Starting phenix.real_space_refine
on Thu Sep 18 02:39:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tt7_26113/09_2025/7tt7_26113.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tt7_26113/09_2025/7tt7_26113.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tt7_26113/09_2025/7tt7_26113.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tt7_26113/09_2025/7tt7_26113.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tt7_26113/09_2025/7tt7_26113.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tt7_26113/09_2025/7tt7_26113.cif"
  }
  resolution = 4.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.006 sd=   0.048
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: 5
    Type Number    sf(0)   Gaussians
     S      26      5.16       5
     C    4323      2.51       5
     N    1158      2.21       5
     O    1321      1.98       5
     H    6468      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13296
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 496, 7625
          Classifications: {'peptide': 496}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 477}
          Chain breaks: 7
    Chain: "C"
      Number of atoms: 396
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 396
          Classifications: {'peptide': 28}
          Link IDs: {'PTRANS': 4, 'TRANS': 23}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1381
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 1381
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 5, 'TRANS': 83}
    Chain: "D"
      Number of atoms: 1599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 1599
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 3, 'TRANS': 98}
          Chain breaks: 3
    Chain: "P"
      Number of atoms: 2295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 152, 2295
          Classifications: {'peptide': 152}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 150}
          Chain breaks: 8
  Time building chain proxies: 2.79, per 1000 atoms: 0.21
  Number of scatterers: 13296
  At special positions: 0
  Unit cell: (92.3485, 94.4962, 128.858, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      26     16.00
     O    1321      8.00
     N    1158      7.00
     C    4323      6.00
     H    6468      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 425 " - pdb=" SG  CYS P1299 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 690 " - pdb=" SG  CYS A 700 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.23
  Conformation dependent library (CDL) restraints added in 763.9 milliseconds
  
  Enol-peptide restraints added in 1.7 microseconds
  

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1568

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 6 sheets defined
      21.0% alpha, 37.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 280 through 289
    Processing helix  chain 'A' and resid 300 through 313
    Processing helix  chain 'A' and resid 361 through 366
      removed outlier: 4.076A  pdb=" N   LEU A 365 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ARG A 366 " --> pdb=" O   ASP A 362 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 361 through 366'
    Processing helix  chain 'A' and resid 367 through 369
      No H-bonds generated for 'chain 'A' and resid 367 through 369'
    Processing helix  chain 'A' and resid 378 through 393
      removed outlier: 3.586A  pdb=" N   VAL A 382 " --> pdb=" O   GLY A 378 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLY A 385 " --> pdb=" O   LEU A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 452
    Processing helix  chain 'A' and resid 542 through 552
      removed outlier: 3.664A  pdb=" N   MET A 552 " --> pdb=" O   TYR A 548 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 651
    Processing helix  chain 'A' and resid 688 through 692
    Processing helix  chain 'C' and resid 39 through 44
    Processing helix  chain 'E' and resid 23 through 27
    Processing helix  chain 'E' and resid 39 through 44
    Processing helix  chain 'E' and resid 51 through 60
    Processing helix  chain 'D' and resid 116 through 121
      removed outlier: 3.991A  pdb=" N   LEU D 119 " --> pdb=" O   ASN D 116 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ASP D 121 " --> pdb=" O   ALA D 118 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 122 through 128
    Processing helix  chain 'D' and resid 137 through 145
      removed outlier: 4.070A  pdb=" N   SER D 145 " --> pdb=" O   ARG D 141 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 166 through 189
      removed outlier: 4.277A  pdb=" N   LEU D 170 " --> pdb=" O   ARG D 166 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 190 through 205
    Processing helix  chain 'D' and resid 209 through 214
    Processing helix  chain 'D' and resid 221 through 225
    Processing helix  chain 'D' and resid 235 through 241
    Processing sheet with id=AA1, first strand: chain 'A' and resid 272 through 276
      removed outlier: 6.528A  pdb=" N   GLU A 272 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   VAL A 341 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   SER A 274 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 348 through 355
      removed outlier: 5.963A  pdb=" N   TYR A 348 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   VAL A 414 " --> pdb=" O   TYR A 348 " (cutoff:3.500A)
      removed outlier: 8.031A  pdb=" N   ARG A 350 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 12.698A  pdb=" N   TYR A 416 " --> pdb=" O   ARG A 350 " (cutoff:3.500A)
      removed outlier: 9.758A  pdb=" N   ILE A 352 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 12.395A  pdb=" N   VAL A 418 " --> pdb=" O   ILE A 352 " (cutoff:3.500A)
      removed outlier: 9.708A  pdb=" N   PHE A 354 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 802 through 806
      removed outlier: 6.429A  pdb=" N   LEU A 783 " --> pdb=" O   TRP A 776 " (cutoff:3.500A)
      removed outlier: 4.839A  pdb=" N   TRP A 776 " --> pdb=" O   LEU A 783 " (cutoff:3.500A)
      removed outlier: 4.944A  pdb=" N   PHE A 785 " --> pdb=" O   LEU A 774 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   TYR A 608 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   PHE A 428 " --> pdb=" O   PHE P1296 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   PHE P1296 " --> pdb=" O   PHE A 428 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ALA P1294 " --> pdb=" O   ILE A 430 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   GLY P1156 " --> pdb=" O   ASP P1120 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   ASP P1120 " --> pdb=" O   GLY P1156 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 671 through 674
      removed outlier: 5.293A  pdb=" N   ASP A 704 " --> pdb=" O   ALA A 672 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   TYR A 674 " --> pdb=" O   SER A 702 " (cutoff:3.500A)
      removed outlier: 8.196A  pdb=" N   SER A 702 " --> pdb=" O   TYR A 674 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 32 through 35
      removed outlier: 3.667A  pdb=" N   MET E  64 " --> pdb=" O   PHE E  74 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 32 through 35
      removed outlier: 6.638A  pdb=" N   THR E  90 " --> pdb=" O   ASN E 106 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   ASN E 106 " --> pdb=" O   THR E  90 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   THR E  92 " --> pdb=" O   ILE E 104 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   ILE E 104 " --> pdb=" O   THR E  92 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   THR E  94 " --> pdb=" O   THR E 102 " (cutoff:3.500A)

    355 hydrogen bonds defined for protein.
    954 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: 3.73

  Time building geometry restraints manager: 1.81 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6468
        1.03 -     1.23: 15
        1.23 -     1.42: 3090
        1.42 -     1.62: 3823
        1.62 -     1.81: 48
  Bond restraints: 13444
  Sorted by residual:
  bond pdb=" C   PHE A 737 "
       pdb=" O   PHE A 737 "
    ideal  model  delta    sigma   weight residual
    1.234  1.221  0.013 1.22e-02 6.72e+03 1.14e+00
  bond pdb=" N   GLY A 631 "
       pdb=" CA  GLY A 631 "
    ideal  model  delta    sigma   weight residual
    1.449  1.439  0.010 1.18e-02 7.18e+03 7.41e-01
  bond pdb=" CA  PRO D 206 "
       pdb=" C   PRO D 206 "
    ideal  model  delta    sigma   weight residual
    1.516  1.531 -0.014 1.75e-02 3.27e+03 6.86e-01
  bond pdb=" C   TRP A 576 "
       pdb=" N   THR A 577 "
    ideal  model  delta    sigma   weight residual
    1.331  1.344 -0.013 1.55e-02 4.16e+03 6.75e-01
  bond pdb=" N   GLN A 371 "
       pdb=" CA  GLN A 371 "
    ideal  model  delta    sigma   weight residual
    1.458  1.447  0.010 1.24e-02 6.50e+03 6.64e-01
  ... (remaining 13439 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 22769
        1.40 -     2.79: 1140
        2.79 -     4.19: 123
        4.19 -     5.59: 22
        5.59 -     6.98: 3
  Bond angle restraints: 24057
  Sorted by residual:
  angle pdb=" N   GLY A 756 "
        pdb=" CA  GLY A 756 "
        pdb=" C   GLY A 756 "
      ideal   model   delta    sigma   weight residual
     115.34  108.94    6.40 1.67e+00 3.59e-01 1.47e+01
  angle pdb=" N   PHE A 478 "
        pdb=" CA  PHE A 478 "
        pdb=" C   PHE A 478 "
      ideal   model   delta    sigma   weight residual
     111.36  107.35    4.01 1.09e+00 8.42e-01 1.36e+01
  angle pdb=" N   ARG D 212 "
        pdb=" CA  ARG D 212 "
        pdb=" C   ARG D 212 "
      ideal   model   delta    sigma   weight residual
     112.45  107.80    4.65 1.39e+00 5.18e-01 1.12e+01
  angle pdb=" N   ASN A 579 "
        pdb=" CA  ASN A 579 "
        pdb=" C   ASN A 579 "
      ideal   model   delta    sigma   weight residual
     107.67  114.65   -6.98 2.09e+00 2.29e-01 1.12e+01
  angle pdb=" N   THR A 577 "
        pdb=" CA  THR A 577 "
        pdb=" C   THR A 577 "
      ideal   model   delta    sigma   weight residual
     109.24  114.52   -5.28 1.67e+00 3.59e-01 9.99e+00
  ... (remaining 24052 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 6019
       17.82 -    35.64: 200
       35.64 -    53.46: 121
       53.46 -    71.28: 46
       71.28 -    89.10: 4
  Dihedral angle restraints: 6390
    sinusoidal: 3362
      harmonic: 3028
  Sorted by residual:
  dihedral pdb=" CB  CYS A 690 "
           pdb=" SG  CYS A 690 "
           pdb=" SG  CYS A 700 "
           pdb=" CB  CYS A 700 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  131.29  -38.29     1      1.00e+01 1.00e-02 2.07e+01
  dihedral pdb=" CA  VAL A 660 "
           pdb=" C   VAL A 660 "
           pdb=" N   ARG A 661 "
           pdb=" CA  ARG A 661 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.45  -19.55     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  PHE A 395 "
           pdb=" C   PHE A 395 "
           pdb=" N   GLU A 396 "
           pdb=" CA  GLU A 396 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.87   18.13     0      5.00e+00 4.00e-02 1.31e+01
  ... (remaining 6387 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 591
       0.034 -    0.068: 245
       0.068 -    0.102: 99
       0.102 -    0.136: 46
       0.136 -    0.170: 12
  Chirality restraints: 993
  Sorted by residual:
  chirality pdb=" CA  ILE P1167 "
            pdb=" N   ILE P1167 "
            pdb=" C   ILE P1167 "
            pdb=" CB  ILE P1167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.20e-01
  chirality pdb=" CA  ILE C  67 "
            pdb=" N   ILE C  67 "
            pdb=" C   ILE C  67 "
            pdb=" CB  ILE C  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.03e-01
  chirality pdb=" CA  TRP D 191 "
            pdb=" N   TRP D 191 "
            pdb=" C   TRP D 191 "
            pdb=" CB  TRP D 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.92e-01
  ... (remaining 990 not shown)

  Planarity restraints: 2040
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 544 "    0.013 2.00e-02 2.50e+03   2.70e-02 7.28e+00
        pdb=" C   ALA A 544 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   ALA A 544 "    0.018 2.00e-02 2.50e+03
        pdb=" N   MET A 545 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 652 "    0.008 2.00e-02 2.50e+03   1.48e-02 6.58e+00
        pdb=" CG  PHE A 652 "    0.012 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 652 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 652 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 652 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 652 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 652 "    0.007 2.00e-02 2.50e+03
        pdb=" HD1 PHE A 652 "   -0.029 2.00e-02 2.50e+03
        pdb=" HD2 PHE A 652 "   -0.005 2.00e-02 2.50e+03
        pdb=" HE1 PHE A 652 "    0.022 2.00e-02 2.50e+03
        pdb=" HE2 PHE A 652 "   -0.018 2.00e-02 2.50e+03
        pdb=" HZ  PHE A 652 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 653 "   -0.010 2.00e-02 2.50e+03   1.33e-02 5.34e+00
        pdb=" CG  TYR A 653 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 653 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 653 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 653 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 653 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 653 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 653 "   -0.003 2.00e-02 2.50e+03
        pdb=" HD1 TYR A 653 "    0.015 2.00e-02 2.50e+03
        pdb=" HD2 TYR A 653 "    0.029 2.00e-02 2.50e+03
        pdb=" HE1 TYR A 653 "    0.008 2.00e-02 2.50e+03
        pdb=" HE2 TYR A 653 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 2037 not shown)

  Histogram of nonbonded interaction distances:
        1.46 -     2.09: 299
        2.09 -     2.72: 22357
        2.72 -     3.34: 35860
        3.34 -     3.97: 46510
        3.97 -     4.60: 71622
  Nonbonded interactions: 176648
  Sorted by model distance:
  nonbonded pdb=" HZ1 LYS A 310 "
            pdb=" OD1 ASP A 380 "
     model   vdw
     1.460 2.450
  nonbonded pdb=" HD1 HIS A 533 "
            pdb=" OD1 ASP A 568 "
     model   vdw
     1.479 2.450
  nonbonded pdb=" H   GLU A 396 "
            pdb=" O   LYS A 419 "
     model   vdw
     1.481 2.450
  nonbonded pdb=" O   ASP P1270 "
            pdb="HH12 ARG P1273 "
     model   vdw
     1.484 2.450
  nonbonded pdb="HD22 ASN E  71 "
            pdb=" O   ASN E  96 "
     model   vdw
     1.535 2.450
  ... (remaining 176643 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             1.330
  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:             0.080
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     15.760
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6494
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   0.024   6978  Z= 0.166
  Angle     :  0.839   6.984   9438  Z= 0.514
  Chirality :  0.048   0.170    993
  Planarity :  0.005   0.027   1228
  Dihedral  : 10.502  89.098   2476
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.28), residues: 819
  helix: -0.22 (0.41), residues: 116
  sheet:  1.37 (0.26), residues: 357
  loop :  0.22 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 314 
 TYR   0.019   0.002   TYR A 416 
 PHE   0.013   0.001   PHE A 652 
 TRP   0.017   0.002   TRP P1042 
 HIS   0.002   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6976)
  covalent geometry    : angle       0.83897 ( 9434)
  SS BOND              : bond        0.00417 (    2)
  SS BOND              : angle       0.79721 (    4)
  hydrogen bonds       : bond        0.12660 (  351)
  hydrogen bonds       : angle       7.84154 (  954)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.357 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  355 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8586 (mm-30)
REVERT: A  362 ASP cc_start: 0.8985 (t70) cc_final: 0.8730 (t0)
REVERT: A  390 ASN cc_start: 0.9511 (m-40) cc_final: 0.9264 (m110)
REVERT: A  400 THR cc_start: 0.7263 (p) cc_final: 0.6842 (p)
REVERT: A  430 ILE cc_start: 0.8925 (tt) cc_final: 0.8709 (tt)
REVERT: A  441 GLN cc_start: 0.8785 (tt0) cc_final: 0.8426 (pm20)
REVERT: A  515 LEU cc_start: 0.9372 (tp) cc_final: 0.9096 (pp)
REVERT: A  709 ASN cc_start: 0.8791 (m110) cc_final: 0.8475 (m110)
REVERT: A  745 TRP cc_start: 0.8303 (p90) cc_final: 0.8022 (p90)
REVERT: E   64 MET cc_start: 0.9210 (mtp) cc_final: 0.8946 (mmm)
REVERT: D  115 THR cc_start: 0.7078 (m) cc_final: 0.6436 (p)
REVERT: D  117 MET cc_start: 0.9113 (mmm) cc_final: 0.8696 (mmm)
REVERT: D  171 LYS cc_start: 0.9402 (mmtt) cc_final: 0.8870 (mmmt)
REVERT: D  176 LYS cc_start: 0.9205 (mtmt) cc_final: 0.8783 (tppt)
REVERT: D  178 GLU cc_start: 0.9023 (mm-30) cc_final: 0.7667 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.2450
  time to fit residues: 74.2094
Evaluate side-chains
  163 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.1980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:   10.0000
   chunk 74 optimal weight:   30.0000
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 506 ASN
A 533 HIS
A 579 ASN
D 139 HIS
** P1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.115812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.084712 restraints weight = 66214.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.086439 restraints weight = 32736.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.088446 restraints weight = 19104.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.088271 restraints weight = 14493.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.088651 restraints weight = 13767.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          0.3296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6978  Z= 0.156
  Angle     :  0.585  11.523   9438  Z= 0.331
  Chirality :  0.044   0.214    993
  Planarity :  0.005   0.053   1228
  Dihedral  :  5.182  57.494    943
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.29), residues: 819
  helix:  0.93 (0.46), residues: 130
  sheet:  0.96 (0.26), residues: 350
  loop :  0.08 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 592 
 TYR   0.011   0.001   TYR A 416 
 PHE   0.023   0.002   PHE P1296 
 TRP   0.005   0.001   TRP P1219 
 HIS   0.006   0.002   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6976)
  covalent geometry    : angle       0.58298 ( 9434)
  SS BOND              : bond        0.00673 (    2)
  SS BOND              : angle       2.43090 (    4)
  hydrogen bonds       : bond        0.04344 (  351)
  hydrogen bonds       : angle       6.49707 (  954)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.440 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  355 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8547 (mm-30)
REVERT: A  390 ASN cc_start: 0.9525 (m-40) cc_final: 0.9279 (m110)
REVERT: A  422 ASN cc_start: 0.8176 (m-40) cc_final: 0.7755 (m-40)
REVERT: A  579 ASN cc_start: 0.8203 (m-40) cc_final: 0.7731 (m110)
REVERT: A  598 LYS cc_start: 0.9472 (ptmt) cc_final: 0.9236 (ptmt)
REVERT: A  745 TRP cc_start: 0.8404 (p90) cc_final: 0.8187 (p90)
REVERT: A  760 TYR cc_start: 0.7690 (m-80) cc_final: 0.7327 (m-10)
REVERT: D  115 THR cc_start: 0.7438 (m) cc_final: 0.6611 (p)
REVERT: D  117 MET cc_start: 0.9249 (mmm) cc_final: 0.8856 (mmm)
REVERT: D  139 HIS cc_start: 0.9245 (m-70) cc_final: 0.8884 (m90)
REVERT: D  171 LYS cc_start: 0.9354 (mmtt) cc_final: 0.8965 (mmmt)
REVERT: D  172 ASP cc_start: 0.8910 (m-30) cc_final: 0.8365 (p0)
REVERT: D  178 GLU cc_start: 0.8708 (mm-30) cc_final: 0.7872 (mm-30)
REVERT: P 1046 MET cc_start: 0.8308 (mpp) cc_final: 0.7888 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.2371
  time to fit residues: 56.1245
Evaluate side-chains
  146 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 59 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 80 optimal weight:    8.9990
   chunk 38 optimal weight:    9.9990
   chunk 79 optimal weight:   20.0000
   chunk 74 optimal weight:    0.5980
   chunk 81 optimal weight:    5.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
P1064 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.115878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.078694 restraints weight = 68767.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.083256 restraints weight = 29611.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.086062 restraints weight = 18043.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 60)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.087869 restraints weight = 13441.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.088768 restraints weight = 11282.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.4108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6978  Z= 0.144
  Angle     :  0.533   7.133   9438  Z= 0.299
  Chirality :  0.043   0.169    993
  Planarity :  0.004   0.034   1228
  Dihedral  :  4.848  48.735    943
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.28), residues: 819
  helix:  0.93 (0.43), residues: 130
  sheet:  0.65 (0.26), residues: 350
  loop :  0.09 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 661 
 TYR   0.010   0.001   TYR A 416 
 PHE   0.012   0.001   PHE A 428 
 TRP   0.008   0.001   TRP A 776 
 HIS   0.004   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6976)
  covalent geometry    : angle       0.53174 ( 9434)
  SS BOND              : bond        0.00689 (    2)
  SS BOND              : angle       2.06005 (    4)
  hydrogen bonds       : bond        0.03736 (  351)
  hydrogen bonds       : angle       5.94924 (  954)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.415 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  390 ASN cc_start: 0.9517 (m-40) cc_final: 0.9254 (m110)
REVERT: A  428 PHE cc_start: 0.8612 (t80) cc_final: 0.8253 (t80)
REVERT: A  447 ASP cc_start: 0.8482 (m-30) cc_final: 0.8108 (p0)
REVERT: A  550 TYR cc_start: 0.8401 (m-10) cc_final: 0.8192 (m-10)
REVERT: A  598 LYS cc_start: 0.9491 (ptmt) cc_final: 0.9289 (ptmt)
REVERT: A  606 ASN cc_start: 0.9291 (t0) cc_final: 0.8728 (t0)
REVERT: A  608 TYR cc_start: 0.9098 (p90) cc_final: 0.8492 (p90)
REVERT: A  760 TYR cc_start: 0.7765 (m-80) cc_final: 0.7497 (m-10)
REVERT: E   92 THR cc_start: 0.9062 (p) cc_final: 0.8828 (p)
REVERT: D  115 THR cc_start: 0.7730 (m) cc_final: 0.6753 (p)
REVERT: D  117 MET cc_start: 0.9095 (mmm) cc_final: 0.8762 (mmm)
REVERT: D  171 LYS cc_start: 0.9331 (mmtt) cc_final: 0.8932 (mmmt)
REVERT: P 1046 MET cc_start: 0.8303 (mpp) cc_final: 0.7815 (mpp)
REVERT: P 1258 MET cc_start: 0.7992 (mmm) cc_final: 0.7370 (mmm)
REVERT: P 1267 GLU cc_start: 0.8693 (mp0) cc_final: 0.8475 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.2278
  time to fit residues: 50.6200
Evaluate side-chains
  145 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   chunk 29 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 57 optimal weight:    7.9990
   chunk 40 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 80 optimal weight:   30.0000
   chunk 17 optimal weight:    4.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 579 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.112127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.079368 restraints weight = 68602.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.081077 restraints weight = 30845.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.082505 restraints weight = 20223.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.082408 restraints weight = 16456.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.082847 restraints weight = 16356.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.4947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071   6978  Z= 0.230
  Angle     :  0.596   7.110   9438  Z= 0.335
  Chirality :  0.043   0.152    993
  Planarity :  0.005   0.042   1228
  Dihedral  :  5.131  52.933    943
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.19 (0.28), residues: 819
  helix:  0.17 (0.42), residues: 129
  sheet:  0.19 (0.25), residues: 349
  loop : -0.44 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 173 
 TYR   0.016   0.001   TYR A 416 
 PHE   0.018   0.002   PHE A 440 
 TRP   0.009   0.001   TRP A 745 
 HIS   0.005   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 6976)
  covalent geometry    : angle       0.59562 ( 9434)
  SS BOND              : bond        0.00424 (    2)
  SS BOND              : angle       1.26681 (    4)
  hydrogen bonds       : bond        0.03961 (  351)
  hydrogen bonds       : angle       5.99898 (  954)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.429 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  369 MET cc_start: 0.9046 (mmt) cc_final: 0.8734 (mmt)
REVERT: A  447 ASP cc_start: 0.8511 (m-30) cc_final: 0.8115 (p0)
REVERT: A  488 ARG cc_start: 0.8915 (ptt180) cc_final: 0.8681 (mtm110)
REVERT: A  598 LYS cc_start: 0.9550 (ptmt) cc_final: 0.9340 (ptmt)
REVERT: A  760 TYR cc_start: 0.7840 (m-80) cc_final: 0.7516 (m-10)
REVERT: E  105 ASP cc_start: 0.7790 (m-30) cc_final: 0.7589 (m-30)
REVERT: D  115 THR cc_start: 0.7879 (m) cc_final: 0.6886 (p)
REVERT: D  117 MET cc_start: 0.9151 (mmm) cc_final: 0.8775 (mmm)
REVERT: P 1258 MET cc_start: 0.7460 (mmm) cc_final: 0.7052 (mmm)
REVERT: P 1267 GLU cc_start: 0.8804 (mp0) cc_final: 0.8600 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.2377
  time to fit residues: 47.1812
Evaluate side-chains
  133 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 45 optimal weight:   10.0000
   chunk 15 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 31 optimal weight:   10.0000
   chunk 65 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 69 optimal weight:   20.0000
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 411 GLN
A 579 ASN
E  34 GLN
P1295 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.114026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.081466 restraints weight = 69750.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.084364 restraints weight = 35893.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.085244 restraints weight = 19683.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.085799 restraints weight = 16346.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.085649 restraints weight = 15039.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.5154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6978  Z= 0.133
  Angle     :  0.504   4.850   9438  Z= 0.280
  Chirality :  0.043   0.171    993
  Planarity :  0.004   0.037   1228
  Dihedral  :  4.964  55.682    943
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.28), residues: 819
  helix:  0.50 (0.43), residues: 129
  sheet:  0.21 (0.26), residues: 341
  loop : -0.37 (0.34), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 173 
 TYR   0.010   0.001   TYR A 649 
 PHE   0.011   0.001   PHE A 648 
 TRP   0.007   0.001   TRP D 191 
 HIS   0.004   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 6976)
  covalent geometry    : angle       0.50335 ( 9434)
  SS BOND              : bond        0.00449 (    2)
  SS BOND              : angle       1.21690 (    4)
  hydrogen bonds       : bond        0.03355 (  351)
  hydrogen bonds       : angle       5.66589 (  954)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.368 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  369 MET cc_start: 0.9145 (mmt) cc_final: 0.8736 (mmt)
REVERT: A  428 PHE cc_start: 0.8961 (t80) cc_final: 0.8326 (t80)
REVERT: A  608 TYR cc_start: 0.9089 (p90) cc_final: 0.8709 (p90)
REVERT: A  760 TYR cc_start: 0.7747 (m-80) cc_final: 0.7521 (m-10)
REVERT: A  768 MET cc_start: 0.7850 (ptp) cc_final: 0.7369 (ptt)
REVERT: D  115 THR cc_start: 0.7966 (m) cc_final: 0.6930 (p)
REVERT: D  117 MET cc_start: 0.9081 (mmm) cc_final: 0.8758 (mmm)
REVERT: D  138 GLN cc_start: 0.8718 (pt0) cc_final: 0.8508 (pt0)
REVERT: D  171 LYS cc_start: 0.9419 (mmtt) cc_final: 0.8991 (tppt)
REVERT: P 1258 MET cc_start: 0.7558 (mmm) cc_final: 0.7174 (mmm)
REVERT: P 1267 GLU cc_start: 0.8838 (mp0) cc_final: 0.8617 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.2257
  time to fit residues: 43.9255
Evaluate side-chains
  130 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 75 optimal weight:   30.0000
   chunk 48 optimal weight:    7.9990
   chunk 23 optimal weight:   10.0000
   chunk 62 optimal weight:    4.9990
   chunk 14 optimal weight:    8.9990
   chunk 55 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   chunk 47 optimal weight:    0.3980
   chunk 68 optimal weight:    2.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 579 ASN
A 775 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.115231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.081904 restraints weight = 67280.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.084557 restraints weight = 33859.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.085678 restraints weight = 18526.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.086315 restraints weight = 16761.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.086303 restraints weight = 14731.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.5320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6978  Z= 0.117
  Angle     :  0.491   5.629   9438  Z= 0.270
  Chirality :  0.042   0.175    993
  Planarity :  0.004   0.037   1228
  Dihedral  :  4.965  69.339    943
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.29), residues: 819
  helix:  0.76 (0.44), residues: 130
  sheet:  0.27 (0.27), residues: 334
  loop : -0.32 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 173 
 TYR   0.008   0.001   TYR A 649 
 PHE   0.010   0.001   PHE P1296 
 TRP   0.011   0.001   TRP A 745 
 HIS   0.004   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 6976)
  covalent geometry    : angle       0.48913 ( 9434)
  SS BOND              : bond        0.00603 (    2)
  SS BOND              : angle       1.86407 (    4)
  hydrogen bonds       : bond        0.03202 (  351)
  hydrogen bonds       : angle       5.49919 (  954)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.345 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  369 MET cc_start: 0.8975 (mmt) cc_final: 0.8724 (mmt)
REVERT: A  428 PHE cc_start: 0.8999 (t80) cc_final: 0.8750 (t80)
REVERT: A  441 GLN cc_start: 0.8013 (pm20) cc_final: 0.7809 (pm20)
REVERT: A  511 THR cc_start: 0.9048 (t) cc_final: 0.8827 (t)
REVERT: A  576 TRP cc_start: 0.8833 (t60) cc_final: 0.8496 (t60)
REVERT: A  760 TYR cc_start: 0.7746 (m-80) cc_final: 0.7490 (m-10)
REVERT: A  768 MET cc_start: 0.7888 (ptp) cc_final: 0.7396 (ptt)
REVERT: E  110 LEU cc_start: 0.7372 (mp) cc_final: 0.6595 (tt)
REVERT: D  115 THR cc_start: 0.7956 (m) cc_final: 0.7147 (p)
REVERT: D  117 MET cc_start: 0.9116 (mmm) cc_final: 0.8798 (mmm)
REVERT: P 1046 MET cc_start: 0.8411 (mpp) cc_final: 0.7929 (mpp)
REVERT: P 1258 MET cc_start: 0.7602 (mmm) cc_final: 0.7212 (mmm)
REVERT: P 1267 GLU cc_start: 0.8872 (mp0) cc_final: 0.8647 (mp0)
REVERT: P 1276 LEU cc_start: 0.9267 (mp) cc_final: 0.9010 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.2401
  time to fit residues: 47.9166
Evaluate side-chains
  138 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   chunk 73 optimal weight:   30.0000
   chunk 13 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 66 optimal weight:    2.9990
   chunk 69 optimal weight:   40.0000
   chunk 62 optimal weight:    0.8980
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 579 ASN
D 139 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.115505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.082892 restraints weight = 68256.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.085532 restraints weight = 34031.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.086700 restraints weight = 19592.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.087008 restraints weight = 16190.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.087090 restraints weight = 14985.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7359
moved from start:          0.5417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6978  Z= 0.098
  Angle     :  0.475   4.392   9438  Z= 0.260
  Chirality :  0.042   0.175    993
  Planarity :  0.004   0.036   1228
  Dihedral  :  4.790  69.318    943
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.19 (0.29), residues: 819
  helix:  0.89 (0.44), residues: 130
  sheet:  0.28 (0.27), residues: 337
  loop : -0.18 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 173 
 TYR   0.010   0.001   TYR D 177 
 PHE   0.007   0.001   PHE A 440 
 TRP   0.006   0.001   TRP D 191 
 HIS   0.004   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 ( 6976)
  covalent geometry    : angle       0.47476 ( 9434)
  SS BOND              : bond        0.00263 (    2)
  SS BOND              : angle       1.29763 (    4)
  hydrogen bonds       : bond        0.03000 (  351)
  hydrogen bonds       : angle       5.28162 (  954)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.364 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  428 PHE cc_start: 0.8995 (t80) cc_final: 0.8293 (t80)
REVERT: A  441 GLN cc_start: 0.8082 (pm20) cc_final: 0.7862 (pm20)
REVERT: A  511 THR cc_start: 0.9059 (t) cc_final: 0.8836 (t)
REVERT: A  760 TYR cc_start: 0.7697 (m-80) cc_final: 0.7477 (m-10)
REVERT: A  768 MET cc_start: 0.7840 (ptp) cc_final: 0.7342 (ptt)
REVERT: E  110 LEU cc_start: 0.7411 (mp) cc_final: 0.6659 (tt)
REVERT: D  115 THR cc_start: 0.7913 (m) cc_final: 0.7078 (p)
REVERT: D  117 MET cc_start: 0.9124 (mmm) cc_final: 0.8806 (mmm)
REVERT: D  199 GLU cc_start: 0.8965 (tt0) cc_final: 0.8743 (tt0)
REVERT: P 1046 MET cc_start: 0.8409 (mpp) cc_final: 0.7903 (mpp)
REVERT: P 1258 MET cc_start: 0.7599 (mmm) cc_final: 0.7210 (mmm)
REVERT: P 1276 LEU cc_start: 0.9303 (mp) cc_final: 0.8984 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.2322
  time to fit residues: 48.0150
Evaluate side-chains
  140 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 18 optimal weight:    0.0670
   chunk 78 optimal weight:    3.9990
   chunk 29 optimal weight:    0.0470
   chunk 10 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 20 optimal weight:    8.9990
   chunk 70 optimal weight:   30.0000
   chunk 58 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 41 optimal weight:    7.9990
   overall best weight:    0.7620

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

Flipped N/Q/H residues before XYZ refinement:
A 579 ASN
D 139 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.115650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.083774 restraints weight = 68131.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.086069 restraints weight = 33288.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.087445 restraints weight = 19134.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.087518 restraints weight = 15745.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.087659 restraints weight = 14347.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.5596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6978  Z= 0.096
  Angle     :  0.460   5.045   9438  Z= 0.252
  Chirality :  0.042   0.170    993
  Planarity :  0.004   0.036   1228
  Dihedral  :  4.530  60.547    943
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.29), residues: 819
  helix:  1.07 (0.45), residues: 130
  sheet:  0.27 (0.27), residues: 339
  loop : -0.03 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 173 
 TYR   0.009   0.001   TYR D 177 
 PHE   0.007   0.001   PHE P1296 
 TRP   0.007   0.001   TRP D 191 
 HIS   0.004   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00198 ( 6976)
  covalent geometry    : angle       0.45902 ( 9434)
  SS BOND              : bond        0.00208 (    2)
  SS BOND              : angle       1.25006 (    4)
  hydrogen bonds       : bond        0.02882 (  351)
  hydrogen bonds       : angle       5.10745 (  954)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.406 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  373 GLU cc_start: 0.8239 (mp0) cc_final: 0.7797 (mp0)
REVERT: A  428 PHE cc_start: 0.8942 (t80) cc_final: 0.8339 (t80)
REVERT: A  449 TRP cc_start: 0.9334 (t-100) cc_final: 0.8987 (t60)
REVERT: A  511 THR cc_start: 0.9043 (t) cc_final: 0.8815 (t)
REVERT: A  760 TYR cc_start: 0.7630 (m-80) cc_final: 0.7409 (m-10)
REVERT: A  768 MET cc_start: 0.7874 (ptp) cc_final: 0.7376 (ptt)
REVERT: E  110 LEU cc_start: 0.7526 (mp) cc_final: 0.6867 (tt)
REVERT: D  115 THR cc_start: 0.7792 (m) cc_final: 0.7159 (p)
REVERT: D  117 MET cc_start: 0.9126 (mmm) cc_final: 0.8572 (mmm)
REVERT: D  199 GLU cc_start: 0.9007 (tt0) cc_final: 0.8786 (tt0)
REVERT: P 1046 MET cc_start: 0.8410 (mpp) cc_final: 0.7904 (mpp)
REVERT: P 1258 MET cc_start: 0.7644 (mmm) cc_final: 0.7262 (mmm)
REVERT: P 1267 GLU cc_start: 0.8929 (mp0) cc_final: 0.8693 (mp0)
REVERT: P 1276 LEU cc_start: 0.9195 (mp) cc_final: 0.8766 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.2256
  time to fit residues: 45.3834
Evaluate side-chains
  148 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 40 optimal weight:   20.0000
   chunk 32 optimal weight:    7.9990
   chunk 36 optimal weight:   10.0000
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9980
   chunk 73 optimal weight:   50.0000
   chunk 49 optimal weight:    0.9980
   chunk 71 optimal weight:    6.9990
   overall best weight:    2.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 579 ASN
E  83 HIS
D 139 HIS
D 226 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.113077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.080390 restraints weight = 73545.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.083407 restraints weight = 33793.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.084291 restraints weight = 20563.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.084160 restraints weight = 17192.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.084912 restraints weight = 17631.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.5890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6978  Z= 0.206
  Angle     :  0.556   6.527   9438  Z= 0.309
  Chirality :  0.042   0.153    993
  Planarity :  0.004   0.048   1228
  Dihedral  :  4.796  50.003    943
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.29), residues: 819
  helix:  0.25 (0.43), residues: 129
  sheet:  0.14 (0.27), residues: 339
  loop : -0.51 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 367 
 TYR   0.015   0.001   TYR A 416 
 PHE   0.012   0.001   PHE D 144 
 TRP   0.021   0.002   TRP A 745 
 HIS   0.003   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 6976)
  covalent geometry    : angle       0.55545 ( 9434)
  SS BOND              : bond        0.00145 (    2)
  SS BOND              : angle       0.99845 (    4)
  hydrogen bonds       : bond        0.03452 (  351)
  hydrogen bonds       : angle       5.46009 (  954)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.371 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 ILE cc_start: 0.9523 (mt) cc_final: 0.9236 (tp)
REVERT: A  428 PHE cc_start: 0.8981 (t80) cc_final: 0.8281 (t80)
REVERT: A  511 THR cc_start: 0.8900 (t) cc_final: 0.8653 (t)
REVERT: A  608 TYR cc_start: 0.9063 (p90) cc_final: 0.8550 (p90)
REVERT: A  711 MET cc_start: 0.9060 (ppp) cc_final: 0.8802 (ppp)
REVERT: A  760 TYR cc_start: 0.7840 (m-80) cc_final: 0.7495 (m-10)
REVERT: A  768 MET cc_start: 0.7897 (ptp) cc_final: 0.7382 (ptt)
REVERT: D  115 THR cc_start: 0.8181 (m) cc_final: 0.7597 (p)
REVERT: D  117 MET cc_start: 0.9038 (mmm) cc_final: 0.8727 (mmm)
REVERT: P 1046 MET cc_start: 0.8434 (mpp) cc_final: 0.7926 (mpp)
REVERT: P 1258 MET cc_start: 0.7596 (mmm) cc_final: 0.7191 (mmm)
REVERT: P 1267 GLU cc_start: 0.8914 (mp0) cc_final: 0.8688 (mp0)
REVERT: P 1276 LEU cc_start: 0.9194 (mp) cc_final: 0.8545 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.2382
  time to fit residues: 45.3611
Evaluate side-chains
  128 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 57 optimal weight:    5.9990
   chunk 72 optimal weight:   50.0000
   chunk 31 optimal weight:    8.9990
   chunk 40 optimal weight:   10.0000
   chunk 82 optimal weight:    5.9990
   chunk 74 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 38 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 579 ASN
E  83 HIS
D 139 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.110866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.079319 restraints weight = 70605.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.081357 restraints weight = 33289.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.082114 restraints weight = 20608.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.082567 restraints weight = 18392.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.082596 restraints weight = 18158.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.6215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   6978  Z= 0.261
  Angle     :  0.635   7.880   9438  Z= 0.351
  Chirality :  0.043   0.145    993
  Planarity :  0.005   0.068   1228
  Dihedral  :  5.157  41.976    943
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.84 (0.29), residues: 819
  helix: -0.61 (0.42), residues: 127
  sheet: -0.06 (0.28), residues: 337
  loop : -0.90 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 188 
 TYR   0.016   0.002   TYR A 416 
 PHE   0.016   0.002   PHE D 144 
 TRP   0.021   0.002   TRP A 745 
 HIS   0.004   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00515 ( 6976)
  covalent geometry    : angle       0.63526 ( 9434)
  SS BOND              : bond        0.00110 (    2)
  SS BOND              : angle       0.90706 (    4)
  hydrogen bonds       : bond        0.03805 (  351)
  hydrogen bonds       : angle       5.80594 (  954)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.381 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  369 MET cc_start: 0.8979 (mmt) cc_final: 0.8441 (mmt)
REVERT: A  428 PHE cc_start: 0.8874 (t80) cc_final: 0.8281 (t80)
REVERT: A  711 MET cc_start: 0.8993 (ppp) cc_final: 0.8715 (ppp)
REVERT: A  768 MET cc_start: 0.7844 (ptp) cc_final: 0.7243 (ptt)
REVERT: E   50 MET cc_start: 0.8507 (ttm) cc_final: 0.8256 (ttm)
REVERT: D  117 MET cc_start: 0.9077 (mmm) cc_final: 0.8689 (tmm)
REVERT: P 1258 MET cc_start: 0.7439 (mmm) cc_final: 0.7028 (mmm)
REVERT: P 1267 GLU cc_start: 0.8791 (mp0) cc_final: 0.8551 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.2473
  time to fit residues: 43.3608
Evaluate side-chains
  124 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 42 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 73 optimal weight:   40.0000
   chunk 23 optimal weight:   10.0000
   chunk 64 optimal weight:    1.9990
   chunk 77 optimal weight:   20.0000
   chunk 4 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 47 optimal weight:    4.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  83 HIS
D 139 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.113306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.081323 restraints weight = 68058.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.083838 restraints weight = 33309.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.084934 restraints weight = 19190.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.084976 restraints weight = 16288.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.085178 restraints weight = 14878.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.6172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6978  Z= 0.119
  Angle     :  0.505   7.003   9438  Z= 0.273
  Chirality :  0.042   0.156    993
  Planarity :  0.004   0.041   1228
  Dihedral  :  4.633  34.175    943
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.39 (0.29), residues: 819
  helix:  0.17 (0.43), residues: 128
  sheet:  0.07 (0.27), residues: 342
  loop : -0.62 (0.35), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 188 
 TYR   0.013   0.001   TYR D 177 
 PHE   0.011   0.001   PHE P1274 
 TRP   0.010   0.001   TRP A 576 
 HIS   0.004   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 6976)
  covalent geometry    : angle       0.50485 ( 9434)
  SS BOND              : bond        0.00120 (    2)
  SS BOND              : angle       0.91752 (    4)
  hydrogen bonds       : bond        0.03150 (  351)
  hydrogen bonds       : angle       5.34735 (  954)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2698.43 seconds
wall clock time: 46 minutes 42.26 seconds (2802.26 seconds total)