Starting phenix.real_space_refine
on Tue Feb 11 21:11:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zyn_60573/02_2025/8zyn_60573.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zyn_60573/02_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_60573/02_2025/8zyn_60573.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zyn_60573/02_2025/8zyn_60573.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zyn_60573/02_2025/8zyn_60573.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zyn_60573/02_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-5592/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: 4.90, per 1000 atoms: 0.74
  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: 1.68
  Conformation dependent library (CDL) restraints added in 891.0 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: 0.55
  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: 1.75

  Time building geometry restraints manager: 1.94 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:             5.870
  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:          0.230
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     18.780
  Find NCS groups from input model:        0.270
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.120
-------------------------------------------------------------------------------
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  : 0.673 
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: 0.2548
  time to fit residues: 35.5806
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  : 0.696 
-------------------------------------------------------------------------------
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 = 0.123510 restraints weight = 8195.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 2.14
r_work: 0.3151 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
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  : 0.726 
Fit side-chains
REVERT: B  552 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8157 (mp)
REVERT: B  591 ASP cc_start: 0.8554 (t0) cc_final: 0.8129 (t0)
REVERT: B  596 PRO cc_start: 0.8079 (Cg_exo) cc_final: 0.7797 (Cg_endo)
REVERT: C  461 ILE cc_start: 0.8532 (mm) cc_final: 0.8236 (mt)
REVERT: C  462 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.7906 (mpp)
REVERT: C  493 TYR cc_start: 0.7634 (t80) cc_final: 0.6958 (t80)
REVERT: D  417 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7529 (mp)
  outliers start: 30
  outliers final: 17
  residues processed: 138
  average time/residue: 0.2158
  time to fit residues: 38.0108
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  : 0.688 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 68 optimal weight:   10.0000
   chunk 70 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   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 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 = 0.4153 r_free = 0.4153 target = 0.185433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.126299 restraints weight = 8225.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 1.90
r_work: 0.3251 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.1220

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= 0.196
  Angle     :  0.512   6.783   9228  Z= 0.273
  Chirality :  0.039   0.171   1092
  Planarity :  0.004   0.035   1088
  Dihedral  :  3.918  30.172    891
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 23.63 %
    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:  1.01 (0.30), residues: 792
  helix:  0.88 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.05 (0.62), 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   0.015   0.001   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
  139 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 116
  time to evaluate  : 0.797 
Fit side-chains
REVERT: B  428 SER cc_start: 0.9007 (t) cc_final: 0.8481 (p)
REVERT: B  596 PRO cc_start: 0.8109 (Cg_exo) cc_final: 0.7870 (Cg_endo)
REVERT: B  624 SER cc_start: 0.8473 (p) cc_final: 0.8025 (m)
REVERT: C  461 ILE cc_start: 0.8538 (mm) cc_final: 0.8289 (mt)
REVERT: C  462 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8169 (mpp)
REVERT: C  493 TYR cc_start: 0.7556 (t80) cc_final: 0.7103 (t80)
REVERT: C  624 SER cc_start: 0.8368 (p) cc_final: 0.7898 (m)
  outliers start: 23
  outliers final: 9
  residues processed: 131
  average time/residue: 0.2513
  time to fit residues: 41.9047
Evaluate side-chains
  117 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    7.9990
   chunk 57 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 48 optimal weight:    0.7980
   chunk 69 optimal weight:    0.1980
   chunk 9 optimal weight:    0.0970
   chunk 44 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.5378

-------------------------------------------------------------------------------
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 = 0.4172 r_free = 0.4172 target = 0.187174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.130326 restraints weight = 8328.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 2.03
r_work: 0.3318 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.1279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   6800  Z= 0.159
  Angle     :  0.484   6.753   9228  Z= 0.255
  Chirality :  0.037   0.159   1092
  Planarity :  0.003   0.033   1088
  Dihedral  :  3.679  22.779    890
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  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 (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:  1.32 (0.31), residues: 792
  helix:  1.07 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.31 (0.64), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 568 
 HIS   0.003   0.001   HIS A 492 
 PHE   0.018   0.001   PHE B 656 
 TYR   0.013   0.001   TYR C 616 
 ARG   0.004   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
  140 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 117
  time to evaluate  : 0.688 
Fit side-chains
REVERT: A  528 ARG cc_start: 0.8708 (mtt-85) cc_final: 0.8478 (mtt180)
REVERT: B  428 SER cc_start: 0.8960 (t) cc_final: 0.8383 (p)
REVERT: B  534 ARG cc_start: 0.8161 (ttm170) cc_final: 0.7886 (mtt180)
REVERT: B  552 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8370 (mt)
REVERT: B  624 SER cc_start: 0.8351 (p) cc_final: 0.7931 (m)
REVERT: C  461 ILE cc_start: 0.8546 (mm) cc_final: 0.8319 (mt)
REVERT: C  462 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8168 (mpp)
REVERT: C  493 TYR cc_start: 0.7452 (t80) cc_final: 0.7011 (t80)
REVERT: C  624 SER cc_start: 0.8232 (p) cc_final: 0.7743 (m)
REVERT: D  633 ASN cc_start: 0.8828 (t0) cc_final: 0.8361 (t0)
  outliers start: 23
  outliers final: 12
  residues processed: 131
  average time/residue: 0.2303
  time to fit residues: 38.5490
Evaluate side-chains
  124 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
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  503 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:    0.0770
   chunk 24 optimal weight:    0.7980
   chunk 16 optimal weight:    0.5980
   chunk 42 optimal weight:    7.9990
   chunk 39 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    5.9990
   chunk 54 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0980
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.4738

-------------------------------------------------------------------------------
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 = 0.187877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.129090 restraints weight = 8230.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 1.89
r_work: 0.3316 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.1360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6800  Z= 0.150
  Angle     :  0.491   7.175   9228  Z= 0.254
  Chirality :  0.037   0.159   1092
  Planarity :  0.003   0.031   1088
  Dihedral  :  3.526  15.481    888
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 23.63 %
    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 (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:  1.44 (0.31), residues: 792
  helix:  1.15 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.30 (0.64), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 568 
 HIS   0.004   0.001   HIS A 492 
 PHE   0.018   0.001   PHE B 656 
 TYR   0.013   0.001   TYR C 616 
 ARG   0.003   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
  132 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.698 
Fit side-chains
REVERT: B  428 SER cc_start: 0.9025 (t) cc_final: 0.8486 (p)
REVERT: B  534 ARG cc_start: 0.8221 (ttm170) cc_final: 0.7913 (mtt180)
REVERT: B  624 SER cc_start: 0.8396 (p) cc_final: 0.7984 (m)
REVERT: C  461 ILE cc_start: 0.8560 (mm) cc_final: 0.8340 (mt)
REVERT: C  462 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8162 (mpp)
REVERT: C  493 TYR cc_start: 0.7488 (t80) cc_final: 0.6981 (t80)
REVERT: C  624 SER cc_start: 0.8302 (p) cc_final: 0.7807 (m)
REVERT: D  529 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8024 (mp)
REVERT: D  633 ASN cc_start: 0.8947 (t0) cc_final: 0.8476 (t0)
  outliers start: 18
  outliers final: 9
  residues processed: 122
  average time/residue: 0.2423
  time to fit residues: 37.5225
Evaluate side-chains
  119 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  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 3 optimal weight:    7.9990
   chunk 26 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 47 optimal weight:    9.9990
   chunk 70 optimal weight:    0.5980
   chunk 30 optimal weight:    6.9990
   chunk 42 optimal weight:    7.9990
   chunk 0 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.4189 r_free = 0.4189 target = 0.186931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.127907 restraints weight = 8163.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 2.09
r_work: 0.3305 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.1509

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= 0.190
  Angle     :  0.512   6.809   9228  Z= 0.265
  Chirality :  0.038   0.162   1092
  Planarity :  0.003   0.029   1088
  Dihedral  :  3.592  15.642    888
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 22.91 %
    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:  1.34 (0.31), residues: 792
  helix:  1.08 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.25 (0.63), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 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   0.005   0.000   ARG C 582 

*********************** 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
  134 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 0.671 
Fit side-chains
REVERT: B  428 SER cc_start: 0.9033 (t) cc_final: 0.8491 (p)
REVERT: B  534 ARG cc_start: 0.8181 (ttm170) cc_final: 0.7849 (mtt180)
REVERT: B  624 SER cc_start: 0.8461 (p) cc_final: 0.8047 (m)
REVERT: C  461 ILE cc_start: 0.8578 (mm) cc_final: 0.8352 (mt)
REVERT: C  462 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8103 (mpp)
REVERT: C  493 TYR cc_start: 0.7419 (t80) cc_final: 0.6866 (t80)
REVERT: C  624 SER cc_start: 0.8325 (p) cc_final: 0.7849 (m)
  outliers start: 24
  outliers final: 16
  residues processed: 124
  average time/residue: 0.2655
  time to fit residues: 41.2774
Evaluate side-chains
  126 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  650 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 83 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0770
   chunk 37 optimal weight:    0.5980
   chunk 50 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   overall best weight:    1.1342

-------------------------------------------------------------------------------
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 = 0.4178 r_free = 0.4178 target = 0.185869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.125529 restraints weight = 8151.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 1.88
r_work: 0.3293 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
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      :  0.004   0.042   6800  Z= 0.238
  Angle     :  0.541   6.885   9228  Z= 0.281
  Chirality :  0.039   0.171   1092
  Planarity :  0.004   0.032   1088
  Dihedral  :  3.704  15.934    888
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 23.63 %
    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:  1.20 (0.31), residues: 792
  helix:  1.00 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.14 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 568 
 HIS   0.004   0.001   HIS A 492 
 PHE   0.020   0.001   PHE B 656 
 TYR   0.016   0.002   TYR C 616 
 ARG   0.002   0.000   ARG A 531 

*********************** 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
  135 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 0.665 
Fit side-chains
REVERT: B  428 SER cc_start: 0.9014 (t) cc_final: 0.8451 (p)
REVERT: B  534 ARG cc_start: 0.8191 (ttm170) cc_final: 0.7840 (mtt180)
REVERT: C  461 ILE cc_start: 0.8573 (mm) cc_final: 0.8341 (mt)
REVERT: C  462 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8034 (mpp)
REVERT: C  493 TYR cc_start: 0.7442 (t80) cc_final: 0.6867 (t80)
REVERT: C  624 SER cc_start: 0.8323 (p) cc_final: 0.7828 (m)
REVERT: D  541 ARG cc_start: 0.8064 (ptm160) cc_final: 0.7846 (ptm160)
REVERT: D  650 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7950 (tt)
  outliers start: 24
  outliers final: 18
  residues processed: 125
  average time/residue: 0.2394
  time to fit residues: 37.6879
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  : 0.726 
-------------------------------------------------------------------------------
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 47 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 8 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 56 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 41 optimal weight:    0.7980
   chunk 81 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.4188 r_free = 0.4188 target = 0.186789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.127028 restraints weight = 8187.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 2.30
r_work: 0.3279 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.1674

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= 0.191
  Angle     :  0.523   6.769   9228  Z= 0.269
  Chirality :  0.038   0.165   1092
  Planarity :  0.003   0.031   1088
  Dihedral  :  3.633  15.768    888
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 23.20 %
    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 (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:  1.25 (0.31), residues: 792
  helix:  1.04 (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   0.013   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   0.003   0.000   ARG A 528 

*********************** 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: 23
    poor density    : 109
  time to evaluate  : 0.731 
Fit side-chains
REVERT: B  428 SER cc_start: 0.8950 (t) cc_final: 0.8311 (p)
REVERT: B  534 ARG cc_start: 0.8085 (ttm170) cc_final: 0.7722 (mtt180)
REVERT: C  461 ILE cc_start: 0.8567 (mm) cc_final: 0.8340 (mt)
REVERT: C  462 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8014 (mpp)
REVERT: C  493 TYR cc_start: 0.7429 (t80) cc_final: 0.6854 (t80)
REVERT: C  624 SER cc_start: 0.8240 (p) cc_final: 0.7709 (m)
REVERT: D  541 ARG cc_start: 0.8060 (ptm160) cc_final: 0.7819 (ptm160)
  outliers start: 23
  outliers final: 17
  residues processed: 123
  average time/residue: 0.2430
  time to fit residues: 37.7427
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  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 21 optimal weight:    6.9990
   chunk 64 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.186451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.129535 restraints weight = 8257.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 2.29
r_work: 0.3272 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.1745

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= 0.205
  Angle     :  0.533   6.809   9228  Z= 0.274
  Chirality :  0.039   0.166   1092
  Planarity :  0.003   0.032   1088
  Dihedral  :  3.643  15.799    888
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 22.77 %
    Favored  : 73.92 %
  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:  1.24 (0.31), residues: 792
  helix:  1.02 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.20 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   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   0.003   0.000   ARG A 528 

*********************** 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
  132 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 109
  time to evaluate  : 0.906 
Fit side-chains
REVERT: B  428 SER cc_start: 0.8946 (t) cc_final: 0.8300 (p)
REVERT: B  534 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7730 (mtt180)
REVERT: C  461 ILE cc_start: 0.8580 (mm) cc_final: 0.8354 (mt)
REVERT: C  462 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8024 (mpp)
REVERT: C  493 TYR cc_start: 0.7439 (t80) cc_final: 0.6875 (t80)
REVERT: C  624 SER cc_start: 0.8230 (p) cc_final: 0.7703 (m)
REVERT: D  541 ARG cc_start: 0.8041 (ptm160) cc_final: 0.7784 (ptm160)
  outliers start: 23
  outliers final: 21
  residues processed: 122
  average time/residue: 0.2505
  time to fit residues: 38.1830
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  : 0.721 
-------------------------------------------------------------------------------
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  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  545 TYR
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 67 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0670
   chunk 70 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9980
   chunk 3 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9980
   chunk 65 optimal weight:    0.2980
   chunk 6 optimal weight:    0.0020
   overall best weight:    0.4726

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.188535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.129545 restraints weight = 8291.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.16
r_work: 0.3331 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.1762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6800  Z= 0.159
  Angle     :  0.516   7.142   9228  Z= 0.263
  Chirality :  0.038   0.159   1092
  Planarity :  0.003   0.028   1088
  Dihedral  :  3.513  15.381    888
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 22.91 %
    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 (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:  1.43 (0.31), residues: 792
  helix:  1.15 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.28 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 568 
 HIS   0.005   0.001   HIS A 492 
 PHE   0.017   0.001   PHE C 656 
 TYR   0.013   0.001   TYR C 616 
 ARG   0.002   0.000   ARG A 665 

********************** 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
  132 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.747 
Fit side-chains
REVERT: B  428 SER cc_start: 0.8926 (t) cc_final: 0.8302 (p)
REVERT: B  534 ARG cc_start: 0.8096 (ttm170) cc_final: 0.7726 (mtt180)
REVERT: B  624 SER cc_start: 0.8414 (p) cc_final: 0.7901 (m)
REVERT: C  461 ILE cc_start: 0.8590 (mm) cc_final: 0.8380 (mt)
REVERT: C  462 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8046 (mpp)
REVERT: C  493 TYR cc_start: 0.7417 (t80) cc_final: 0.6874 (t80)
REVERT: C  624 SER cc_start: 0.8195 (p) cc_final: 0.7675 (m)
REVERT: D  541 ARG cc_start: 0.8096 (ptm160) cc_final: 0.7858 (ptm160)
REVERT: D  633 ASN cc_start: 0.8884 (t0) cc_final: 0.8373 (t0)
  outliers start: 21
  outliers final: 19
  residues processed: 122
  average time/residue: 0.2346
  time to fit residues: 36.0522
Evaluate side-chains
  130 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
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  606 SER
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  545 TYR
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  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:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 3 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 70 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.8784

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.186497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.126507 restraints weight = 8299.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 1.94
r_work: 0.3270 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.1810

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= 0.202
  Angle     :  0.535   7.001   9228  Z= 0.275
  Chirality :  0.039   0.163   1092
  Planarity :  0.004   0.030   1088
  Dihedral  :  3.584  15.333    888
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 23.05 %
    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 (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:  1.33 (0.31), residues: 792
  helix:  1.08 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.26 (0.61), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 568 
 HIS   0.005   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 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3543.17 seconds
wall clock time: 64 minutes 11.60 seconds (3851.60 seconds total)