Starting phenix.real_space_refine
on Wed Mar 12 12:38:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tti_26116/03_2025/7tti_26116_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tti_26116/03_2025/7tti_26116.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tti_26116/03_2025/7tti_26116.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tti_26116/03_2025/7tti_26116.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tti_26116/03_2025/7tti_26116_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tti_26116/03_2025/7tti_26116_trim.cif"
  }
  resolution = 3.5
  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=   0.000 sd=   0.043
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      62      5.16       5
     C    5030      2.51       5
     N    1208      2.21       5
     O    1370      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7670
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3753
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 542, 3753
          Classifications: {'peptide': 542}
          Incomplete info: {'truncation_to_alanine': 88}
          Link IDs: {'PTRANS': 27, 'TRANS': 514}
          Unresolved non-hydrogen bonds: 370
          Unresolved non-hydrogen angles: 464
          Unresolved non-hydrogen dihedrals: 316
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 11, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 233
    Chain: "B"
      Number of atoms: 3753
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 542, 3753
          Classifications: {'peptide': 542}
          Incomplete info: {'truncation_to_alanine': 88}
          Link IDs: {'PTRANS': 27, 'TRANS': 514}
          Unresolved non-hydrogen bonds: 370
          Unresolved non-hydrogen angles: 464
          Unresolved non-hydrogen dihedrals: 316
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 11, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 233
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Unusual residues: {'JUX': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Unusual residues: {'JUX': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.41, per 1000 atoms: 0.71
  Number of scatterers: 7670
  At special positions: 0
  Unit cell: (85.905, 108.675, 104.535, 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      62     16.00
     O    1370      8.00
     N    1208      7.00
     C    5030      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 163 " - pdb=" SG  CYS A 626 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 308 " - pdb=" SG  CYS A 323 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 343 " - pdb=" SG  CYS A 353 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 163 " - pdb=" SG  CYS B 626 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 308 " - pdb=" SG  CYS B 323 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 343 " - pdb=" SG  CYS B 353 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 312 "
      " NAG D   1 " - " ASN A 361 "
      " NAG E   1 " - " ASN B 312 "
      " NAG F   1 " - " ASN B 361 "
  Time building additional restraints: 2.63
  Conformation dependent library (CDL) restraints added in 995.0 milliseconds
  

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1984

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 2 sheets defined
      71.0% alpha, 1.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 120 through 134
      removed outlier: 4.442A  pdb=" N   LEU A 126 " --> pdb=" O   MET A 122 " (cutoff:3.500A)
      Proline residue:  A 127  - end of helix
      removed outlier: 3.522A  pdb=" N   PHE A 133 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   GLY A 134 " --> pdb=" O   GLN A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 176
      removed outlier: 4.239A  pdb=" N   TRP A 143 " --> pdb=" O   LEU A 139 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   VAL A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
      removed outlier: 8.979A  pdb=" N   LEU A 151 " --> pdb=" O   THR A 147 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   GLN A 152 " --> pdb=" O   ALA A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 193
      removed outlier: 3.587A  pdb=" N   MET A 188 " --> pdb=" O   GLY A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 227
      removed outlier: 3.841A  pdb=" N   ALA A 200 " --> pdb=" O   GLU A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 234
      No H-bonds generated for 'chain 'A' and resid 232 through 234'
    Processing helix  chain 'A' and resid 235 through 240
    Processing helix  chain 'A' and resid 243 through 268
      removed outlier: 3.748A  pdb=" N   THR A 247 " --> pdb=" O   THR A 243 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   THR A 256 " --> pdb=" O   ARG A 252 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   PHE A 261 " --> pdb=" O   ILE A 257 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL A 268 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 272
    Processing helix  chain 'A' and resid 273 through 301
    Processing helix  chain 'A' and resid 336 through 341
    Processing helix  chain 'A' and resid 354 through 360
      removed outlier: 4.170A  pdb=" N   MET A 358 " --> pdb=" O   ASP A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 379
    Processing helix  chain 'A' and resid 419 through 428
    Processing helix  chain 'A' and resid 429 through 432
      removed outlier: 3.515A  pdb=" N   THR A 432 " --> pdb=" O   PRO A 429 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 429 through 432'
    Processing helix  chain 'A' and resid 435 through 440
      removed outlier: 3.577A  pdb=" N   ARG A 440 " --> pdb=" O   ALA A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 449
    Processing helix  chain 'A' and resid 450 through 477
    Processing helix  chain 'A' and resid 478 through 483
      removed outlier: 3.713A  pdb=" N   ARG A 483 " --> pdb=" O   GLY A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 488
      removed outlier: 4.030A  pdb=" N   ASP A 488 " --> pdb=" O   LYS A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 500
      removed outlier: 3.503A  pdb=" N   THR A 498 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LEU A 499 " --> pdb=" O   VAL A 495 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ALA A 500 " --> pdb=" O   VAL A 496 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 494 through 500'
    Processing helix  chain 'A' and resid 503 through 536
      removed outlier: 4.083A  pdb=" N   ILE A 507 " --> pdb=" O   SER A 503 " (cutoff:3.500A)
      Proline residue:  A 527  - end of helix
      removed outlier: 3.782A  pdb=" N   ASP A 536 " --> pdb=" O   ALA A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 543
      removed outlier: 3.663A  pdb=" N   ARG A 543 " --> pdb=" O   PRO A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 553
      removed outlier: 3.858A  pdb=" N   GLU A 553 " --> pdb=" O   VAL A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 572
    Processing helix  chain 'A' and resid 578 through 602
      removed outlier: 3.823A  pdb=" N   SER A 582 " --> pdb=" O   ALA A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 613 through 656
      removed outlier: 4.243A  pdb=" N   ALA A 617 " --> pdb=" O   TYR A 613 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   MET A 630 " --> pdb=" O   CYS A 626 " (cutoff:3.500A)
      removed outlier: 7.469A  pdb=" N   TYR A 636 " --> pdb=" O   VAL A 632 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   TYR A 637 " --> pdb=" O   SER A 633 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   VAL A 640 " --> pdb=" O   TYR A 636 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 134
      removed outlier: 4.428A  pdb=" N   LEU B 126 " --> pdb=" O   MET B 122 " (cutoff:3.500A)
      Proline residue:  B 127  - end of helix
      removed outlier: 4.561A  pdb=" N   GLY B 134 " --> pdb=" O   GLN B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 176
      removed outlier: 4.245A  pdb=" N   TRP B 143 " --> pdb=" O   LEU B 139 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   VAL B 150 " --> pdb=" O   GLY B 146 " (cutoff:3.500A)
      removed outlier: 8.963A  pdb=" N   LEU B 151 " --> pdb=" O   THR B 147 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLN B 152 " --> pdb=" O   ALA B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 193
      removed outlier: 3.595A  pdb=" N   MET B 188 " --> pdb=" O   GLY B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 227
      removed outlier: 3.763A  pdb=" N   ALA B 200 " --> pdb=" O   GLU B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 234
      No H-bonds generated for 'chain 'B' and resid 232 through 234'
    Processing helix  chain 'B' and resid 235 through 240
    Processing helix  chain 'B' and resid 243 through 268
      removed outlier: 3.734A  pdb=" N   THR B 247 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   THR B 256 " --> pdb=" O   ARG B 252 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   PHE B 261 " --> pdb=" O   ILE B 257 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   VAL B 268 " --> pdb=" O   LEU B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 272
    Processing helix  chain 'B' and resid 273 through 301
    Processing helix  chain 'B' and resid 336 through 341
    Processing helix  chain 'B' and resid 354 through 360
      removed outlier: 4.153A  pdb=" N   MET B 358 " --> pdb=" O   ASP B 354 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 379
    Processing helix  chain 'B' and resid 419 through 428
    Processing helix  chain 'B' and resid 429 through 432
    Processing helix  chain 'B' and resid 435 through 440
      removed outlier: 3.575A  pdb=" N   ARG B 440 " --> pdb=" O   ALA B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 449
    Processing helix  chain 'B' and resid 450 through 477
    Processing helix  chain 'B' and resid 478 through 483
      removed outlier: 3.725A  pdb=" N   ARG B 483 " --> pdb=" O   GLY B 479 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 488
      removed outlier: 4.028A  pdb=" N   ASP B 488 " --> pdb=" O   LYS B 485 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 494 through 500
      removed outlier: 3.564A  pdb=" N   LEU B 499 " --> pdb=" O   VAL B 495 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ALA B 500 " --> pdb=" O   VAL B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 503 through 536
      removed outlier: 4.081A  pdb=" N   ILE B 507 " --> pdb=" O   SER B 503 " (cutoff:3.500A)
      Proline residue:  B 527  - end of helix
      removed outlier: 3.763A  pdb=" N   ASP B 536 " --> pdb=" O   ALA B 532 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 539 through 543
      removed outlier: 3.652A  pdb=" N   ARG B 543 " --> pdb=" O   PRO B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 549 through 553
      removed outlier: 3.864A  pdb=" N   GLU B 553 " --> pdb=" O   VAL B 550 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 557 through 572
    Processing helix  chain 'B' and resid 578 through 602
      removed outlier: 3.810A  pdb=" N   SER B 582 " --> pdb=" O   ALA B 578 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 613 through 656
      removed outlier: 4.240A  pdb=" N   ALA B 617 " --> pdb=" O   TYR B 613 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   MET B 630 " --> pdb=" O   CYS B 626 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   TYR B 636 " --> pdb=" O   VAL B 632 " (cutoff:3.500A)
      removed outlier: 7.317A  pdb=" N   TYR B 637 " --> pdb=" O   SER B 633 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   VAL B 640 " --> pdb=" O   TYR B 636 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314
    Processing sheet with id=AA2, first strand: chain 'B' and resid 306 through 310

    515 hydrogen bonds defined for protein.
    1509 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: 2.16

  Time building geometry restraints manager: 2.95 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2346
        1.34 -     1.46: 1915
        1.46 -     1.58: 3503
        1.58 -     1.70: 0
        1.70 -     1.82: 88
  Bond restraints: 7852
  Sorted by residual:
  bond pdb=" C5  JUX B1201 "
       pdb=" S1  JUX B1201 "
    ideal  model  delta    sigma   weight residual
    1.734  1.400  0.334 2.00e-02 2.50e+03 2.80e+02
  bond pdb=" C5  JUX A1201 "
       pdb=" S1  JUX A1201 "
    ideal  model  delta    sigma   weight residual
    1.734  1.400  0.334 2.00e-02 2.50e+03 2.79e+02
  bond pdb=" C8  JUX A1201 "
       pdb=" S1  JUX A1201 "
    ideal  model  delta    sigma   weight residual
    1.721  1.394  0.327 2.00e-02 2.50e+03 2.67e+02
  bond pdb=" C8  JUX B1201 "
       pdb=" S1  JUX B1201 "
    ideal  model  delta    sigma   weight residual
    1.721  1.394  0.327 2.00e-02 2.50e+03 2.67e+02
  bond pdb=" C9  JUX A1201 "
       pdb=" S2  JUX A1201 "
    ideal  model  delta    sigma   weight residual
    1.823  1.745  0.078 2.00e-02 2.50e+03 1.52e+01
  ... (remaining 7847 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.13: 10748
        3.13 -     6.26: 42
        6.26 -     9.39: 8
        9.39 -    12.51: 4
       12.51 -    15.64: 2
  Bond angle restraints: 10804
  Sorted by residual:
  angle pdb=" C7  JUX A1201 "
        pdb=" C6  JUX A1201 "
        pdb=" N2  JUX A1201 "
      ideal   model   delta    sigma   weight residual
     119.28  134.92  -15.64 3.00e+00 1.11e-01 2.72e+01
  angle pdb=" C7  JUX B1201 "
        pdb=" C6  JUX B1201 "
        pdb=" N2  JUX B1201 "
      ideal   model   delta    sigma   weight residual
     119.28  134.81  -15.53 3.00e+00 1.11e-01 2.68e+01
  angle pdb=" N   JUX A1201 "
        pdb=" CA  JUX A1201 "
        pdb=" C   JUX A1201 "
      ideal   model   delta    sigma   weight residual
     119.72  108.51   11.21 3.00e+00 1.11e-01 1.40e+01
  angle pdb=" N   JUX B1201 "
        pdb=" CA  JUX B1201 "
        pdb=" C   JUX B1201 "
      ideal   model   delta    sigma   weight residual
     119.72  108.96   10.76 3.00e+00 1.11e-01 1.29e+01
  angle pdb=" N   ILE A 538 "
        pdb=" CA  ILE A 538 "
        pdb=" C   ILE A 538 "
      ideal   model   delta    sigma   weight residual
     111.81  108.78    3.03 8.60e-01 1.35e+00 1.24e+01
  ... (remaining 10799 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.81: 4279
       22.81 -    45.61: 277
       45.61 -    68.41: 44
       68.41 -    91.22: 18
       91.22 -   114.02: 8
  Dihedral angle restraints: 4626
    sinusoidal: 1526
      harmonic: 3100
  Sorted by residual:
  dihedral pdb=" CA  CYS B 626 "
           pdb=" C   CYS B 626 "
           pdb=" N   LEU B 627 "
           pdb=" CA  LEU B 627 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.56   33.44     0      5.00e+00 4.00e-02 4.47e+01
  dihedral pdb=" CA  CYS A 626 "
           pdb=" C   CYS A 626 "
           pdb=" N   LEU A 627 "
           pdb=" CA  LEU A 627 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.63   33.37     0      5.00e+00 4.00e-02 4.45e+01
  dihedral pdb=" CB  CYS A 308 "
           pdb=" SG  CYS A 308 "
           pdb=" SG  CYS A 323 "
           pdb=" CB  CYS A 323 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -133.74   47.74     1      1.00e+01 1.00e-02 3.14e+01
  ... (remaining 4623 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1011
       0.037 -    0.074: 276
       0.074 -    0.111: 77
       0.111 -    0.149: 12
       0.149 -    0.186: 2
  Chirality restraints: 1378
  Sorted by residual:
  chirality pdb=" CA  CYS B 626 "
            pdb=" N   CYS B 626 "
            pdb=" C   CYS B 626 "
            pdb=" CB  CYS B 626 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.62e-01
  chirality pdb=" CA  CYS A 626 "
            pdb=" N   CYS A 626 "
            pdb=" C   CYS A 626 "
            pdb=" CB  CYS A 626 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.19 2.00e-01 2.50e+01 8.57e-01
  chirality pdb=" CA  JUX B1201 "
            pdb=" N   JUX B1201 "
            pdb=" C   JUX B1201 "
            pdb=" C4  JUX B1201 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.30   -2.44   -0.14 2.00e-01 2.50e+01 4.90e-01
  ... (remaining 1375 not shown)

  Planarity restraints: 1332
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" N   JUX B1201 "    0.122 2.00e-02 2.50e+03   9.89e-02 1.47e+02
        pdb=" CA  JUX B1201 "   -0.138 2.00e-02 2.50e+03
        pdb=" OH  JUX B1201 "   -0.131 2.00e-02 2.50e+03
        pdb=" C1  JUX B1201 "    0.038 2.00e-02 2.50e+03
        pdb=" C5  JUX B1201 "    0.042 2.00e-02 2.50e+03
        pdb=" C9  JUX B1201 "    0.066 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" N   JUX A1201 "   -0.109 2.00e-02 2.50e+03   9.67e-02 1.40e+02
        pdb=" CA  JUX A1201 "    0.135 2.00e-02 2.50e+03
        pdb=" OH  JUX A1201 "    0.130 2.00e-02 2.50e+03
        pdb=" C1  JUX A1201 "   -0.033 2.00e-02 2.50e+03
        pdb=" C5  JUX A1201 "   -0.051 2.00e-02 2.50e+03
        pdb=" C9  JUX A1201 "   -0.073 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 236 "   -0.025 5.00e-02 4.00e+02   3.89e-02 2.43e+00
        pdb=" N   PRO A 237 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 237 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 237 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1329 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 59
        2.57 -     3.15: 7531
        3.15 -     3.74: 12544
        3.74 -     4.32: 14879
        4.32 -     4.90: 25317
  Nonbonded interactions: 60330
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 292 "
            pdb=" OG  SER B 468 "
     model   vdw
     1.990 3.040
  nonbonded pdb=" OH  TYR A 292 "
            pdb=" OG  SER A 468 "
     model   vdw
     1.995 3.040
  nonbonded pdb=" OG  SER A 345 "
            pdb=" OD1 ASN A 347 "
     model   vdw
     1.997 3.040
  nonbonded pdb=" OG  SER B 345 "
            pdb=" OD1 ASN B 347 "
     model   vdw
     1.999 3.040
  nonbonded pdb=" O6  NAG F   1 "
            pdb=" O5  NAG F   2 "
     model   vdw
     2.093 3.040
  ... (remaining 60325 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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 group one per residue
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:             0.980
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.130
  Find NCS groups from input model:        0.290
  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:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6192
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      :  0.008   0.334   7852  Z= 0.470
  Angle     :  0.627  15.643  10804  Z= 0.280
  Chirality :  0.038   0.186   1378
  Planarity :  0.005   0.099   1328
  Dihedral  : 16.783 114.025   2624
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 50.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 17.98 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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:  1.88 (0.28), residues: 1080
  helix:  3.18 (0.21), residues: 626
  sheet:  None (None), residues: 0
  loop : -1.75 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 616 
 HIS   0.001   0.000   HIS A 344 
 PHE   0.007   0.001   PHE A 541 
 TYR   0.006   0.001   TYR A 186 
 ARG   0.001   0.000   ARG A 140 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 198
  time to evaluate  : 0.698 
Fit side-chains
REVERT: A  410 LEU cc_start: 0.7355 (mt) cc_final: 0.6821 (tp)
REVERT: A  571 ILE cc_start: 0.7071 (mm) cc_final: 0.6725 (mt)
REVERT: A  583 MET cc_start: 0.7334 (mmm) cc_final: 0.6946 (mmm)
REVERT: B  357 PHE cc_start: 0.5113 (m-80) cc_final: 0.4851 (t80)
REVERT: B  410 LEU cc_start: 0.7478 (mt) cc_final: 0.7037 (tp)
REVERT: B  411 TYR cc_start: 0.8196 (m-10) cc_final: 0.7992 (m-80)
REVERT: B  528 ARG cc_start: 0.7469 (mpt-90) cc_final: 0.7259 (mmt90)
REVERT: B  571 ILE cc_start: 0.7164 (mm) cc_final: 0.6844 (mt)
REVERT: B  583 MET cc_start: 0.7313 (mmm) cc_final: 0.6864 (mmm)
REVERT: B  643 LEU cc_start: 0.6008 (OUTLIER) cc_final: 0.5802 (mt)
  outliers start: 2
  outliers final: 0
  residues processed: 200
  average time/residue: 0.1432
  time to fit residues: 41.8452
Evaluate side-chains
  130 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  643 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.5980
   chunk 81 optimal weight:    7.9990
   chunk 45 optimal weight:    0.3980
   chunk 27 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 43 optimal weight:    0.3980
   chunk 84 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 98 optimal weight:    2.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A 249 ASN
** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 ASN
B 250 ASN
B 347 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.179543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.152626 restraints weight = 9694.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.156215 restraints weight = 5557.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.158184 restraints weight = 3872.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.1921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7852  Z= 0.254
  Angle     :  0.748   8.707  10804  Z= 0.361
  Chirality :  0.047   0.220   1378
  Planarity :  0.005   0.064   1328
  Dihedral  : 13.746  98.920   1326
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 21.35 %
    Favored  : 73.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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:  1.03 (0.27), residues: 1080
  helix:  2.22 (0.20), residues: 634
  sheet:  None (None), residues: 0
  loop : -1.74 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 339 
 HIS   0.001   0.000   HIS A 344 
 PHE   0.017   0.002   PHE A 541 
 TYR   0.010   0.001   TYR A 186 
 ARG   0.003   0.001   ARG A 252 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 146
  time to evaluate  : 0.804 
Fit side-chains
REVERT: A  571 ILE cc_start: 0.8538 (mm) cc_final: 0.8233 (mt)
REVERT: A  573 SER cc_start: 0.7566 (t) cc_final: 0.7286 (t)
REVERT: B  130 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7902 (tm-30)
REVERT: B  197 PHE cc_start: 0.6565 (m-80) cc_final: 0.6363 (m-80)
REVERT: B  571 ILE cc_start: 0.8471 (mm) cc_final: 0.8189 (mt)
  outliers start: 37
  outliers final: 24
  residues processed: 171
  average time/residue: 0.1494
  time to fit residues: 37.2051
Evaluate side-chains
  160 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 136
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  364 GLU
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  619 SER
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain B residue  364 GLU
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  471 VAL
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  507 ILE
Chi-restraints excluded: chain B residue  619 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 74 optimal weight:    5.9990
   chunk 88 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN
** B 130 GLN ** 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 = 0.4062 r_free = 0.4062 target = 0.181018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.154095 restraints weight = 9889.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.157603 restraints weight = 5725.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.159679 restraints weight = 4031.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7852  Z= 0.253
  Angle     :  0.683   9.305  10804  Z= 0.332
  Chirality :  0.046   0.224   1378
  Planarity :  0.005   0.050   1328
  Dihedral  : 12.743  91.335   1324
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  6.88 %
    Allowed  : 20.65 %
    Favored  : 72.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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:  0.81 (0.26), residues: 1080
  helix:  2.04 (0.20), residues: 632
  sheet:  None (None), residues: 0
  loop : -1.80 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 501 
 HIS   0.002   0.001   HIS B 394 
 PHE   0.014   0.002   PHE A 541 
 TYR   0.009   0.001   TYR B 411 
 ARG   0.003   0.001   ARG B 252 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 143
  time to evaluate  : 0.794 
Fit side-chains
REVERT: A  137 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8173 (tp)
REVERT: A  490 VAL cc_start: 0.7625 (m) cc_final: 0.7284 (p)
REVERT: A  571 ILE cc_start: 0.8695 (mm) cc_final: 0.8422 (mt)
REVERT: A  630 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8090 (ptm)
REVERT: B  137 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8242 (tp)
REVERT: B  223 ILE cc_start: 0.8533 (mm) cc_final: 0.8327 (mt)
REVERT: B  571 ILE cc_start: 0.8674 (mm) cc_final: 0.8415 (mt)
  outliers start: 49
  outliers final: 28
  residues processed: 177
  average time/residue: 0.1411
  time to fit residues: 36.9184
Evaluate side-chains
  161 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 130
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  163 CYS
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  364 GLU
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  619 SER
Chi-restraints excluded: chain A residue  630 MET
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  163 CYS
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  507 ILE
Chi-restraints excluded: chain B residue  619 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 74 optimal weight:    5.9990
   chunk 100 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0570
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.181887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.154858 restraints weight = 9811.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.158375 restraints weight = 5690.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.160603 restraints weight = 4008.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7852  Z= 0.215
  Angle     :  0.673   9.638  10804  Z= 0.323
  Chirality :  0.044   0.244   1378
  Planarity :  0.005   0.054   1328
  Dihedral  : 12.076  85.418   1324
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  6.88 %
    Allowed  : 21.77 %
    Favored  : 71.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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:  0.88 (0.27), residues: 1080
  helix:  1.95 (0.21), residues: 648
  sheet:  None (None), residues: 0
  loop : -1.65 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 339 
 HIS   0.001   0.000   HIS B 394 
 PHE   0.021   0.002   PHE A 591 
 TYR   0.008   0.001   TYR A 186 
 ARG   0.003   0.001   ARG A 440 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 140
  time to evaluate  : 0.805 
Fit side-chains
REVERT: A  137 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8132 (tp)
REVERT: A  155 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7504 (tt)
REVERT: A  571 ILE cc_start: 0.8694 (mm) cc_final: 0.8429 (mt)
REVERT: A  630 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8094 (ptm)
REVERT: B  137 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8134 (tp)
REVERT: B  571 ILE cc_start: 0.8671 (mm) cc_final: 0.8410 (mt)
  outliers start: 49
  outliers final: 30
  residues processed: 174
  average time/residue: 0.1635
  time to fit residues: 42.8532
Evaluate side-chains
  164 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 130
  time to evaluate  : 1.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  163 CYS
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  453 VAL
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  619 SER
Chi-restraints excluded: chain A residue  630 MET
Chi-restraints excluded: chain A residue  654 TYR
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  453 VAL
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  507 ILE
Chi-restraints excluded: chain B residue  619 SER
Chi-restraints excluded: chain B residue  654 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 89 optimal weight:    0.6980
   chunk 95 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 100 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 107 optimal weight:    0.7980
   chunk 36 optimal weight:    0.1980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 130 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.181595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.154686 restraints weight = 9807.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.158092 restraints weight = 5667.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.160124 restraints weight = 4021.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.2766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7852  Z= 0.220
  Angle     :  0.663   9.704  10804  Z= 0.318
  Chirality :  0.044   0.255   1378
  Planarity :  0.005   0.056   1328
  Dihedral  : 11.600  82.226   1324
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  6.74 %
    Allowed  : 23.31 %
    Favored  : 69.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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:  0.96 (0.27), residues: 1080
  helix:  2.08 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -1.63 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 339 
 HIS   0.001   0.000   HIS B 394 
 PHE   0.019   0.001   PHE B 428 
 TYR   0.007   0.001   TYR A 186 
 ARG   0.002   0.000   ARG A 252 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 133
  time to evaluate  : 0.880 
Fit side-chains
REVERT: A  137 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8182 (tp)
REVERT: A  571 ILE cc_start: 0.8686 (mm) cc_final: 0.8447 (mt)
REVERT: A  630 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8131 (ptm)
REVERT: B  137 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8225 (tp)
REVERT: B  155 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7509 (tt)
REVERT: B  571 ILE cc_start: 0.8669 (mm) cc_final: 0.8415 (mt)
REVERT: B  643 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7391 (mt)
  outliers start: 48
  outliers final: 30
  residues processed: 168
  average time/residue: 0.1904
  time to fit residues: 47.1715
Evaluate side-chains
  162 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 127
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  163 CYS
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  619 SER
Chi-restraints excluded: chain A residue  630 MET
Chi-restraints excluded: chain A residue  654 TYR
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  163 CYS
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  507 ILE
Chi-restraints excluded: chain B residue  570 LEU
Chi-restraints excluded: chain B residue  619 SER
Chi-restraints excluded: chain B residue  643 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 104 optimal weight:    2.9990
   chunk 91 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 12 optimal weight:    0.2980
   chunk 85 optimal weight:    1.9990
   chunk 103 optimal weight:   30.0000
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.6982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.180860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.154068 restraints weight = 9863.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.157503 restraints weight = 5692.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.159693 restraints weight = 4034.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.2883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7852  Z= 0.226
  Angle     :  0.673   9.719  10804  Z= 0.321
  Chirality :  0.045   0.261   1378
  Planarity :  0.005   0.057   1328
  Dihedral  : 11.227  84.769   1324
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  6.88 %
    Allowed  : 24.30 %
    Favored  : 68.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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:  0.94 (0.27), residues: 1080
  helix:  1.90 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.55 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 339 
 HIS   0.001   0.000   HIS B 344 
 PHE   0.022   0.001   PHE B 591 
 TYR   0.007   0.001   TYR A 186 
 ARG   0.002   0.001   ARG A 252 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 126
  time to evaluate  : 0.751 
Fit side-chains
REVERT: A  137 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8215 (tp)
REVERT: A  248 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7833 (mp)
REVERT: A  571 ILE cc_start: 0.8678 (mm) cc_final: 0.8443 (mt)
REVERT: A  630 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8073 (ptm)
REVERT: B  137 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8277 (tp)
REVERT: B  248 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7914 (mp)
REVERT: B  571 ILE cc_start: 0.8654 (mm) cc_final: 0.8421 (mt)
REVERT: B  643 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7378 (mt)
  outliers start: 49
  outliers final: 34
  residues processed: 165
  average time/residue: 0.1438
  time to fit residues: 34.8930
Evaluate side-chains
  162 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 122
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  163 CYS
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  453 VAL
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  619 SER
Chi-restraints excluded: chain A residue  630 MET
Chi-restraints excluded: chain A residue  631 PHE
Chi-restraints excluded: chain A residue  654 TYR
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  163 CYS
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  453 VAL
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  507 ILE
Chi-restraints excluded: chain B residue  570 LEU
Chi-restraints excluded: chain B residue  619 SER
Chi-restraints excluded: chain B residue  643 LEU
Chi-restraints excluded: chain B residue  654 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 106 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 30 optimal weight:    0.2980
   chunk 68 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.179726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.153035 restraints weight = 9784.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.156421 restraints weight = 5695.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.158234 restraints weight = 4046.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.3042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7852  Z= 0.236
  Angle     :  0.674   9.745  10804  Z= 0.321
  Chirality :  0.045   0.261   1378
  Planarity :  0.005   0.058   1328
  Dihedral  : 10.770  89.521   1324
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  7.02 %
    Allowed  : 24.16 %
    Favored  : 68.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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:  0.96 (0.27), residues: 1080
  helix:  1.97 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -1.54 (0.32), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 339 
 HIS   0.001   0.000   HIS B 344 
 PHE   0.015   0.001   PHE A 428 
 TYR   0.007   0.001   TYR A 186 
 ARG   0.002   0.000   ARG A 252 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 123
  time to evaluate  : 0.797 
Fit side-chains
REVERT: A  137 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8273 (tp)
REVERT: A  248 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7837 (mp)
REVERT: A  571 ILE cc_start: 0.8674 (mm) cc_final: 0.8437 (mt)
REVERT: B  137 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8385 (tp)
REVERT: B  248 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7924 (mp)
REVERT: B  571 ILE cc_start: 0.8671 (mm) cc_final: 0.8465 (mt)
  outliers start: 50
  outliers final: 40
  residues processed: 163
  average time/residue: 0.1441
  time to fit residues: 34.5473
Evaluate side-chains
  161 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 117
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  163 CYS
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  418 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  453 VAL
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  619 SER
Chi-restraints excluded: chain A residue  654 TYR
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  163 CYS
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  344 HIS
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  453 VAL
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  507 ILE
Chi-restraints excluded: chain B residue  570 LEU
Chi-restraints excluded: chain B residue  619 SER
Chi-restraints excluded: chain B residue  654 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 100 optimal weight:    0.7980
   chunk 85 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0870
   chunk 102 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 86 optimal weight:    0.6980
   overall best weight:    0.6158

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.180681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.154006 restraints weight = 9900.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.157494 restraints weight = 5741.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.159330 restraints weight = 4051.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.3101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7852  Z= 0.224
  Angle     :  0.678   9.741  10804  Z= 0.322
  Chirality :  0.044   0.261   1378
  Planarity :  0.005   0.058   1328
  Dihedral  : 10.434  89.698   1324
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  6.60 %
    Allowed  : 25.00 %
    Favored  : 68.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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:  0.98 (0.27), residues: 1080
  helix:  1.98 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -1.53 (0.32), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 501 
 HIS   0.001   0.000   HIS B 394 
 PHE   0.016   0.001   PHE B 428 
 TYR   0.007   0.001   TYR A 186 
 ARG   0.002   0.000   ARG A 252 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 128
  time to evaluate  : 0.723 
Fit side-chains
REVERT: A  137 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8251 (tp)
REVERT: A  248 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7857 (mp)
REVERT: A  571 ILE cc_start: 0.8634 (mm) cc_final: 0.8402 (mt)
REVERT: B  137 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8364 (tp)
REVERT: B  248 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7931 (mp)
REVERT: B  571 ILE cc_start: 0.8641 (mm) cc_final: 0.8428 (mt)
  outliers start: 47
  outliers final: 39
  residues processed: 165
  average time/residue: 0.1431
  time to fit residues: 35.0092
Evaluate side-chains
  160 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 117
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  163 CYS
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  418 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  453 VAL
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  619 SER
Chi-restraints excluded: chain A residue  631 PHE
Chi-restraints excluded: chain A residue  654 TYR
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  163 CYS
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  344 HIS
Chi-restraints excluded: chain B residue  418 THR
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  453 VAL
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  507 ILE
Chi-restraints excluded: chain B residue  570 LEU
Chi-restraints excluded: chain B residue  619 SER
Chi-restraints excluded: chain B residue  654 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 105 optimal weight:    0.7980
   chunk 96 optimal weight:    0.3980
   chunk 74 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.9382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.178064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.151441 restraints weight = 9931.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.154572 restraints weight = 5760.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.156990 restraints weight = 4127.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.3188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7852  Z= 0.263
  Angle     :  0.719  10.098  10804  Z= 0.337
  Chirality :  0.045   0.252   1378
  Planarity :  0.005   0.059   1328
  Dihedral  : 10.010  88.189   1324
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  6.04 %
    Allowed  : 25.98 %
    Favored  : 67.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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:  0.87 (0.27), residues: 1080
  helix:  1.88 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -1.55 (0.32), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 501 
 HIS   0.001   0.000   HIS A 394 
 PHE   0.019   0.002   PHE B 428 
 TYR   0.008   0.001   TYR A 186 
 ARG   0.002   0.000   ARG A 252 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 125
  time to evaluate  : 0.720 
Fit side-chains
REVERT: A  137 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8324 (tp)
REVERT: A  248 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7935 (mp)
REVERT: A  571 ILE cc_start: 0.8642 (mm) cc_final: 0.8427 (mt)
REVERT: A  573 SER cc_start: 0.7515 (t) cc_final: 0.7209 (t)
REVERT: B  137 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8444 (tp)
REVERT: B  248 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7985 (mp)
REVERT: B  573 SER cc_start: 0.7473 (t) cc_final: 0.7175 (t)
  outliers start: 43
  outliers final: 38
  residues processed: 162
  average time/residue: 0.1395
  time to fit residues: 33.1829
Evaluate side-chains
  160 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 118
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  163 CYS
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  418 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  453 VAL
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  619 SER
Chi-restraints excluded: chain A residue  631 PHE
Chi-restraints excluded: chain A residue  654 TYR
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  163 CYS
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  344 HIS
Chi-restraints excluded: chain B residue  418 THR
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  453 VAL
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  507 ILE
Chi-restraints excluded: chain B residue  570 LEU
Chi-restraints excluded: chain B residue  619 SER
Chi-restraints excluded: chain B residue  654 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 99 optimal weight:    0.9980
   chunk 97 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 90 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 85 optimal weight:    0.5980
   chunk 0 optimal weight:    0.6980
   chunk 48 optimal weight:    8.9990
   chunk 68 optimal weight:    2.9990
   chunk 59 optimal weight:    0.5980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.179273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.152713 restraints weight = 9853.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.156148 restraints weight = 5705.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.158321 restraints weight = 4031.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.3283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7852  Z= 0.234
  Angle     :  0.707   9.748  10804  Z= 0.331
  Chirality :  0.045   0.240   1378
  Planarity :  0.005   0.059   1328
  Dihedral  :  9.630  88.720   1324
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  6.04 %
    Allowed  : 26.69 %
    Favored  : 67.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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:  0.93 (0.27), residues: 1080
  helix:  1.93 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -1.53 (0.32), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 501 
 HIS   0.001   0.000   HIS A 394 
 PHE   0.020   0.001   PHE B 428 
 TYR   0.007   0.001   TYR A 186 
 ARG   0.002   0.000   ARG A 252 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 120
  time to evaluate  : 0.800 
Fit side-chains
REVERT: A  137 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8278 (tp)
REVERT: A  248 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7935 (mp)
REVERT: A  571 ILE cc_start: 0.8619 (mm) cc_final: 0.8401 (mt)
REVERT: A  573 SER cc_start: 0.7491 (t) cc_final: 0.7183 (t)
REVERT: B  137 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8417 (tp)
REVERT: B  248 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7984 (mp)
  outliers start: 43
  outliers final: 37
  residues processed: 156
  average time/residue: 0.1320
  time to fit residues: 31.2197
Evaluate side-chains
  158 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 117
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  163 CYS
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  418 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  453 VAL
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  619 SER
Chi-restraints excluded: chain A residue  631 PHE
Chi-restraints excluded: chain A residue  654 TYR
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  163 CYS
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  344 HIS
Chi-restraints excluded: chain B residue  418 THR
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  453 VAL
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  507 ILE
Chi-restraints excluded: chain B residue  570 LEU
Chi-restraints excluded: chain B residue  619 SER
Chi-restraints excluded: chain B residue  654 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 78 optimal weight:    8.9990
   chunk 9 optimal weight:    0.5980
   chunk 93 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 86 optimal weight:    0.4980
   chunk 10 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0570
   chunk 28 optimal weight:    0.1980
   chunk 18 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   overall best weight:    0.4098

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

Flipped N/Q/H residues before XYZ refinement:
B 379 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.182442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.156148 restraints weight = 9768.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.159275 restraints weight = 5617.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.161664 restraints weight = 4026.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.3364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7852  Z= 0.202
  Angle     :  0.698   9.725  10804  Z= 0.323
  Chirality :  0.044   0.221   1378
  Planarity :  0.005   0.058   1328
  Dihedral  :  9.206  89.201   1324
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 27.25 %
    Favored  : 67.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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 (0.27), residues: 1080
  helix:  2.04 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -1.49 (0.32), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 501 
 HIS   0.000   0.000   HIS A 615 
 PHE   0.019   0.001   PHE B 428 
 TYR   0.006   0.001   TYR A 186 
 ARG   0.002   0.000   ARG A 440 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2398.65 seconds
wall clock time: 43 minutes 11.39 seconds (2591.39 seconds total)