Starting phenix.real_space_refine
on Fri Mar 14 04:09:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xf5_33169/03_2025/7xf5_33169.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xf5_33169/03_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_33169/03_2025/7xf5_33169.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xf5_33169/03_2025/7xf5_33169.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xf5_33169/03_2025/7xf5_33169.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xf5_33169/03_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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 6.16, per 1000 atoms: 0.64
  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: 2.49
  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: 2.79

  Time building geometry restraints manager: 2.94 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:             1.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.470
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     24.790
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.890
-------------------------------------------------------------------------------
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  : 0.978 
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: 0.2351
  time to fit residues: 111.4012
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  : 1.070 
-------------------------------------------------------------------------------
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 = 0.159022 restraints weight = 15651.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.162693 restraints weight = 8678.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.165294 restraints weight = 5960.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7208
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  : 1.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  274 ASN cc_start: 0.8141 (m-40) cc_final: 0.7938 (m110)
REVERT: A  309 ARG cc_start: 0.7367 (ttp-170) cc_final: 0.7084 (mtm110)
REVERT: A  374 ILE cc_start: 0.8576 (tt) cc_final: 0.8085 (mt)
REVERT: A  453 PRO cc_start: 0.8322 (Cg_endo) cc_final: 0.8093 (Cg_exo)
REVERT: B  178 GLU cc_start: 0.6288 (OUTLIER) cc_final: 0.5967 (pm20)
REVERT: B  214 MET cc_start: 0.7588 (mtp) cc_final: 0.7342 (mtp)
REVERT: B  252 PHE cc_start: 0.5767 (m-80) cc_final: 0.4931 (m-80)
REVERT: B  374 ILE cc_start: 0.8632 (tt) cc_final: 0.8329 (mt)
REVERT: B  383 PHE cc_start: 0.8313 (t80) cc_final: 0.8015 (t80)
REVERT: B  453 PRO cc_start: 0.8354 (Cg_endo) cc_final: 0.8094 (Cg_exo)
  outliers start: 31
  outliers final: 20
  residues processed: 269
  average time/residue: 0.2359
  time to fit residues: 89.7072
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  : 1.231 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 98 optimal weight:   10.0000
   chunk 119 optimal weight:    0.7980
   chunk 84 optimal weight:    0.0050
   chunk 111 optimal weight:    0.4980
   chunk 97 optimal weight:    0.7980
   chunk 102 optimal weight:    0.0970
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.4192

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

Flipped N/Q/H residues before XYZ refinement:
A 409 GLN
A 631 GLN
** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 422 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.202862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.155552 restraints weight = 15722.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.159165 restraints weight = 9172.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.161614 restraints weight = 6472.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.4357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9861  Z= 0.172
  Angle     :  0.567  13.786  13399  Z= 0.284
  Chirality :  0.042   0.155   1578
  Planarity :  0.004   0.046   1671
  Dihedral  :  3.656  18.531   1321
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 13.69 %
    Favored  : 83.98 %
  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:  1.37 (0.24), residues: 1223
  helix:  1.74 (0.18), residues: 827
  sheet:  None (None), residues: 0
  loop : -0.87 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  91 
 HIS   0.005   0.001   HIS A 210 
 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
  245 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 221
  time to evaluate  : 1.451 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 ARG cc_start: 0.7373 (ttp-170) cc_final: 0.5934 (ttp-170)
REVERT: A  314 PHE cc_start: 0.5763 (m-80) cc_final: 0.5483 (m-80)
REVERT: A  374 ILE cc_start: 0.8569 (tt) cc_final: 0.8275 (mt)
REVERT: A  453 PRO cc_start: 0.8390 (Cg_endo) cc_final: 0.8185 (Cg_exo)
REVERT: B  178 GLU cc_start: 0.6210 (OUTLIER) cc_final: 0.5900 (pm20)
REVERT: B  344 LYS cc_start: 0.7868 (mmtm) cc_final: 0.7657 (mmmm)
REVERT: B  360 MET cc_start: 0.4832 (ptp) cc_final: 0.4561 (ptm)
REVERT: B  374 ILE cc_start: 0.8576 (tt) cc_final: 0.8364 (mt)
REVERT: B  383 PHE cc_start: 0.8276 (t80) cc_final: 0.8004 (t80)
REVERT: B  453 PRO cc_start: 0.8346 (Cg_endo) cc_final: 0.8137 (Cg_exo)
  outliers start: 24
  outliers final: 14
  residues processed: 233
  average time/residue: 0.2594
  time to fit residues: 86.6902
Evaluate side-chains
  215 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 200
  time to evaluate  : 1.749 
-------------------------------------------------------------------------------
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  387 MET
Chi-restraints excluded: chain A residue  420 THR
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  420 THR
Chi-restraints excluded: chain B residue  515 VAL
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:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0770
   chunk 103 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0040
   chunk 41 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 73 optimal weight:    0.2980
   chunk 29 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.4150

-------------------------------------------------------------------------------
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 = 0.4334 r_free = 0.4334 target = 0.203230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.155974 restraints weight = 15545.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.159622 restraints weight = 8868.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.162050 restraints weight = 6198.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7161
moved from start:          0.4602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9861  Z= 0.166
  Angle     :  0.551  13.731  13399  Z= 0.273
  Chirality :  0.041   0.173   1578
  Planarity :  0.004   0.035   1671
  Dihedral  :  3.517  16.529   1321
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 13.59 %
    Favored  : 83.98 %
  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:  1.51 (0.24), residues: 1223
  helix:  1.81 (0.18), residues: 829
  sheet:  None (None), residues: 0
  loop : -0.76 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 444 
 HIS   0.004   0.001   HIS B 210 
 PHE   0.019   0.001   PHE A 287 
 TYR   0.013   0.001   TYR B 134 
 ARG   0.003   0.000   ARG A 273 

*********************** 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
  249 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 224
  time to evaluate  : 1.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  314 PHE cc_start: 0.5766 (m-80) cc_final: 0.5515 (m-80)
REVERT: B  344 LYS cc_start: 0.7935 (mmtm) cc_final: 0.7656 (mmmm)
REVERT: B  383 PHE cc_start: 0.8211 (t80) cc_final: 0.7916 (t80)
REVERT: B  453 PRO cc_start: 0.8392 (Cg_endo) cc_final: 0.8156 (Cg_exo)
  outliers start: 25
  outliers final: 16
  residues processed: 235
  average time/residue: 0.2785
  time to fit residues: 92.5789
Evaluate side-chains
  222 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 206
  time to evaluate  : 1.396 
-------------------------------------------------------------------------------
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  387 MET
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  387 MET
Chi-restraints excluded: chain B residue  420 THR
Chi-restraints excluded: chain B residue  515 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 3 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 105 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.4314 r_free = 0.4314 target = 0.201061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.153715 restraints weight = 15679.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.157350 restraints weight = 8986.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.159529 restraints weight = 6316.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7204
moved from start:          0.4926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9861  Z= 0.181
  Angle     :  0.578  14.407  13399  Z= 0.283
  Chirality :  0.042   0.213   1578
  Planarity :  0.004   0.057   1671
  Dihedral  :  3.482  15.906   1321
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 15.63 %
    Favored  : 81.75 %
  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:  1.55 (0.24), residues: 1223
  helix:  1.83 (0.18), residues: 829
  sheet:  None (None), residues: 0
  loop : -0.69 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 276 
 HIS   0.004   0.001   HIS A 513 
 PHE   0.026   0.001   PHE B 289 
 TYR   0.013   0.001   TYR A 140 
 ARG   0.008   0.000   ARG B 357 

*********************** 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
  236 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 209
  time to evaluate  : 1.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  218 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.6585 (mt)
REVERT: B  383 PHE cc_start: 0.8218 (t80) cc_final: 0.7950 (t80)
REVERT: B  453 PRO cc_start: 0.8376 (Cg_endo) cc_final: 0.8136 (Cg_exo)
  outliers start: 27
  outliers final: 20
  residues processed: 220
  average time/residue: 0.2293
  time to fit residues: 70.2494
Evaluate side-chains
  224 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 203
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
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  252 PHE
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  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  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  515 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 32 optimal weight:    8.9990
   chunk 67 optimal weight:    2.9990
   chunk 112 optimal weight:    8.9990
   chunk 117 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 122 optimal weight:    5.9990
   chunk 16 optimal weight:    0.8980
   chunk 62 optimal weight:    4.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 817 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.192917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.147912 restraints weight = 15888.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.147678 restraints weight = 11608.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.148737 restraints weight = 8874.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.5719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9861  Z= 0.263
  Angle     :  0.657  16.055  13399  Z= 0.326
  Chirality :  0.044   0.171   1578
  Planarity :  0.005   0.051   1671
  Dihedral  :  3.773  17.672   1321
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 17.09 %
    Favored  : 79.81 %
  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:  1.26 (0.24), residues: 1223
  helix:  1.59 (0.18), residues: 829
  sheet:  None (None), residues: 0
  loop : -0.77 (0.33), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 276 
 HIS   0.005   0.001   HIS B 210 
 PHE   0.017   0.002   PHE A 287 
 TYR   0.017   0.002   TYR A 140 
 ARG   0.004   0.000   ARG A 361 

*********************** 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
  249 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 217
  time to evaluate  : 1.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  297 ARG cc_start: 0.6688 (mtp85) cc_final: 0.5954 (tmm160)
REVERT: A  314 PHE cc_start: 0.5967 (m-80) cc_final: 0.5621 (m-80)
REVERT: A  819 TYR cc_start: 0.5700 (m-80) cc_final: 0.5359 (m-10)
REVERT: B  214 MET cc_start: 0.7705 (ptp) cc_final: 0.7418 (ptp)
REVERT: B  218 LEU cc_start: 0.7449 (tt) cc_final: 0.6545 (mt)
REVERT: B  344 LYS cc_start: 0.8018 (mmtm) cc_final: 0.7705 (mmmm)
REVERT: B  383 PHE cc_start: 0.8256 (t80) cc_final: 0.7955 (t80)
  outliers start: 32
  outliers final: 23
  residues processed: 235
  average time/residue: 0.2101
  time to fit residues: 69.5421
Evaluate side-chains
  223 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 200
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  160 VAL
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  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  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  182 LEU
Chi-restraints excluded: chain B residue  208 PHE
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  501 VAL
Chi-restraints excluded: chain B residue  515 VAL
Chi-restraints excluded: chain B residue  806 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 98 optimal weight:    0.0970
   chunk 91 optimal weight:    0.7980
   chunk 83 optimal weight:    2.9990
   chunk 118 optimal weight:    0.0670
   chunk 12 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 39 optimal weight:    7.9990
   chunk 36 optimal weight:    4.9990
   chunk 109 optimal weight:    0.0020
   chunk 104 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.3724

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

Flipped N/Q/H residues before XYZ refinement:
A 232 ASN
A 274 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.195061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.149912 restraints weight = 15959.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.151615 restraints weight = 10906.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.152317 restraints weight = 8021.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.5811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9861  Z= 0.171
  Angle     :  0.595  13.985  13399  Z= 0.290
  Chirality :  0.042   0.176   1578
  Planarity :  0.005   0.059   1671
  Dihedral  :  3.579  15.508   1321
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 18.83 %
    Favored  : 78.83 %
  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:  1.49 (0.24), residues: 1223
  helix:  1.78 (0.18), residues: 829
  sheet:  None (None), residues: 0
  loop : -0.71 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 121 
 HIS   0.005   0.001   HIS A 210 
 PHE   0.021   0.001   PHE A 287 
 TYR   0.020   0.001   TYR B 140 
 ARG   0.005   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
  242 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 218
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  218 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6601 (mt)
REVERT: B  383 PHE cc_start: 0.8252 (t80) cc_final: 0.7921 (t80)
REVERT: B  832 LEU cc_start: -0.2673 (OUTLIER) cc_final: -0.3014 (mp)
  outliers start: 24
  outliers final: 16
  residues processed: 226
  average time/residue: 0.2093
  time to fit residues: 66.1450
Evaluate side-chains
  223 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 205
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  256 ILE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  621 MET
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  292 LEU
Chi-restraints excluded: chain B residue  420 THR
Chi-restraints excluded: chain B residue  515 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:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 92 optimal weight:    0.3980
   chunk 80 optimal weight:    6.9990
   chunk 13 optimal weight:    0.8980
   chunk 40 optimal weight:    9.9990
   chunk 101 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 88 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 274 ASN
A 817 HIS
B 133 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.194575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.147507 restraints weight = 16177.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.150576 restraints weight = 10008.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.152650 restraints weight = 7375.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.5960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9861  Z= 0.188
  Angle     :  0.607  15.048  13399  Z= 0.295
  Chirality :  0.043   0.210   1578
  Planarity :  0.004   0.055   1671
  Dihedral  :  3.553  15.280   1321
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 18.74 %
    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:  1.47 (0.24), residues: 1223
  helix:  1.74 (0.18), residues: 834
  sheet:  None (None), residues: 0
  loop : -0.68 (0.32), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 406 
 HIS   0.004   0.001   HIS A 210 
 PHE   0.022   0.001   PHE B 287 
 TYR   0.016   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
  239 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 213
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  218 LEU cc_start: 0.7417 (tt) cc_final: 0.6652 (mt)
REVERT: B  340 TYR cc_start: 0.7208 (t80) cc_final: 0.6922 (t80)
REVERT: B  383 PHE cc_start: 0.8155 (t80) cc_final: 0.7848 (t80)
REVERT: B  611 MET cc_start: 0.1156 (mmp) cc_final: 0.0860 (mtp)
  outliers start: 26
  outliers final: 19
  residues processed: 223
  average time/residue: 0.2093
  time to fit residues: 67.2309
Evaluate side-chains
  223 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 204
  time to evaluate  : 1.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  501 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  166 GLU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  252 PHE
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  420 THR
Chi-restraints excluded: chain B residue  501 VAL
Chi-restraints excluded: chain B residue  515 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 90 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 89 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 15 optimal weight:    5.9990
   chunk 110 optimal weight:    6.9990
   chunk 100 optimal weight:    3.9990
   chunk 111 optimal weight:    5.9990
   chunk 74 optimal weight:    0.6980
   chunk 78 optimal weight:    3.9990
   chunk 82 optimal weight:    0.4980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A 274 ASN
A 817 HIS
B 274 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.195494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.149731 restraints weight = 15865.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.153080 restraints weight = 9226.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.155296 restraints weight = 6535.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.6248

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= 0.212
  Angle     :  0.639  15.174  13399  Z= 0.310
  Chirality :  0.044   0.196   1578
  Planarity :  0.005   0.054   1671
  Dihedral  :  3.614  15.640   1321
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 19.42 %
    Favored  : 77.96 %
  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:  1.37 (0.24), residues: 1223
  helix:  1.66 (0.18), residues: 835
  sheet:  None (None), residues: 0
  loop : -0.72 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 121 
 HIS   0.004   0.001   HIS A 210 
 PHE   0.025   0.001   PHE B 287 
 TYR   0.022   0.002   TYR B 140 
 ARG   0.006   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
  235 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 208
  time to evaluate  : 1.063 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 ILE cc_start: 0.8572 (mm) cc_final: 0.8366 (mm)
REVERT: A  817 HIS cc_start: 0.5666 (t-170) cc_final: 0.5413 (t70)
REVERT: B  167 MET cc_start: 0.7193 (mmm) cc_final: 0.6798 (mmm)
REVERT: B  214 MET cc_start: 0.7779 (ptp) cc_final: 0.7399 (ptp)
REVERT: B  218 LEU cc_start: 0.7458 (tt) cc_final: 0.6679 (mt)
REVERT: B  340 TYR cc_start: 0.7298 (t80) cc_final: 0.6985 (t80)
REVERT: B  383 PHE cc_start: 0.8172 (t80) cc_final: 0.7838 (t80)
  outliers start: 27
  outliers final: 24
  residues processed: 220
  average time/residue: 0.2019
  time to fit residues: 63.3747
Evaluate side-chains
  229 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 205
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 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  256 ILE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  341 LEU
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  252 PHE
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  420 THR
Chi-restraints excluded: chain B residue  501 VAL
Chi-restraints excluded: chain B residue  515 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 112 optimal weight:    4.9990
   chunk 100 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 63 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 48 optimal weight:   10.0000
   chunk 103 optimal weight:    0.6980
   chunk 105 optimal weight:    0.5980
   chunk 16 optimal weight:    0.4980
   chunk 59 optimal weight:    0.0670
   overall best weight:    0.5118

-------------------------------------------------------------------------------
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 = 0.4266 r_free = 0.4266 target = 0.196752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.151027 restraints weight = 16087.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.153738 restraints weight = 10191.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.154830 restraints weight = 6875.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7287
moved from start:          0.6302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9861  Z= 0.177
  Angle     :  0.630  15.165  13399  Z= 0.304
  Chirality :  0.043   0.185   1578
  Planarity :  0.005   0.062   1671
  Dihedral  :  3.532  15.086   1321
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 20.00 %
    Favored  : 77.67 %
  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:  1.49 (0.24), residues: 1223
  helix:  1.74 (0.18), residues: 834
  sheet:  None (None), residues: 0
  loop : -0.64 (0.32), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 406 
 HIS   0.004   0.000   HIS A 210 
 PHE   0.039   0.001   PHE B 287 
 TYR   0.022   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
  242 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 218
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  167 MET cc_start: 0.7070 (mmm) cc_final: 0.6677 (mmm)
REVERT: B  218 LEU cc_start: 0.7434 (tt) cc_final: 0.6657 (mt)
REVERT: B  340 TYR cc_start: 0.7213 (t80) cc_final: 0.6849 (t80)
REVERT: B  344 LYS cc_start: 0.7964 (mmtm) cc_final: 0.7614 (mmmm)
REVERT: B  383 PHE cc_start: 0.8217 (t80) cc_final: 0.7877 (t80)
REVERT: B  611 MET cc_start: 0.1082 (mmp) cc_final: 0.0814 (mtp)
  outliers start: 24
  outliers final: 21
  residues processed: 227
  average time/residue: 0.2013
  time to fit residues: 65.1682
Evaluate side-chains
  236 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 215
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  292 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  621 MET
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  252 PHE
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  420 THR
Chi-restraints excluded: chain B residue  501 VAL
Chi-restraints excluded: chain B residue  515 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 96 optimal weight:    0.0670
   chunk 51 optimal weight:    4.9990
   chunk 2 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 92 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 121 optimal weight:    3.9990
   overall best weight:    0.6118

-------------------------------------------------------------------------------
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 = 0.4265 r_free = 0.4265 target = 0.196367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.150116 restraints weight = 15857.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.153600 restraints weight = 9174.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.155596 restraints weight = 6433.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
moved from start:          0.6395

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= 0.178
  Angle     :  0.619  15.051  13399  Z= 0.302
  Chirality :  0.043   0.191   1578
  Planarity :  0.004   0.061   1671
  Dihedral  :  3.513  14.907   1321
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 20.29 %
    Favored  : 77.57 %
  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:  1.50 (0.24), residues: 1223
  helix:  1.71 (0.18), residues: 837
  sheet:  None (None), residues: 0
  loop : -0.57 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 406 
 HIS   0.003   0.001   HIS A 513 
 PHE   0.040   0.001   PHE B 287 
 TYR   0.024   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: 3539.22 seconds
wall clock time: 64 minutes 54.20 seconds (3894.20 seconds total)