Starting phenix.real_space_refine
on Tue Mar 11 20:41:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zyn_60573/03_2025/8zyn_60573.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zyn_60573/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zyn_60573/03_2025/8zyn_60573.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zyn_60573/03_2025/8zyn_60573.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zyn_60573/03_2025/8zyn_60573.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zyn_60573/03_2025/8zyn_60573.cif"
  }
  resolution = 3.27
  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=   0.004 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.70, per 1000 atoms: 0.71
  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: 1.42
  Conformation dependent library (CDL) restraints added in 826.1 milliseconds
  

  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: 0.53
  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: 1.57

  Time building geometry restraints manager: 1.72 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: 0.02
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:             2.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.830
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.030
  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:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.800
-------------------------------------------------------------------------------
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= 0.179
  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 (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:  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
 TRP   0.014   0.001   TRP D 568 
 HIS   0.004   0.001   HIS A 492 
 PHE   0.017   0.001   PHE C 656 
 TYR   0.013   0.001   TYR C 616 
 ARG   0.004   0.000   ARG B 665 

*********************** 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  : 0.742 
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: 0.2448
  time to fit residues: 34.5120
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  : 0.772 
-------------------------------------------------------------------------------
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 70 optimal weight:    2.9990
   chunk 63 optimal weight:    6.9990
   chunk 35 optimal weight:    4.9990
   chunk 21 optimal weight:    6.9990
   chunk 42 optimal weight:    7.9990
   chunk 34 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 633 ASN
D 573 ASN
D 576 GLN
D 588 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.181554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.123514 restraints weight = 8195.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 2.14
r_work: 0.3155 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.1272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.068   6800  Z= 0.463
  Angle     :  0.664   7.438   9228  Z= 0.350
  Chirality :  0.045   0.192   1092
  Planarity :  0.005   0.045   1088
  Dihedral  :  4.485  33.947    893
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 22.62 %
    Favored  : 73.05 %
  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:  0.57 (0.30), residues: 792
  helix:  0.58 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -0.14 (0.59), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D 585 
 HIS   0.005   0.001   HIS B 562 
 PHE   0.025   0.002   PHE B 656 
 TYR   0.021   0.002   TYR C 616 
 ARG   0.003   0.001   ARG C 531 

*********************** 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
  144 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 114
  time to evaluate  : 0.720 
Fit side-chains
REVERT: B  552 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8152 (mp)
REVERT: B  591 ASP cc_start: 0.8558 (t0) cc_final: 0.8132 (t0)
REVERT: B  596 PRO cc_start: 0.8086 (Cg_exo) cc_final: 0.7805 (Cg_endo)
REVERT: C  461 ILE cc_start: 0.8532 (mm) cc_final: 0.8237 (mt)
REVERT: C  462 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.7894 (mpp)
REVERT: C  493 TYR cc_start: 0.7625 (t80) cc_final: 0.6948 (t80)
REVERT: D  417 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7525 (mp)
  outliers start: 30
  outliers final: 17
  residues processed: 138
  average time/residue: 0.2132
  time to fit residues: 37.7192
Evaluate side-chains
  133 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
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  521 ILE
Chi-restraints excluded: chain B residue  535 VAL
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  417 LEU
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  573 ASN
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 7 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 68 optimal weight:   10.0000
   chunk 70 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.4148 r_free = 0.4148 target = 0.185059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 87)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.125744 restraints weight = 8234.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 1.88
r_work: 0.3228 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3085 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.1250

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= 0.212
  Angle     :  0.520   6.825   9228  Z= 0.277
  Chirality :  0.039   0.173   1092
  Planarity :  0.004   0.036   1088
  Dihedral  :  3.960  30.855    891
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 24.06 %
    Favored  : 72.62 %
  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:  0.95 (0.30), residues: 792
  helix:  0.84 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.01 (0.61), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 568 
 HIS   0.004   0.001   HIS C 578 
 PHE   0.020   0.001   PHE B 656 
 TYR   0.016   0.002   TYR C 616 
 ARG   0.002   0.000   ARG A 665 

*********************** 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
  140 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 117
  time to evaluate  : 0.675 
Fit side-chains
REVERT: B  428 SER cc_start: 0.9005 (t) cc_final: 0.8484 (p)
REVERT: B  596 PRO cc_start: 0.8129 (Cg_exo) cc_final: 0.7889 (Cg_endo)
REVERT: C  434 LYS cc_start: 0.6436 (mmtm) cc_final: 0.5867 (ptpt)
REVERT: C  461 ILE cc_start: 0.8534 (mm) cc_final: 0.8284 (mt)
REVERT: C  462 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8147 (mpp)
REVERT: C  493 TYR cc_start: 0.7522 (t80) cc_final: 0.7066 (t80)
REVERT: C  624 SER cc_start: 0.8355 (p) cc_final: 0.7866 (m)
  outliers start: 23
  outliers final: 11
  residues processed: 132
  average time/residue: 0.2261
  time to fit residues: 37.7474
Evaluate side-chains
  120 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
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  665 ARG
Chi-restraints excluded: chain B residue  469 ILE
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  499 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 72 optimal weight:    6.9990
   chunk 57 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 48 optimal weight:    0.7980
   chunk 69 optimal weight:    8.9990
   chunk 9 optimal weight:    0.0570
   chunk 44 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.1102

-------------------------------------------------------------------------------
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**
C 633 ASN
D 573 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.184272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.127747 restraints weight = 8359.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 2.04
r_work: 0.3258 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6800  Z= 0.232
  Angle     :  0.525   6.957   9228  Z= 0.278
  Chirality :  0.039   0.168   1092
  Planarity :  0.004   0.035   1088
  Dihedral  :  3.906  28.506    890
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 22.62 %
    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 (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:  1.00 (0.30), residues: 792
  helix:  0.87 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.08 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 568 
 HIS   0.003   0.001   HIS A 492 
 PHE   0.020   0.001   PHE B 656 
 TYR   0.017   0.002   TYR C 616 
 ARG   0.002   0.000   ARG C 582 

*********************** 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
  143 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 0.706 
Fit side-chains
REVERT: A  528 ARG cc_start: 0.8735 (mtt-85) cc_final: 0.8095 (mtt180)
REVERT: B  428 SER cc_start: 0.8940 (t) cc_final: 0.8411 (p)
REVERT: B  534 ARG cc_start: 0.8211 (ttm170) cc_final: 0.7929 (mtt180)
REVERT: B  552 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8400 (mt)
REVERT: B  596 PRO cc_start: 0.8048 (Cg_exo) cc_final: 0.7831 (Cg_endo)
REVERT: C  434 LYS cc_start: 0.6404 (mmtm) cc_final: 0.5907 (ptpt)
REVERT: C  461 ILE cc_start: 0.8508 (mm) cc_final: 0.8266 (mt)
REVERT: C  462 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8159 (mpp)
REVERT: C  493 TYR cc_start: 0.7524 (t80) cc_final: 0.7081 (t80)
REVERT: C  624 SER cc_start: 0.8295 (p) cc_final: 0.7775 (m)
REVERT: D  650 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7963 (tt)
  outliers start: 26
  outliers final: 14
  residues processed: 133
  average time/residue: 0.2627
  time to fit residues: 44.4974
Evaluate side-chains
  130 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
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  665 ARG
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  533 VAL
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  552 LEU
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  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  650 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 80 optimal weight:    0.0020
   chunk 24 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 42 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.9794

-------------------------------------------------------------------------------
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 = 0.4144 r_free = 0.4144 target = 0.184712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.127342 restraints weight = 8235.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 2.09
r_work: 0.3210 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.1440

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= 0.212
  Angle     :  0.524   6.904   9228  Z= 0.272
  Chirality :  0.039   0.170   1092
  Planarity :  0.004   0.034   1088
  Dihedral  :  3.830  25.148    890
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 23.20 %
    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 (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:  1.06 (0.31), residues: 792
  helix:  0.90 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.08 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 568 
 HIS   0.003   0.001   HIS A 492 
 PHE   0.020   0.001   PHE B 656 
 TYR   0.016   0.001   TYR C 616 
 ARG   0.002   0.000   ARG C 582 

*********************** 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
  139 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 0.637 
Fit side-chains
REVERT: B  428 SER cc_start: 0.8979 (t) cc_final: 0.8385 (p)
REVERT: B  534 ARG cc_start: 0.8165 (ttm170) cc_final: 0.7856 (mtt180)
REVERT: B  624 SER cc_start: 0.8403 (p) cc_final: 0.7946 (m)
REVERT: C  434 LYS cc_start: 0.6422 (mmtm) cc_final: 0.5894 (ptpt)
REVERT: C  461 ILE cc_start: 0.8531 (mm) cc_final: 0.8284 (mt)
REVERT: C  462 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8122 (mpp)
REVERT: C  493 TYR cc_start: 0.7449 (t80) cc_final: 0.6970 (t80)
REVERT: C  624 SER cc_start: 0.8286 (p) cc_final: 0.7799 (m)
REVERT: D  650 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7939 (tt)
  outliers start: 27
  outliers final: 16
  residues processed: 130
  average time/residue: 0.2256
  time to fit residues: 36.9321
Evaluate side-chains
  127 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
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  665 ARG
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  533 VAL
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  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  631 SER
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 3 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 47 optimal weight:   10.0000
   chunk 70 optimal weight:    9.9990
   chunk 30 optimal weight:    3.9990
   chunk 42 optimal weight:    7.9990
   chunk 0 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0870
   overall best weight:    2.0166

-------------------------------------------------------------------------------
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 = 0.4119 r_free = 0.4119 target = 0.182203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.121563 restraints weight = 8272.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 2.15
r_work: 0.3189 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   6800  Z= 0.367
  Angle     :  0.616   7.190   9228  Z= 0.322
  Chirality :  0.042   0.183   1092
  Planarity :  0.005   0.053   1088
  Dihedral  :  4.036  17.117    888
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 22.91 %
    Favored  : 72.62 %
  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:  0.63 (0.30), residues: 792
  helix:  0.64 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -0.22 (0.60), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 568 
 HIS   0.004   0.001   HIS A 492 
 PHE   0.022   0.002   PHE B 656 
 TYR   0.019   0.002   TYR C 616 
 ARG   0.002   0.001   ARG D 537 

*********************** 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
  144 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 113
  time to evaluate  : 0.830 
Fit side-chains
REVERT: B  428 SER cc_start: 0.8934 (t) cc_final: 0.8378 (p)
REVERT: C  434 LYS cc_start: 0.6426 (mmtm) cc_final: 0.5920 (ptpt)
REVERT: C  461 ILE cc_start: 0.8540 (mm) cc_final: 0.8298 (mt)
REVERT: C  462 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.7956 (mpp)
REVERT: C  493 TYR cc_start: 0.7509 (t80) cc_final: 0.7037 (t80)
REVERT: D  650 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8036 (tt)
  outliers start: 31
  outliers final: 24
  residues processed: 131
  average time/residue: 0.2398
  time to fit residues: 40.4662
Evaluate side-chains
  137 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
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  665 ARG
Chi-restraints excluded: chain B residue  461 ILE
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  521 ILE
Chi-restraints excluded: chain B residue  533 VAL
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  591 ASP
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  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  414 ILE
Chi-restraints excluded: chain D residue  456 ASP
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  631 SER
Chi-restraints excluded: chain D residue  650 LEU
Chi-restraints excluded: chain D residue  655 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 7 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0980
   chunk 44 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 4 optimal weight:    8.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4179 r_free = 0.4179 target = 0.186071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.125668 restraints weight = 8179.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 1.87
r_work: 0.3304 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.1652

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= 0.189
  Angle     :  0.526   6.723   9228  Z= 0.274
  Chirality :  0.038   0.170   1092
  Planarity :  0.004   0.035   1088
  Dihedral  :  3.758  16.337    888
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 23.34 %
    Favored  : 73.34 %
  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:  1.02 (0.30), residues: 792
  helix:  0.90 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -0.05 (0.61), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 568 
 HIS   0.004   0.001   HIS A 492 
 PHE   0.019   0.001   PHE B 656 
 TYR   0.015   0.001   TYR C 616 
 ARG   0.002   0.000   ARG A 665 

*********************** 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
  132 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 109
  time to evaluate  : 0.746 
Fit side-chains
REVERT: B  428 SER cc_start: 0.9040 (t) cc_final: 0.8461 (p)
REVERT: B  534 ARG cc_start: 0.8217 (ttm170) cc_final: 0.7823 (mtt180)
REVERT: B  624 SER cc_start: 0.8434 (p) cc_final: 0.7984 (m)
REVERT: C  434 LYS cc_start: 0.6407 (mmtm) cc_final: 0.5814 (ptpt)
REVERT: C  461 ILE cc_start: 0.8569 (mm) cc_final: 0.8328 (mt)
REVERT: C  462 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8125 (mpp)
REVERT: C  493 TYR cc_start: 0.7445 (t80) cc_final: 0.6912 (t80)
REVERT: C  624 SER cc_start: 0.8301 (p) cc_final: 0.7838 (m)
REVERT: D  650 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8004 (tt)
  outliers start: 23
  outliers final: 16
  residues processed: 123
  average time/residue: 0.2394
  time to fit residues: 37.1463
Evaluate side-chains
  126 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
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  521 ILE
Chi-restraints excluded: chain B residue  533 VAL
Chi-restraints excluded: chain B residue  591 ASP
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  414 ILE
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  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 15 optimal weight:    0.7980
   chunk 47 optimal weight:    9.9990
   chunk 26 optimal weight:    0.0980
   chunk 8 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 67 optimal weight:    0.3980
   chunk 41 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.4179 r_free = 0.4179 target = 0.185895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.126678 restraints weight = 8213.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 2.16
r_work: 0.3283 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.1664

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= 0.193
  Angle     :  0.529   6.797   9228  Z= 0.274
  Chirality :  0.038   0.162   1092
  Planarity :  0.003   0.033   1088
  Dihedral  :  3.685  15.927    888
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 24.21 %
    Favored  : 72.77 %
  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:  1.17 (0.31), residues: 792
  helix:  0.98 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.13 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 568 
 HIS   0.004   0.001   HIS A 492 
 PHE   0.019   0.001   PHE B 656 
 TYR   0.015   0.001   TYR C 616 
 ARG   0.004   0.000   ARG A 531 

*********************** 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
  131 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.724 
Fit side-chains
REVERT: B  428 SER cc_start: 0.8957 (t) cc_final: 0.8332 (p)
REVERT: B  534 ARG cc_start: 0.8117 (ttm170) cc_final: 0.7710 (mtt180)
REVERT: B  624 SER cc_start: 0.8368 (p) cc_final: 0.7911 (m)
REVERT: C  434 LYS cc_start: 0.6320 (mmtm) cc_final: 0.5804 (ptpt)
REVERT: C  461 ILE cc_start: 0.8568 (mm) cc_final: 0.8327 (mt)
REVERT: C  462 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8051 (mpp)
REVERT: C  493 TYR cc_start: 0.7497 (t80) cc_final: 0.6960 (t80)
REVERT: C  624 SER cc_start: 0.8250 (p) cc_final: 0.7751 (m)
REVERT: D  650 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7963 (tt)
  outliers start: 21
  outliers final: 17
  residues processed: 121
  average time/residue: 0.2380
  time to fit residues: 36.2893
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  : 0.767 
-------------------------------------------------------------------------------
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  665 ARG
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  533 VAL
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  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  414 ILE
Chi-restraints excluded: chain D residue  497 TRP
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 21 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   chunk 17 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.4178 r_free = 0.4178 target = 0.186022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.125709 restraints weight = 8262.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 1.90
r_work: 0.3320 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3168 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.1698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6800  Z= 0.191
  Angle     :  0.530   6.777   9228  Z= 0.273
  Chirality :  0.038   0.166   1092
  Planarity :  0.004   0.033   1088
  Dihedral  :  3.655  15.772    888
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 24.78 %
    Favored  : 72.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.22 (0.31), residues: 792
  helix:  1.01 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.15 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 568 
 HIS   0.004   0.001   HIS A 492 
 PHE   0.019   0.001   PHE B 656 
 TYR   0.015   0.001   TYR C 616 
 ARG   0.002   0.000   ARG D 537 

*********************** 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
  131 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.676 
Fit side-chains
REVERT: A  531 ARG cc_start: 0.8063 (mtt90) cc_final: 0.7715 (mtt180)
REVERT: B  428 SER cc_start: 0.9060 (t) cc_final: 0.8488 (p)
REVERT: B  534 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7732 (mtt180)
REVERT: B  624 SER cc_start: 0.8426 (p) cc_final: 0.7991 (m)
REVERT: C  434 LYS cc_start: 0.6311 (mmtm) cc_final: 0.5760 (ptpt)
REVERT: C  461 ILE cc_start: 0.8596 (mm) cc_final: 0.8363 (mt)
REVERT: C  462 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8044 (mpp)
REVERT: C  493 TYR cc_start: 0.7473 (t80) cc_final: 0.6923 (t80)
REVERT: C  624 SER cc_start: 0.8315 (p) cc_final: 0.7825 (m)
REVERT: D  541 ARG cc_start: 0.8140 (ptm160) cc_final: 0.7909 (ptm160)
  outliers start: 20
  outliers final: 19
  residues processed: 122
  average time/residue: 0.2378
  time to fit residues: 36.6956
Evaluate side-chains
  129 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
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  665 ARG
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  533 VAL
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  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  414 ILE
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  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 67 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 63 optimal weight:    5.9990
   chunk 81 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0270
   chunk 10 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 6 optimal weight:    9.9990
   overall best weight:    0.8842

-------------------------------------------------------------------------------
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 = 0.4173 r_free = 0.4173 target = 0.185513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.125089 restraints weight = 8314.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 1.90
r_work: 0.3290 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3150 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.1750

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= 0.206
  Angle     :  0.541   6.844   9228  Z= 0.278
  Chirality :  0.038   0.164   1092
  Planarity :  0.004   0.033   1088
  Dihedral  :  3.682  15.812    888
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 24.64 %
    Favored  : 72.19 %
  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:  1.19 (0.31), residues: 792
  helix:  0.99 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.16 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 568 
 HIS   0.004   0.001   HIS A 492 
 PHE   0.019   0.001   PHE B 656 
 TYR   0.016   0.001   TYR C 616 
 ARG   0.003   0.000   ARG D 537 

********************** 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
  133 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 111
  time to evaluate  : 0.737 
Fit side-chains
REVERT: B  428 SER cc_start: 0.9048 (t) cc_final: 0.8452 (p)
REVERT: B  534 ARG cc_start: 0.8160 (ttm170) cc_final: 0.7758 (mtt180)
REVERT: B  624 SER cc_start: 0.8421 (p) cc_final: 0.7971 (m)
REVERT: C  434 LYS cc_start: 0.6265 (mmtm) cc_final: 0.5712 (ptpt)
REVERT: C  461 ILE cc_start: 0.8588 (mm) cc_final: 0.8352 (mt)
REVERT: C  462 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8046 (mpp)
REVERT: C  493 TYR cc_start: 0.7458 (t80) cc_final: 0.6897 (t80)
REVERT: C  575 GLU cc_start: 0.7440 (tm-30) cc_final: 0.7231 (tm-30)
REVERT: C  624 SER cc_start: 0.8320 (p) cc_final: 0.7835 (m)
REVERT: D  541 ARG cc_start: 0.8147 (ptm160) cc_final: 0.7893 (ptm160)
REVERT: D  650 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7946 (tt)
  outliers start: 22
  outliers final: 20
  residues processed: 123
  average time/residue: 0.2421
  time to fit residues: 37.2496
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  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  497 TRP
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  533 VAL
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  414 ILE
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  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 79 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 3 optimal weight:    4.9990
   chunk 51 optimal weight:    0.4980
   chunk 70 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.8186

-------------------------------------------------------------------------------
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 = 0.4177 r_free = 0.4177 target = 0.185894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.125434 restraints weight = 8265.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 1.90
r_work: 0.3303 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.1755

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= 0.198
  Angle     :  0.539   7.140   9228  Z= 0.277
  Chirality :  0.038   0.166   1092
  Planarity :  0.004   0.032   1088
  Dihedral  :  3.651  15.738    888
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 24.64 %
    Favored  : 72.05 %
  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:  1.23 (0.31), residues: 792
  helix:  1.01 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.19 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 568 
 HIS   0.004   0.001   HIS A 492 
 PHE   0.018   0.001   PHE B 656 
 TYR   0.015   0.001   TYR C 616 
 ARG   0.002   0.000   ARG D 537 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3591.03 seconds
wall clock time: 62 minutes 12.62 seconds (3732.62 seconds total)