.1131
  time to fit residues: 17.2801
Evaluate side-chains
  124 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  665 ARG
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  545 TYR
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  591 ASP
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  462 MET
Chi-restraints excluded: chain C residue  467 ILE
Chi-restraints excluded: chain C residue  591 ASP
Chi-restraints excluded: chain C residue  606 SER
Chi-restraints excluded: chain C residue  636 SER
Chi-restraints excluded: chain D residue  499 LEU
Chi-restraints excluded: chain D residue  631 SER
Chi-restraints excluded: chain D residue  650 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 9 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0570
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.9902

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

Flipped N/Q/H residues before XYZ refinement:
A 492 HIS
** C 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 573 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.185567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.124515 restraints weight = 8249.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 1.96
r_work: 0.3275 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.3133 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.1620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6800  Z= 0.143
  Angle     :  0.534   6.842   9228  Z= 0.275
  Chirality :  0.039   0.167   1092
  Planarity :  0.003   0.029   1088
  Dihedral  :  3.685  15.799    888
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 23.20 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.31), residues: 792
  helix:  1.03 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.22 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 534 
 TYR   0.016   0.001   TYR C 616 
 PHE   0.020   0.001   PHE B 656 
 TRP   0.012   0.001   TRP A 568 
 HIS   0.004   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 6800)
  covalent geometry    : angle       0.53361 ( 9228)
  hydrogen bonds       : bond        0.03923 (  487)
  hydrogen bonds       : angle       3.85433 ( 1377)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.264 
Fit side-chains
REVERT: B  428 SER cc_start: 0.9021 (t) cc_final: 0.8453 (p)
REVERT: B  534 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7763 (mtt180)
REVERT: C  434 LYS cc_start: 0.6300 (mmtm) cc_final: 0.5731 (ptpt)
REVERT: C  461 ILE cc_start: 0.8579 (mm) cc_final: 0.8348 (mt)
REVERT: C  462 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.7990 (mpp)
REVERT: C  493 TYR cc_start: 0.7401 (t80) cc_final: 0.6799 (t80)
REVERT: C  624 SER cc_start: 0.8328 (p) cc_final: 0.7822 (m)
REVERT: D  541 ARG cc_start: 0.8212 (ptm160) cc_final: 0.7975 (ptm160)
REVERT: D  550 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8234 (tt)
  outliers start: 22
  outliers final: 18
  residues processed: 123
  average time/residue: 0.1058
  time to fit residues: 16.5811
Evaluate side-chains
  126 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  665 ARG
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  545 TYR
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  591 ASP
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  462 MET
Chi-restraints excluded: chain C residue  467 ILE
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  591 ASP
Chi-restraints excluded: chain C residue  606 SER
Chi-restraints excluded: chain C residue  636 SER
Chi-restraints excluded: chain D residue  499 LEU
Chi-restraints excluded: chain D residue  521 ILE
Chi-restraints excluded: chain D residue  550 LEU
Chi-restraints excluded: chain D residue  631 SER
Chi-restraints excluded: chain D residue  650 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 49 optimal weight:    7.9990
   chunk 75 optimal weight:    0.5980
   chunk 23 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 9 optimal weight:    9.9990
   chunk 2 optimal weight:    0.3980
   chunk 19 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 492 HIS
** C 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 573 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.186511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.128992 restraints weight = 8252.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 2.21
r_work: 0.3302 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.1635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6800  Z= 0.122
  Angle     :  0.515   6.918   9228  Z= 0.264
  Chirality :  0.038   0.163   1092
  Planarity :  0.003   0.028   1088
  Dihedral  :  3.592  15.582    888
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 23.92 %
    Favored  : 72.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.36 (0.31), residues: 792
  helix:  1.09 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.33 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 534 
 TYR   0.014   0.001   TYR C 616 
 PHE   0.018   0.001   PHE B 656 
 TRP   0.013   0.001   TRP D 568 
 HIS   0.004   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6800)
  covalent geometry    : angle       0.51507 ( 9228)
  hydrogen bonds       : bond        0.03788 (  487)
  hydrogen bonds       : angle       3.79387 ( 1377)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 0.258 
Fit side-chains
REVERT: B  428 SER cc_start: 0.8954 (t) cc_final: 0.8319 (p)
REVERT: B  534 ARG cc_start: 0.8094 (ttm170) cc_final: 0.7719 (mtt180)
REVERT: C  461 ILE cc_start: 0.8574 (mm) cc_final: 0.8354 (mt)
REVERT: C  462 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8066 (mpp)
REVERT: C  493 TYR cc_start: 0.7416 (t80) cc_final: 0.6865 (t80)
REVERT: C  575 GLU cc_start: 0.7025 (tm-30) cc_final: 0.6817 (tm-30)
REVERT: C  624 SER cc_start: 0.8237 (p) cc_final: 0.7701 (m)
REVERT: D  541 ARG cc_start: 0.8287 (ptm160) cc_final: 0.8064 (ptm160)
  outliers start: 22
  outliers final: 20
  residues processed: 119
  average time/residue: 0.1155
  time to fit residues: 17.3037
Evaluate side-chains
  128 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  497 TRP
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  665 ARG
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  545 TYR
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  591 ASP
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  462 MET
Chi-restraints excluded: chain C residue  467 ILE
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  591 ASP
Chi-restraints excluded: chain C residue  606 SER
Chi-restraints excluded: chain C residue  636 SER
Chi-restraints excluded: chain D residue  499 LEU
Chi-restraints excluded: chain D residue  521 ILE
Chi-restraints excluded: chain D residue  573 ASN
Chi-restraints excluded: chain D residue  631 SER
Chi-restraints excluded: chain D residue  650 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 21 optimal weight:    6.9990
   chunk 75 optimal weight:    0.8980
   chunk 48 optimal weight:    5.9990
   chunk 23 optimal weight:    0.4980
   chunk 62 optimal weight:    0.3980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 492 HIS
** C 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 573 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.186010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.125569 restraints weight = 8225.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 1.91
r_work: 0.3304 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.1678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6800  Z= 0.140
  Angle     :  0.551   9.126   9228  Z= 0.279
  Chirality :  0.038   0.166   1092
  Planarity :  0.003   0.029   1088
  Dihedral  :  3.641  15.699    888
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 23.78 %
    Favored  : 72.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.31), residues: 792
  helix:  1.05 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.32 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 534 
 TYR   0.015   0.001   TYR C 616 
 PHE   0.019   0.001   PHE B 656 
 TRP   0.014   0.001   TRP D 568 
 HIS   0.004   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6800)
  covalent geometry    : angle       0.55090 ( 9228)
  hydrogen bonds       : bond        0.03859 (  487)
  hydrogen bonds       : angle       3.84004 ( 1377)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.252 
Fit side-chains
REVERT: B  428 SER cc_start: 0.9062 (t) cc_final: 0.8502 (p)
REVERT: B  534 ARG cc_start: 0.8172 (ttm170) cc_final: 0.7809 (mtt180)
REVERT: C  461 ILE cc_start: 0.8586 (mm) cc_final: 0.8371 (mt)
REVERT: C  462 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8067 (mpp)
REVERT: C  493 TYR cc_start: 0.7443 (t80) cc_final: 0.6838 (t80)
REVERT: C  575 GLU cc_start: 0.7268 (tm-30) cc_final: 0.7056 (tm-30)
REVERT: C  624 SER cc_start: 0.8359 (p) cc_final: 0.7831 (m)
REVERT: D  541 ARG cc_start: 0.8346 (ptm160) cc_final: 0.8106 (ptm160)
  outliers start: 23
  outliers final: 20
  residues processed: 118
  average time/residue: 0.1133
  time to fit residues: 16.9437
Evaluate side-chains
  126 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  497 TRP
Chi-restraints excluded: chain A residue  606 SER
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  665 ARG
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  545 TYR
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  591 ASP
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  462 MET
Chi-restraints excluded: chain C residue  467 ILE
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  591 ASP
Chi-restraints excluded: chain C residue  606 SER
Chi-restraints excluded: chain C residue  636 SER
Chi-restraints excluded: chain D residue  499 LEU
Chi-restraints excluded: chain D residue  521 ILE
Chi-restraints excluded: chain D residue  573 ASN
Chi-restraints excluded: chain D residue  631 SER
Chi-restraints excluded: chain D residue  650 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 57 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 70 optimal weight:    8.9990
   chunk 22 optimal weight:    0.8980
   chunk 63 optimal weight:    6.9990
   chunk 25 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 50 optimal weight:    0.2980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 492 HIS
D 573 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.186951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.129643 restraints weight = 8150.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 2.15
r_work: 0.3307 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.1675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6800  Z= 0.122
  Angle     :  0.528   7.157   9228  Z= 0.269
  Chirality :  0.038   0.162   1092
  Planarity :  0.003   0.028   1088
  Dihedral  :  3.598  15.557    888
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 24.06 %
    Favored  : 72.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.31), residues: 792
  helix:  1.09 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.39 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 534 
 TYR   0.014   0.001   TYR C 616 
 PHE   0.018   0.001   PHE B 656 
 TRP   0.014   0.001   TRP D 568 
 HIS   0.004   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6800)
  covalent geometry    : angle       0.52846 ( 9228)
  hydrogen bonds       : bond        0.03787 (  487)
  hydrogen bonds       : angle       3.79966 ( 1377)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1915.91 seconds
wall clock time: 33 minutes 35.09 seconds (2015.09 seconds total)