Starting phenix.real_space_refine
on Fri Feb 14 00:11:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xf5_33169/02_2025/7xf5_33169.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xf5_33169/02_2025/7xf5_33169.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xf5_33169/02_2025/7xf5_33169.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xf5_33169/02_2025/7xf5_33169.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xf5_33169/02_2025/7xf5_33169.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xf5_33169/02_2025/7xf5_33169.cif"
  }
  resolution = 3.9
  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=   0.003
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      57      5.16       5
     C    6294      2.51       5
     N    1615      2.21       5
     O    1674      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9640
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 622, 4837
          Classifications: {'peptide': 622}
          Link IDs: {'PTRANS': 29, 'TRANS': 592}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 4803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 617, 4803
          Classifications: {'peptide': 617}
          Link IDs: {'PTRANS': 28, 'TRANS': 588}
          Chain breaks: 3
  Time building chain proxies: 6.02, per 1000 atoms: 0.62
  Number of scatterers: 9640
  At special positions: 0
  Unit cell: (111.915, 113.573, 116.06, 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      57     16.00
     O    1674      8.00
     N    1615      7.00
     C    6294      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.55
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2312

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 3 sheets defined
      74.6% alpha, 1.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 89 through 126
    Processing helix  chain 'A' and resid 129 through 156
      Proline residue:  A 141  - end of helix
    Processing helix  chain 'A' and resid 157 through 160
    Processing helix  chain 'A' and resid 163 through 172
    Processing helix  chain 'A' and resid 176 through 180
    Processing helix  chain 'A' and resid 181 through 198
    Processing helix  chain 'A' and resid 204 through 225
    Processing helix  chain 'A' and resid 226 through 231
      removed outlier: 6.910A  pdb=" N   ILE A 229 " --> pdb=" O   PHE A 226 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   TYR A 230 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 253
      removed outlier: 3.609A  pdb=" N   PHE A 252 " --> pdb=" O   VAL A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 267
      removed outlier: 3.614A  pdb=" N   SER A 267 " --> pdb=" O   ILE A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 296
    Processing helix  chain 'A' and resid 317 through 319
      No H-bonds generated for 'chain 'A' and resid 317 through 319'
    Processing helix  chain 'A' and resid 320 through 352
      removed outlier: 3.514A  pdb=" N   GLN A 352 " --> pdb=" O   VAL A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 362
    Processing helix  chain 'A' and resid 364 through 378
      removed outlier: 3.556A  pdb=" N   ALA A 368 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 386
      removed outlier: 3.726A  pdb=" N   GLN A 385 " --> pdb=" O   GLY A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 401
    Processing helix  chain 'A' and resid 419 through 425
    Processing helix  chain 'A' and resid 430 through 450
      removed outlier: 4.142A  pdb=" N   TRP A 444 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 481
    Processing helix  chain 'A' and resid 495 through 513
      removed outlier: 3.872A  pdb=" N   TYR A 499 " --> pdb=" O   VAL A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 526
      removed outlier: 4.425A  pdb=" N   VAL A 519 " --> pdb=" O   VAL A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 549
    Processing helix  chain 'A' and resid 551 through 560
    Processing helix  chain 'A' and resid 573 through 578
      removed outlier: 3.828A  pdb=" N   TYR A 576 " --> pdb=" O   HIS A 573 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   VAL A 578 " --> pdb=" O   GLN A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 584
    Processing helix  chain 'A' and resid 596 through 607
      removed outlier: 4.203A  pdb=" N   LEU A 600 " --> pdb=" O   THR A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 640
      removed outlier: 3.643A  pdb=" N   LEU A 640 " --> pdb=" O   LEU A 636 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 641 through 648
      removed outlier: 3.706A  pdb=" N   ARG A 645 " --> pdb=" O   SER A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 767 through 778
      removed outlier: 4.057A  pdb=" N   ILE A 771 " --> pdb=" O   SER A 767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 814
      removed outlier: 3.709A  pdb=" N   LEU A 813 " --> pdb=" O   ILE A 809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 831 through 844
      removed outlier: 4.120A  pdb=" N   LEU A 835 " --> pdb=" O   THR A 831 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 126
      removed outlier: 3.514A  pdb=" N   LEU B 126 " --> pdb=" O   MET B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 156
      Proline residue:  B 141  - end of helix
    Processing helix  chain 'B' and resid 157 through 160
    Processing helix  chain 'B' and resid 163 through 173
    Processing helix  chain 'B' and resid 176 through 180
    Processing helix  chain 'B' and resid 181 through 198
    Processing helix  chain 'B' and resid 204 through 225
      removed outlier: 3.854A  pdb=" N   LEU B 225 " --> pdb=" O   LYS B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 231
      removed outlier: 7.085A  pdb=" N   ILE B 229 " --> pdb=" O   PHE B 226 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   TYR B 230 " --> pdb=" O   GLY B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 253
      removed outlier: 3.647A  pdb=" N   PHE B 252 " --> pdb=" O   VAL B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 267
      removed outlier: 3.716A  pdb=" N   VAL B 259 " --> pdb=" O   PRO B 255 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   SER B 267 " --> pdb=" O   ILE B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 296
    Processing helix  chain 'B' and resid 317 through 319
      No H-bonds generated for 'chain 'B' and resid 317 through 319'
    Processing helix  chain 'B' and resid 320 through 352
    Processing helix  chain 'B' and resid 352 through 363
    Processing helix  chain 'B' and resid 364 through 378
      removed outlier: 3.574A  pdb=" N   ALA B 368 " --> pdb=" O   LEU B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 382 through 386
      removed outlier: 3.674A  pdb=" N   GLN B 385 " --> pdb=" O   GLY B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 401
    Processing helix  chain 'B' and resid 405 through 409
    Processing helix  chain 'B' and resid 419 through 425
    Processing helix  chain 'B' and resid 430 through 450
      removed outlier: 4.073A  pdb=" N   TRP B 444 " --> pdb=" O   LEU B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 481
    Processing helix  chain 'B' and resid 495 through 513
      removed outlier: 3.866A  pdb=" N   TYR B 499 " --> pdb=" O   VAL B 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 516 through 526
    Processing helix  chain 'B' and resid 530 through 549
    Processing helix  chain 'B' and resid 551 through 560
    Processing helix  chain 'B' and resid 573 through 578
      removed outlier: 3.847A  pdb=" N   TYR B 576 " --> pdb=" O   HIS B 573 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL B 578 " --> pdb=" O   GLN B 575 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 580 through 584
      removed outlier: 3.576A  pdb=" N   MET B 584 " --> pdb=" O   GLU B 581 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 596 through 607
      removed outlier: 3.867A  pdb=" N   LEU B 600 " --> pdb=" O   THR B 596 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 628 through 640
      removed outlier: 3.751A  pdb=" N   LEU B 640 " --> pdb=" O   LEU B 636 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 641 through 648
      removed outlier: 4.552A  pdb=" N   ARG B 645 " --> pdb=" O   SER B 641 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   HIS B 648 " --> pdb=" O   ARG B 644 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 770 through 778
    Processing helix  chain 'B' and resid 802 through 810
    Processing helix  chain 'B' and resid 832 through 841
    Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 271
    Processing sheet with id=AA2, first strand: chain 'A' and resid 485 through 487
    Processing sheet with id=AA3, first strand: chain 'B' and resid 485 through 487

    649 hydrogen bonds defined for protein.
    1860 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: 2.83

  Time building geometry restraints manager: 2.92 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: 3038
        1.34 -     1.46: 2194
        1.46 -     1.58: 4533
        1.58 -     1.70: 0
        1.70 -     1.82: 96
  Bond restraints: 9861
  Sorted by residual:
  bond pdb=" CA  LEU B 812 "
       pdb=" C   LEU B 812 "
    ideal  model  delta    sigma   weight residual
    1.523  1.495  0.028 1.34e-02 5.57e+03 4.52e+00
  bond pdb=" CA  LEU B 813 "
       pdb=" C   LEU B 813 "
    ideal  model  delta    sigma   weight residual
    1.521  1.503  0.018 1.36e-02 5.41e+03 1.71e+00
  bond pdb=" N   ILE B 170 "
       pdb=" CA  ILE B 170 "
    ideal  model  delta    sigma   weight residual
    1.461  1.447  0.014 1.19e-02 7.06e+03 1.34e+00
  bond pdb=" C   LYS B 168 "
       pdb=" O   LYS B 168 "
    ideal  model  delta    sigma   weight residual
    1.237  1.223  0.014 1.19e-02 7.06e+03 1.30e+00
  bond pdb=" C   THR B 169 "
       pdb=" O   THR B 169 "
    ideal  model  delta    sigma   weight residual
    1.237  1.223  0.014 1.19e-02 7.06e+03 1.30e+00
  ... (remaining 9856 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.71: 13301
        2.71 -     5.43: 86
        5.43 -     8.14: 8
        8.14 -    10.86: 3
       10.86 -    13.57: 1
  Bond angle restraints: 13399
  Sorted by residual:
  angle pdb=" N   LEU B 813 "
        pdb=" CA  LEU B 813 "
        pdb=" C   LEU B 813 "
      ideal   model   delta    sigma   weight residual
     113.41   99.84   13.57 1.22e+00 6.72e-01 1.24e+02
  angle pdb=" N   SER B 811 "
        pdb=" CA  SER B 811 "
        pdb=" C   SER B 811 "
      ideal   model   delta    sigma   weight residual
     114.64  109.05    5.59 1.52e+00 4.33e-01 1.35e+01
  angle pdb=" N   PHE B 810 "
        pdb=" CA  PHE B 810 "
        pdb=" C   PHE B 810 "
      ideal   model   delta    sigma   weight residual
     113.37  108.50    4.87 1.38e+00 5.25e-01 1.25e+01
  angle pdb=" CB  MET A 167 "
        pdb=" CG  MET A 167 "
        pdb=" SD  MET A 167 "
      ideal   model   delta    sigma   weight residual
     112.70  104.08    8.62 3.00e+00 1.11e-01 8.26e+00
  angle pdb=" C   TYR B 230 "
        pdb=" N   GLU B 231 "
        pdb=" CA  GLU B 231 "
      ideal   model   delta    sigma   weight residual
     121.94  116.23    5.71 2.00e+00 2.50e-01 8.16e+00
  ... (remaining 13394 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.22: 5322
       17.22 -    34.43: 377
       34.43 -    51.65: 81
       51.65 -    68.87: 27
       68.87 -    86.08: 22
  Dihedral angle restraints: 5829
    sinusoidal: 2262
      harmonic: 3567
  Sorted by residual:
  dihedral pdb=" CB  GLU B 166 "
           pdb=" CG  GLU B 166 "
           pdb=" CD  GLU B 166 "
           pdb=" OE1 GLU B 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.33   85.33     1      3.00e+01 1.11e-03 9.80e+00
  dihedral pdb=" CA  LEU B 813 "
           pdb=" CB  LEU B 813 "
           pdb=" CG  LEU B 813 "
           pdb=" CD1 LEU B 813 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  116.27  -56.27     3      1.50e+01 4.44e-03 9.39e+00
  dihedral pdb=" CG  ARG A 558 "
           pdb=" CD  ARG A 558 "
           pdb=" NE  ARG A 558 "
           pdb=" CZ  ARG A 558 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -138.50  -41.50     2      1.50e+01 4.44e-03 9.37e+00
  ... (remaining 5826 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1194
       0.043 -    0.085: 298
       0.085 -    0.127: 79
       0.127 -    0.170: 5
       0.170 -    0.212: 2
  Chirality restraints: 1578
  Sorted by residual:
  chirality pdb=" CA  LEU B 813 "
            pdb=" N   LEU B 813 "
            pdb=" C   LEU B 813 "
            pdb=" CB  LEU B 813 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  LEU B 812 "
            pdb=" N   LEU B 812 "
            pdb=" C   LEU B 812 "
            pdb=" CB  LEU B 812 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.57e-01
  chirality pdb=" CA  GLU B 231 "
            pdb=" N   GLU B 231 "
            pdb=" C   GLU B 231 "
            pdb=" CB  GLU B 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.10e-01
  ... (remaining 1575 not shown)

  Planarity restraints: 1671
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 444 "   -0.019 2.00e-02 2.50e+03   1.45e-02 5.28e+00
        pdb=" CG  TRP A 444 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 444 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 444 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 444 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 444 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 444 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 444 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 444 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 444 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 444 "    0.012 2.00e-02 2.50e+03   1.25e-02 3.89e+00
        pdb=" CG  TRP B 444 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 444 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 444 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 444 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 444 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 444 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 444 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 444 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 444 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 379 "   -0.026 5.00e-02 4.00e+02   4.00e-02 2.56e+00
        pdb=" N   PRO B 380 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B 380 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 380 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1668 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1459
        2.76 -     3.29: 9581
        3.29 -     3.83: 16013
        3.83 -     4.36: 17154
        4.36 -     4.90: 30157
  Nonbonded interactions: 74364
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 320 "
            pdb=" OH  TYR A 499 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" OE2 GLU B 320 "
            pdb=" OH  TYR B 499 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   GLU A 166 "
            pdb=" OG1 THR A 169 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   ASP A 402 "
            pdb=" NH1 ARG A 471 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" O   ARG B 601 "
            pdb=" ND1 HIS B 605 "
     model   vdw
     2.308 3.120
  ... (remaining 74359 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 89 through 649 or resid 769 through 845))
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.990
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.040
  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:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6657
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9861  Z= 0.164
  Angle     :  0.607  13.571  13399  Z= 0.348
  Chirality :  0.040   0.212   1578
  Planarity :  0.004   0.040   1671
  Dihedral  : 14.141  86.085   3517
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.29 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  0.29 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.24), residues: 1223
  helix:  1.51 (0.18), residues: 832
  sheet:  None (None), residues: 0
  loop : -0.93 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.001   TRP A 444 
 HIS   0.012   0.001   HIS B 210 
 PHE   0.021   0.001   PHE B 147 
 TYR   0.016   0.001   TYR A 140 
 ARG   0.011   0.000   ARG B 277 

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 344
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 HIS cc_start: 0.7891 (t-170) cc_final: 0.7565 (t70)
REVERT: A  239 MET cc_start: 0.7214 (mmt) cc_final: 0.6759 (ptm)
REVERT: A  309 ARG cc_start: 0.6994 (ttp-170) cc_final: 0.6200 (mtm110)
REVERT: A  340 TYR cc_start: 0.6818 (t80) cc_final: 0.6472 (t80)
REVERT: A  374 ILE cc_start: 0.8639 (tt) cc_final: 0.8155 (mt)
REVERT: A  439 ILE cc_start: 0.8192 (mm) cc_final: 0.7980 (mt)
REVERT: A  531 ILE cc_start: 0.9316 (tt) cc_final: 0.9045 (tt)
REVERT: A  549 GLN cc_start: 0.7704 (tp-100) cc_final: 0.7359 (tt0)
REVERT: A  558 ARG cc_start: 0.6490 (mmt180) cc_final: 0.5991 (mtt-85)
REVERT: A  801 THR cc_start: 0.5389 (m) cc_final: 0.5177 (m)
REVERT: B  219 LEU cc_start: 0.8581 (tp) cc_final: 0.8373 (tp)
REVERT: B  374 ILE cc_start: 0.8657 (tt) cc_final: 0.8180 (mt)
REVERT: B  558 ARG cc_start: 0.6348 (mmt180) cc_final: 0.5626 (mtt180)
REVERT: B  815 VAL cc_start: 0.5453 (OUTLIER) cc_final: 0.5240 (m)
  outliers start: 6
  outliers final: 1
  residues processed: 347
  average time/residue: 0.2390
  time to fit residues: 113.0557
Evaluate side-chains
  217 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 215
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  813 LEU
Chi-restraints excluded: chain B residue  815 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 51 optimal weight:   20.0000
   chunk 31 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   chunk 49 optimal weight:    6.9990
   chunk 96 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 58 optimal weight:   10.0000
   chunk 71 optimal weight:    5.9990
   chunk 111 optimal weight:    0.0980
   overall best weight:    2.4188

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

Flipped N/Q/H residues before XYZ refinement:
A 119 GLN
A 133 GLN
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 513 HIS
A 530 HIS
A 546 GLN
B 133 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.205521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.159035 restraints weight = 15651.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.162709 restraints weight = 8676.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.165277 restraints weight = 5962.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.3920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   9861  Z= 0.364
  Angle     :  0.710   9.040  13399  Z= 0.367
  Chirality :  0.048   0.227   1578
  Planarity :  0.005   0.043   1671
  Dihedral  :  4.467  50.717   1324
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  :  9.51 %
    Favored  : 87.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.24), residues: 1223
  helix:  1.29 (0.17), residues: 827
  sheet:  None (None), residues: 0
  loop : -0.92 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  91 
 HIS   0.007   0.001   HIS B 210 
 PHE   0.027   0.003   PHE B 522 
 TYR   0.025   0.003   TYR B 134 
 ARG   0.005   0.001   ARG B 343 

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 251
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  274 ASN cc_start: 0.8076 (m-40) cc_final: 0.7863 (m110)
REVERT: A  309 ARG cc_start: 0.7353 (ttp-170) cc_final: 0.7091 (mtm110)
REVERT: A  374 ILE cc_start: 0.8552 (tt) cc_final: 0.8051 (mt)
REVERT: A  453 PRO cc_start: 0.8292 (Cg_endo) cc_final: 0.8064 (Cg_exo)
REVERT: B  178 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.5933 (pm20)
REVERT: B  214 MET cc_start: 0.7484 (mtp) cc_final: 0.7232 (mtp)
REVERT: B  252 PHE cc_start: 0.5681 (m-80) cc_final: 0.4850 (m-80)
REVERT: B  374 ILE cc_start: 0.8607 (tt) cc_final: 0.8291 (mt)
REVERT: B  383 PHE cc_start: 0.8241 (t80) cc_final: 0.7974 (t80)
REVERT: B  453 PRO cc_start: 0.8326 (Cg_endo) cc_final: 0.8059 (Cg_exo)
  outliers start: 31
  outliers final: 20
  residues processed: 269
  average time/residue: 0.2179
  time to fit residues: 81.6916
Evaluate side-chains
  233 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 212
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  555 SER
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  405 THR
Chi-restraints excluded: chain B residue  421 SER
Chi-restraints excluded: chain B residue  555 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 98 optimal weight:    4.9990
   chunk 119 optimal weight:    0.8980
   chunk 84 optimal weight:    0.6980
   chunk 111 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9980
   chunk 102 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 409 GLN
B 133 GLN
B 422 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.201062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.153021 restraints weight = 15709.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.156515 restraints weight = 9038.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.159022 restraints weight = 6426.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7202
moved from start:          0.4482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9861  Z= 0.194
  Angle     :  0.572  13.803  13399  Z= 0.288
  Chirality :  0.042   0.155   1578
  Planarity :  0.004   0.046   1671
  Dihedral  :  3.696  18.639   1321
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 13.98 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.24), residues: 1223
  helix:  1.72 (0.18), residues: 827
  sheet:  None (None), residues: 0
  loop : -0.93 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 121 
 HIS   0.005   0.001   HIS A 513 
 PHE   0.015   0.001   PHE B 185 
 TYR   0.020   0.001   TYR B 140 
 ARG   0.005   0.000   ARG A 273 

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 214
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 GLN cc_start: 0.7539 (mt0) cc_final: 0.7159 (tp40)
REVERT: A  292 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8086 (mm)
REVERT: A  314 PHE cc_start: 0.5761 (m-80) cc_final: 0.5495 (m-80)
REVERT: A  374 ILE cc_start: 0.8586 (tt) cc_final: 0.8359 (mt)
REVERT: A  477 MET cc_start: 0.7477 (mmm) cc_final: 0.7254 (mmm)
REVERT: B  344 LYS cc_start: 0.7890 (mmtm) cc_final: 0.7647 (mmmm)
REVERT: B  374 ILE cc_start: 0.8584 (tt) cc_final: 0.8357 (mt)
REVERT: B  383 PHE cc_start: 0.8297 (t80) cc_final: 0.7999 (t80)
REVERT: B  453 PRO cc_start: 0.8380 (Cg_endo) cc_final: 0.8163 (Cg_exo)
REVERT: B  584 MET cc_start: 0.0108 (tpt) cc_final: -0.0122 (tpt)
  outliers start: 26
  outliers final: 16
  residues processed: 228
  average time/residue: 0.2117
  time to fit residues: 67.9529
Evaluate side-chains
  223 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 206
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  420 THR
Chi-restraints excluded: chain B residue  806 THR
Chi-restraints excluded: chain B residue  816 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 103 optimal weight:    0.5980
   chunk 49 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 409 GLN
B 133 GLN
B 210 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.205485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.158973 restraints weight = 15540.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.162382 restraints weight = 9165.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.164594 restraints weight = 6522.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
moved from start:          0.4830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9861  Z= 0.189
  Angle     :  0.555  14.135  13399  Z= 0.278
  Chirality :  0.041   0.172   1578
  Planarity :  0.004   0.054   1671
  Dihedral  :  3.566  17.256   1321
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 12.82 %
    Favored  : 84.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.24), residues: 1223
  helix:  1.80 (0.18), residues: 829
  sheet:  None (None), residues: 0
  loop : -0.90 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 444 
 HIS   0.005   0.001   HIS B 210 
 PHE   0.020   0.001   PHE A 279 
 TYR   0.015   0.001   TYR A 179 
 ARG   0.003   0.000   ARG B 343 

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 229
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 ILE cc_start: 0.8702 (mt) cc_final: 0.8447 (mm)
REVERT: A  314 PHE cc_start: 0.5778 (m-80) cc_final: 0.5529 (m-80)
REVERT: B  178 GLU cc_start: 0.6208 (OUTLIER) cc_final: 0.5868 (pm20)
REVERT: B  292 LEU cc_start: 0.8147 (mt) cc_final: 0.7917 (mm)
REVERT: B  344 LYS cc_start: 0.8018 (mmtm) cc_final: 0.7729 (mmmm)
REVERT: B  383 PHE cc_start: 0.8328 (t80) cc_final: 0.8025 (t80)
  outliers start: 29
  outliers final: 19
  residues processed: 243
  average time/residue: 0.2152
  time to fit residues: 73.3469
Evaluate side-chains
  229 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 209
  time to evaluate  : 1.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  420 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   chunk 36 optimal weight:    7.9990
   chunk 97 optimal weight:    0.5980
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.4286 r_free = 0.4286 target = 0.198436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.151320 restraints weight = 15668.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.154792 restraints weight = 9079.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.157213 restraints weight = 6433.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.5301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9861  Z= 0.220
  Angle     :  0.605  15.481  13399  Z= 0.299
  Chirality :  0.043   0.244   1578
  Planarity :  0.005   0.057   1671
  Dihedral  :  3.611  17.112   1321
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.34 %
    Favored  : 81.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.24), residues: 1223
  helix:  1.75 (0.18), residues: 830
  sheet:  None (None), residues: 0
  loop : -0.75 (0.32), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 121 
 HIS   0.004   0.001   HIS A 513 
 PHE   0.023   0.002   PHE B 289 
 TYR   0.016   0.002   TYR A 140 
 ARG   0.006   0.000   ARG A 273 

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 224
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  395 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6907 (mt-10)
REVERT: B  218 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.6490 (mt)
REVERT: B  383 PHE cc_start: 0.8286 (t80) cc_final: 0.8000 (t80)
  outliers start: 34
  outliers final: 27
  residues processed: 239
  average time/residue: 0.2127
  time to fit residues: 71.6006
Evaluate side-chains
  238 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 210
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  252 PHE
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  806 THR
Chi-restraints excluded: chain B residue  166 GLU
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  420 THR
Chi-restraints excluded: chain B residue  421 SER
Chi-restraints excluded: chain B residue  501 VAL
Chi-restraints excluded: chain B residue  806 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0000
   chunk 67 optimal weight:    2.9990
   chunk 112 optimal weight:    7.9990
   chunk 117 optimal weight:    3.9990
   chunk 23 optimal weight:    0.5980
   chunk 122 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   overall best weight:    0.7188

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

Flipped N/Q/H residues before XYZ refinement:
A 274 ASN
** B 274 ASN ** 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 = 0.4290 r_free = 0.4290 target = 0.198861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.152184 restraints weight = 15766.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.155586 restraints weight = 9094.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.157899 restraints weight = 6443.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7235
moved from start:          0.5452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9861  Z= 0.175
  Angle     :  0.581  15.691  13399  Z= 0.282
  Chirality :  0.041   0.179   1578
  Planarity :  0.004   0.055   1671
  Dihedral  :  3.520  15.649   1321
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 17.77 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.24), residues: 1223
  helix:  1.83 (0.18), residues: 829
  sheet:  None (None), residues: 0
  loop : -0.66 (0.33), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 444 
 HIS   0.004   0.001   HIS A 513 
 PHE   0.023   0.001   PHE A 279 
 TYR   0.017   0.001   TYR A 140 
 ARG   0.006   0.000   ARG A 273 

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 219
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6776 (pm20)
REVERT: A  314 PHE cc_start: 0.5846 (m-80) cc_final: 0.5419 (m-80)
REVERT: B  218 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.6501 (mt)
REVERT: B  292 LEU cc_start: 0.8193 (mt) cc_final: 0.7989 (mm)
REVERT: B  344 LYS cc_start: 0.7933 (mmtm) cc_final: 0.7586 (mmmm)
REVERT: B  383 PHE cc_start: 0.8278 (t80) cc_final: 0.7987 (t80)
  outliers start: 27
  outliers final: 17
  residues processed: 230
  average time/residue: 0.2207
  time to fit residues: 70.7206
Evaluate side-chains
  231 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 212
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  806 THR
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain B residue  166 GLU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  252 PHE
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  420 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 98 optimal weight:    0.0010
   chunk 91 optimal weight:    0.1980
   chunk 83 optimal weight:    0.9980
   chunk 118 optimal weight:    5.9990
   chunk 12 optimal weight:    0.6980
   chunk 61 optimal weight:    0.1980
   chunk 39 optimal weight:    8.9990
   chunk 36 optimal weight:   10.0000
   chunk 109 optimal weight:    6.9990
   chunk 104 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 274 ASN
B 133 GLN
B 274 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.197035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.152658 restraints weight = 15771.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.153171 restraints weight = 10839.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.154989 restraints weight = 8476.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.5528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9861  Z= 0.169
  Angle     :  0.575  14.378  13399  Z= 0.281
  Chirality :  0.042   0.184   1578
  Planarity :  0.004   0.057   1671
  Dihedral  :  3.485  14.951   1321
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 18.54 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.24), residues: 1223
  helix:  1.87 (0.18), residues: 829
  sheet:  None (None), residues: 0
  loop : -0.66 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 444 
 HIS   0.006   0.001   HIS A 210 
 PHE   0.024   0.001   PHE B 287 
 TYR   0.018   0.001   TYR B 140 
 ARG   0.007   0.000   ARG A 273 

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 221
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 TRP cc_start: 0.7022 (t-100) cc_final: 0.6004 (t60)
REVERT: A  186 ILE cc_start: 0.8547 (mm) cc_final: 0.8342 (mm)
REVERT: A  205 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6719 (pm20)
REVERT: A  314 PHE cc_start: 0.5649 (m-80) cc_final: 0.5408 (m-80)
REVERT: B  167 MET cc_start: 0.7259 (mmm) cc_final: 0.7051 (mmm)
REVERT: B  218 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.6575 (mt)
REVERT: B  292 LEU cc_start: 0.8161 (mt) cc_final: 0.7953 (mm)
REVERT: B  344 LYS cc_start: 0.7930 (mmtm) cc_final: 0.7592 (mmmm)
REVERT: B  383 PHE cc_start: 0.8205 (t80) cc_final: 0.7935 (t80)
REVERT: B  832 LEU cc_start: -0.2723 (OUTLIER) cc_final: -0.3135 (mp)
  outliers start: 28
  outliers final: 19
  residues processed: 231
  average time/residue: 0.2152
  time to fit residues: 69.6984
Evaluate side-chains
  234 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 212
  time to evaluate  : 1.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  252 PHE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  806 THR
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain B residue  166 GLU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  252 PHE
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  420 THR
Chi-restraints excluded: chain B residue  421 SER
Chi-restraints excluded: chain B residue  501 VAL
Chi-restraints excluded: chain B residue  832 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 113 optimal weight:    0.0170
   chunk 4 optimal weight:    0.9980
   chunk 64 optimal weight:    0.6980
   chunk 92 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 13 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 101 optimal weight:    4.9990
   chunk 18 optimal weight:    0.4980
   chunk 88 optimal weight:    0.6980
   chunk 14 optimal weight:    5.9990
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
A 274 ASN
B 274 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.199075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.152309 restraints weight = 15948.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.155811 restraints weight = 9098.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.158226 restraints weight = 6364.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
moved from start:          0.5665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9861  Z= 0.172
  Angle     :  0.591  14.686  13399  Z= 0.286
  Chirality :  0.042   0.183   1578
  Planarity :  0.004   0.058   1671
  Dihedral  :  3.462  15.044   1321
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 19.32 %
    Favored  : 77.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.24), residues: 1223
  helix:  1.87 (0.18), residues: 829
  sheet:  None (None), residues: 0
  loop : -0.57 (0.33), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 276 
 HIS   0.004   0.000   HIS A 210 
 PHE   0.026   0.001   PHE B  93 
 TYR   0.020   0.001   TYR B 140 
 ARG   0.007   0.000   ARG A 273 

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 220
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 TRP cc_start: 0.6998 (t-100) cc_final: 0.6038 (t60)
REVERT: A  205 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6759 (pm20)
REVERT: A  314 PHE cc_start: 0.5693 (m-80) cc_final: 0.5467 (m-80)
REVERT: B  218 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.6579 (mt)
REVERT: B  344 LYS cc_start: 0.7969 (mmtm) cc_final: 0.7655 (mmmm)
REVERT: B  383 PHE cc_start: 0.8140 (t80) cc_final: 0.7872 (t80)
  outliers start: 30
  outliers final: 22
  residues processed: 233
  average time/residue: 0.2126
  time to fit residues: 70.0118
Evaluate side-chains
  238 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 214
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  252 PHE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  806 THR
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  252 PHE
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  420 THR
Chi-restraints excluded: chain B residue  421 SER
Chi-restraints excluded: chain B residue  501 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 90 optimal weight:    7.9990
   chunk 38 optimal weight:    0.5980
   chunk 89 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9980
   chunk 15 optimal weight:    7.9990
   chunk 110 optimal weight:   20.0000
   chunk 100 optimal weight:    0.7980
   chunk 111 optimal weight:    0.5980
   chunk 74 optimal weight:    0.5980
   chunk 78 optimal weight:    0.7980
   chunk 82 optimal weight:    0.0970
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A 274 ASN
B 274 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.198773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.151832 restraints weight = 15699.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.155258 restraints weight = 9188.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.157690 restraints weight = 6484.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7233
moved from start:          0.5785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9861  Z= 0.172
  Angle     :  0.603  15.260  13399  Z= 0.293
  Chirality :  0.042   0.181   1578
  Planarity :  0.004   0.060   1671
  Dihedral  :  3.445  15.338   1321
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 19.32 %
    Favored  : 78.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.25), residues: 1223
  helix:  1.79 (0.18), residues: 835
  sheet:  None (None), residues: 0
  loop : -0.55 (0.33), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 295 
 HIS   0.004   0.001   HIS A 210 
 PHE   0.031   0.001   PHE B 287 
 TYR   0.023   0.001   TYR B 140 
 ARG   0.007   0.000   ARG A 273 

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 219
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 TRP cc_start: 0.6943 (t-100) cc_final: 0.6015 (t60)
REVERT: A  186 ILE cc_start: 0.8458 (mm) cc_final: 0.8219 (mm)
REVERT: A  205 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6706 (pm20)
REVERT: A  314 PHE cc_start: 0.5784 (m-80) cc_final: 0.5261 (m-80)
REVERT: A  492 TYR cc_start: 0.6788 (m-80) cc_final: 0.6485 (m-80)
REVERT: B  218 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.6666 (mt)
REVERT: B  344 LYS cc_start: 0.7959 (mmtm) cc_final: 0.7603 (mmmm)
REVERT: B  383 PHE cc_start: 0.8035 (t80) cc_final: 0.7832 (t80)
REVERT: B  611 MET cc_start: 0.0781 (mmp) cc_final: 0.0421 (mtp)
REVERT: B  832 LEU cc_start: -0.2665 (OUTLIER) cc_final: -0.2975 (mp)
  outliers start: 27
  outliers final: 20
  residues processed: 229
  average time/residue: 0.2287
  time to fit residues: 74.8719
Evaluate side-chains
  236 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 213
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  252 PHE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  621 MET
Chi-restraints excluded: chain A residue  806 THR
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  420 THR
Chi-restraints excluded: chain B residue  421 SER
Chi-restraints excluded: chain B residue  832 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 112 optimal weight:    0.9990
   chunk 100 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 63 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 48 optimal weight:   20.0000
   chunk 103 optimal weight:    0.5980
   chunk 105 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 59 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 274 ASN
B 274 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.198158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.152219 restraints weight = 15973.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.155820 restraints weight = 9042.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.158158 restraints weight = 6241.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7234
moved from start:          0.5998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9861  Z= 0.190
  Angle     :  0.640  15.580  13399  Z= 0.306
  Chirality :  0.043   0.196   1578
  Planarity :  0.004   0.062   1671
  Dihedral  :  3.475  16.041   1321
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 20.58 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.25), residues: 1223
  helix:  1.76 (0.18), residues: 835
  sheet:  None (None), residues: 0
  loop : -0.49 (0.33), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 276 
 HIS   0.004   0.001   HIS A 817 
 PHE   0.031   0.001   PHE B 287 
 TYR   0.027   0.001   TYR B 140 
 ARG   0.007   0.000   ARG A 273 

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 211
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 TRP cc_start: 0.6848 (t-100) cc_final: 0.5934 (t60)
REVERT: A  314 PHE cc_start: 0.5877 (m-80) cc_final: 0.5359 (m-80)
REVERT: A  492 TYR cc_start: 0.6841 (m-80) cc_final: 0.6566 (m-80)
REVERT: A  817 HIS cc_start: 0.5714 (t70) cc_final: 0.5460 (t70)
REVERT: B  218 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.6655 (mt)
REVERT: B  219 LEU cc_start: 0.8848 (tp) cc_final: 0.8581 (tp)
REVERT: B  344 LYS cc_start: 0.8022 (mmtm) cc_final: 0.7674 (mmmm)
REVERT: B  383 PHE cc_start: 0.8102 (t80) cc_final: 0.7841 (t80)
REVERT: B  832 LEU cc_start: -0.2654 (OUTLIER) cc_final: -0.2993 (mp)
  outliers start: 26
  outliers final: 23
  residues processed: 221
  average time/residue: 0.2109
  time to fit residues: 65.5558
Evaluate side-chains
  234 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 209
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  252 PHE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  621 MET
Chi-restraints excluded: chain A residue  806 THR
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  420 THR
Chi-restraints excluded: chain B residue  421 SER
Chi-restraints excluded: chain B residue  832 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0570
   chunk 2 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 40 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9980
   chunk 121 optimal weight:    2.9990
   overall best weight:    0.7300

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

Flipped N/Q/H residues before XYZ refinement:
A 274 ASN
B 274 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.198982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.152706 restraints weight = 15872.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.156275 restraints weight = 9047.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.158239 restraints weight = 6330.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
moved from start:          0.6160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9861  Z= 0.187
  Angle     :  0.633  15.415  13399  Z= 0.305
  Chirality :  0.043   0.198   1578
  Planarity :  0.004   0.062   1671
  Dihedral  :  3.496  16.107   1321
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 20.78 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.24), residues: 1223
  helix:  1.81 (0.18), residues: 828
  sheet:  None (None), residues: 0
  loop : -0.46 (0.32), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 276 
 HIS   0.003   0.001   HIS A 210 
 PHE   0.032   0.001   PHE B 287 
 TYR   0.028   0.001   TYR B 140 
 ARG   0.007   0.000   ARG A 273 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3233.85 seconds
wall clock time: 58 minutes 51.69 seconds (3531.69 seconds total)