Starting phenix.real_space_refine
on Fri Aug 22 16:06:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wvw_37874/08_2025/8wvw_37874.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wvw_37874/08_2025/8wvw_37874.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wvw_37874/08_2025/8wvw_37874.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wvw_37874/08_2025/8wvw_37874.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wvw_37874/08_2025/8wvw_37874.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wvw_37874/08_2025/8wvw_37874.map"
  }
  resolution = 3.53
  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=  -0.001 sd=   0.063
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      26      5.16       5
     C    3634      2.51       5
     N     920      2.21       5
     O    1014      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5594
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 722, 5594
          Classifications: {'peptide': 722}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 36, 'TRANS': 685}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 47
          Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 35
  Time building chain proxies: 1.57, per 1000 atoms: 0.28
  Number of scatterers: 5594
  At special positions: 0
  Unit cell: (97.75, 79.05, 147.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      26     16.00
     O    1014      8.00
     N     920      7.00
     C    3634      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  33 " - pdb=" SG  CYS A  43 " distance=1.98
    Simple disulfide: pdb=" SG  CYS A 339 " - pdb=" SG  CYS A 364 " distance=1.96
    Simple disulfide: pdb=" SG  CYS A 470 " - pdb=" SG  CYS A 522 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 471 " - pdb=" SG  CYS A 532 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A 618 " - pdb=" SG  CYS A 693 " distance=2.06

  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: 0.30
  Conformation dependent library (CDL) restraints added in 187.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1416 Ramachandran restraints generated.
    708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1366

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 6 sheets defined
      32.4% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 169 through 174
    Processing helix  chain 'A' and resid 241 through 247
      removed outlier: 3.525A  pdb=" N   LYS A 245 " --> pdb=" O   GLN A 242 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ALA A 246 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 342
    Processing helix  chain 'A' and resid 407 through 411
      removed outlier: 4.340A  pdb=" N   THR A 411 " --> pdb=" O   ALA A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 474
      removed outlier: 3.912A  pdb=" N   ALA A 472 " --> pdb=" O   GLN A 469 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   TRP A 474 " --> pdb=" O   CYS A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 564
      removed outlier: 3.922A  pdb=" N   ASN A 556 " --> pdb=" O   ALA A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 601
      removed outlier: 3.621A  pdb=" N   ASN A 584 " --> pdb=" O   ILE A 580 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   MET A 587 " --> pdb=" O   SER A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 614
      removed outlier: 4.110A  pdb=" N   ILE A 610 " --> pdb=" O   ALA A 606 " (cutoff:3.500A)
      removed outlier: 4.737A  pdb=" N   TRP A 611 " --> pdb=" O   GLU A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 631
      removed outlier: 3.661A  pdb=" N   VAL A 620 " --> pdb=" O   SER A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 647
      removed outlier: 3.892A  pdb=" N   ALA A 647 " --> pdb=" O   SER A 644 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 658 through 666
    Processing helix  chain 'A' and resid 666 through 679
      removed outlier: 3.832A  pdb=" N   PHE A 670 " --> pdb=" O   ALA A 666 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLY A 672 " --> pdb=" O   LEU A 668 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   THR A 674 " --> pdb=" O   PHE A 670 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ALA A 676 " --> pdb=" O   GLY A 672 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLY A 677 " --> pdb=" O   ALA A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 730
    Processing helix  chain 'A' and resid 741 through 768
      removed outlier: 3.792A  pdb=" N   CYS A 761 " --> pdb=" O   CYS A 757 " (cutoff:3.500A)
      Proline residue:  A 762  - end of helix
      removed outlier: 3.729A  pdb=" N   PHE A 768 " --> pdb=" O   ALA A 764 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 768 through 773
      removed outlier: 3.623A  pdb=" N   ILE A 772 " --> pdb=" O   PHE A 768 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 778 through 789
    Processing helix  chain 'A' and resid 792 through 804
      removed outlier: 3.661A  pdb=" N   LEU A 796 " --> pdb=" O   LEU A 792 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ASN A 797 " --> pdb=" O   PRO A 793 " (cutoff:3.500A)
      Proline residue:  A 798  - end of helix
      removed outlier: 3.785A  pdb=" N   VAL A 802 " --> pdb=" O   PRO A 798 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   PHE A 803 " --> pdb=" O   VAL A 799 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE A 804 " --> pdb=" O   LEU A 800 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 805 through 815
      removed outlier: 4.168A  pdb=" N   LYS A 809 " --> pdb=" O   ASN A 805 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   GLU A 810 " --> pdb=" O   PRO A 806 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42
      removed outlier: 6.344A  pdb=" N   VAL A  41 " --> pdb=" O   ASP A  63 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   LEU A  62 " --> pdb=" O   GLN A  87 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   THR A 111 " --> pdb=" O   LEU A  86 " (cutoff:3.500A)
      removed outlier: 7.244A  pdb=" N   LEU A 110 " --> pdb=" O   ARG A 135 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   TRP A 159 " --> pdb=" O   LEU A 134 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   HIS A 207 " --> pdb=" O   LEU A 182 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   LEU A 253 " --> pdb=" O   HIS A 278 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 192
      removed outlier: 3.740A  pdb=" N   ILE A 192 " --> pdb=" O   SER A 215 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 263
    Processing sheet with id=AA4, first strand: chain 'A' and resid 302 through 304
      removed outlier: 6.281A  pdb=" N   LEU A 324 " --> pdb=" O   ASP A 349 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 379 through 380
    Processing sheet with id=AA6, first strand: chain 'A' and resid 393 through 395
      removed outlier: 6.909A  pdb=" N   LEU A 394 " --> pdb=" O   ASP A 419 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   LEU A 418 " --> pdb=" O   LYS A 440 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6

    147 hydrogen bonds defined for protein.
    426 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.02

  Time building geometry restraints manager: 0.45 seconds

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

  Histogram of bond lengths:
        1.15 -     1.28: 990
        1.28 -     1.42: 1335
        1.42 -     1.55: 3360
        1.55 -     1.69: 2
        1.69 -     1.82: 34
  Bond restraints: 5721
  Sorted by residual:
  bond pdb=" C   TYR A 234 "
       pdb=" N   ASN A 235 "
    ideal  model  delta    sigma   weight residual
    1.328  1.466 -0.138 8.50e-03 1.38e+04 2.63e+02
  bond pdb=" C   THR A 698 "
       pdb=" N   GLY A 699 "
    ideal  model  delta    sigma   weight residual
    1.329  1.497 -0.168 1.40e-02 5.10e+03 1.44e+02
  bond pdb=" C   LEU A 400 "
       pdb=" N   ILE A 401 "
    ideal  model  delta    sigma   weight residual
    1.331  1.462 -0.130 1.11e-02 8.12e+03 1.37e+02
  bond pdb=" C   SER A  94 "
       pdb=" N   PHE A  95 "
    ideal  model  delta    sigma   weight residual
    1.331  1.496 -0.165 1.43e-02 4.89e+03 1.33e+02
  bond pdb=" C   GLY A 432 "
       pdb=" N   LEU A 433 "
    ideal  model  delta    sigma   weight residual
    1.330  1.493 -0.163 1.52e-02 4.33e+03 1.15e+02
  ... (remaining 5716 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.03: 7316
        4.03 -     8.05: 421
        8.05 -    12.08: 31
       12.08 -    16.10: 8
       16.10 -    20.13: 2
  Bond angle restraints: 7778
  Sorted by residual:
  angle pdb=" N   TRP A 474 "
        pdb=" CA  TRP A 474 "
        pdb=" C   TRP A 474 "
      ideal   model   delta    sigma   weight residual
     112.58  132.71  -20.13 1.22e+00 6.72e-01 2.72e+02
  angle pdb=" N   CYS A 532 "
        pdb=" CA  CYS A 532 "
        pdb=" CB  CYS A 532 "
      ideal   model   delta    sigma   weight residual
     110.73   93.96   16.77 1.55e+00 4.16e-01 1.17e+02
  angle pdb=" C   PRO A 531 "
        pdb=" CA  PRO A 531 "
        pdb=" CB  PRO A 531 "
      ideal   model   delta    sigma   weight residual
     111.46   97.63   13.83 1.29e+00 6.01e-01 1.15e+02
  angle pdb=" C   ASN A 805 "
        pdb=" CA  ASN A 805 "
        pdb=" CB  ASN A 805 "
      ideal   model   delta    sigma   weight residual
     109.65   96.32   13.33 1.30e+00 5.92e-01 1.05e+02
  angle pdb=" O   PRO A 697 "
        pdb=" C   PRO A 697 "
        pdb=" N   THR A 698 "
      ideal   model   delta    sigma   weight residual
     122.23  133.18  -10.95 1.20e+00 6.94e-01 8.32e+01
  ... (remaining 7773 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.39: 2807
       16.39 -    32.78: 443
       32.78 -    49.17: 129
       49.17 -    65.56: 21
       65.56 -    81.94: 9
  Dihedral angle restraints: 3409
    sinusoidal: 1317
      harmonic: 2092
  Sorted by residual:
  dihedral pdb=" N   TRP A 474 "
           pdb=" C   TRP A 474 "
           pdb=" CA  TRP A 474 "
           pdb=" CB  TRP A 474 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  142.90  -20.10     0      2.50e+00 1.60e-01 6.47e+01
  dihedral pdb=" C   TRP A 474 "
           pdb=" N   TRP A 474 "
           pdb=" CA  TRP A 474 "
           pdb=" CB  TRP A 474 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -141.75   19.15     0      2.50e+00 1.60e-01 5.87e+01
  dihedral pdb=" N   CYS A 532 "
           pdb=" C   CYS A 532 "
           pdb=" CA  CYS A 532 "
           pdb=" CB  CYS A 532 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  103.74   19.06     0      2.50e+00 1.60e-01 5.82e+01
  ... (remaining 3406 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.206: 903
       0.206 -    0.411: 19
       0.411 -    0.617: 0
       0.617 -    0.823: 0
       0.823 -    1.029: 1
  Chirality restraints: 923
  Sorted by residual:
  chirality pdb=" CA  TRP A 474 "
            pdb=" N   TRP A 474 "
            pdb=" C   TRP A 474 "
            pdb=" CB  TRP A 474 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.48    1.03 2.00e-01 2.50e+01 2.64e+01
  chirality pdb=" CA  SER A 538 "
            pdb=" N   SER A 538 "
            pdb=" C   SER A 538 "
            pdb=" CB  SER A 538 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.86   -0.35 2.00e-01 2.50e+01 2.99e+00
  chirality pdb=" CA  PHE A 473 "
            pdb=" N   PHE A 473 "
            pdb=" C   PHE A 473 "
            pdb=" CB  PHE A 473 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.58e+00
  ... (remaining 920 not shown)

  Planarity restraints: 982
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 680 "    0.022 2.00e-02 2.50e+03   4.21e-02 1.78e+01
        pdb=" C   PRO A 680 "   -0.073 2.00e-02 2.50e+03
        pdb=" O   PRO A 680 "    0.026 2.00e-02 2.50e+03
        pdb=" N   LEU A 681 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 541 "    0.019 2.00e-02 2.50e+03   3.89e-02 1.52e+01
        pdb=" C   ILE A 541 "   -0.067 2.00e-02 2.50e+03
        pdb=" O   ILE A 541 "    0.024 2.00e-02 2.50e+03
        pdb=" N   ARG A 542 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 526 "   -0.019 2.00e-02 2.50e+03   3.89e-02 1.51e+01
        pdb=" C   THR A 526 "    0.067 2.00e-02 2.50e+03
        pdb=" O   THR A 526 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   GLY A 527 "   -0.023 2.00e-02 2.50e+03
  ... (remaining 979 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 240
        2.68 -     3.23: 5142
        3.23 -     3.79: 8174
        3.79 -     4.34: 10645
        4.34 -     4.90: 17524
  Nonbonded interactions: 41725
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A  67 "
            pdb=" ND2 ASN A  91 "
     model   vdw
     2.124 3.120
  nonbonded pdb=" O   THR A 523 "
            pdb=" C   PRO A 524 "
     model   vdw
     2.229 3.270
  nonbonded pdb=" OE1 GLU A 146 "
            pdb=" ND1 HIS A 171 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" O   THR A 523 "
            pdb=" N   SER A 525 "
     model   vdw
     2.333 3.120
  nonbonded pdb=" O   SER A 463 "
            pdb=" OG  SER A 463 "
     model   vdw
     2.346 3.040
  ... (remaining 41720 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             3.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.210
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
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      :  0.019   0.168   5726  Z= 1.400
  Angle     :  1.926  20.130   7788  Z= 1.343
  Chirality :  0.078   1.029    923
  Planarity :  0.010   0.088    982
  Dihedral  : 17.268  81.943   2028
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 18.79
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.90 %
    Favored  : 90.96 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 26.11 %
    Favored  : 70.54 %
  Cbeta Deviations :  1.90 %
  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: -3.16 (0.30), residues: 708
  helix: -1.45 (0.32), residues: 222
  sheet: -2.83 (0.54), residues: 96
  loop : -2.32 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 542 
 TYR   0.033   0.003   TYR A 468 
 PHE   0.031   0.002   PHE A 547 
 TRP   0.010   0.001   TRP A 812 
 HIS   0.010   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.01937 ( 5721)
  covalent geometry    : angle       1.90975 ( 7778)
  SS BOND              : bond        0.04474 (    5)
  SS BOND              : angle       7.13231 (   10)
  hydrogen bonds       : bond        0.28261 (  147)
  hydrogen bonds       : angle       7.70707 (  426)

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

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

  1416 Ramachandran restraints generated.
    708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1416 Ramachandran restraints generated.
    708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 89
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 MET cc_start: 0.7693 (mmm) cc_final: 0.7400 (mmt)
REVERT: A   99 LYS cc_start: 0.7570 (ttpt) cc_final: 0.6928 (tptt)
REVERT: A  212 LYS cc_start: 0.7525 (tmtt) cc_final: 0.7075 (tptp)
REVERT: A  289 ASN cc_start: 0.7871 (p0) cc_final: 0.7644 (p0)
REVERT: A  344 MET cc_start: 0.7636 (mtt) cc_final: 0.7358 (mtm)
  outliers start: 21
  outliers final: 7
  residues processed: 107
  average time/residue: 0.0624
  time to fit residues: 9.0786
Evaluate side-chains
  69 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 ILE
Chi-restraints excluded: chain A residue  339 CYS
Chi-restraints excluded: chain A residue  517 GLN
Chi-restraints excluded: chain A residue  523 THR
Chi-restraints excluded: chain A residue  583 SER
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain A residue  802 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.0470
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 340 GLN
A 386 GLN
A 458 ASN
A 658 HIS
A 683 HIS
A 797 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.167550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.133705 restraints weight = 7427.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.132223 restraints weight = 5749.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.133093 restraints weight = 5537.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.133331 restraints weight = 4898.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.133512 restraints weight = 4729.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5726  Z= 0.145
  Angle     :  0.674   6.934   7788  Z= 0.340
  Chirality :  0.044   0.133    923
  Planarity :  0.005   0.046    982
  Dihedral  :  5.338  55.760    755
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 23.73 %
    Favored  : 73.41 %
  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: -2.29 (0.30), residues: 708
  helix: -0.08 (0.36), residues: 214
  sheet: -2.78 (0.61), residues: 75
  loop : -2.14 (0.27), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 542 
 TYR   0.015   0.002   TYR A 725 
 PHE   0.017   0.001   PHE A 696 
 TRP   0.011   0.001   TRP A 159 
 HIS   0.007   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 5721)
  covalent geometry    : angle       0.67033 ( 7778)
  SS BOND              : bond        0.00731 (    5)
  SS BOND              : angle       2.04926 (   10)
  hydrogen bonds       : bond        0.06906 (  147)
  hydrogen bonds       : angle       5.11785 (  426)

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

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

  1416 Ramachandran restraints generated.
    708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1416 Ramachandran restraints generated.
    708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A   99 LYS cc_start: 0.7699 (ttpt) cc_final: 0.7188 (tptt)
REVERT: A  105 LYS cc_start: 0.7894 (ptpp) cc_final: 0.7556 (mtmm)
REVERT: A  132 GLN cc_start: 0.7908 (mt0) cc_final: 0.7556 (mt0)
REVERT: A  262 VAL cc_start: 0.8721 (m) cc_final: 0.8511 (p)
  outliers start: 18
  outliers final: 8
  residues processed: 88
  average time/residue: 0.0588
  time to fit residues: 7.3138
Evaluate side-chains
  69 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  194 ASP
Chi-restraints excluded: chain A residue  339 CYS
Chi-restraints excluded: chain A residue  517 GLN
Chi-restraints excluded: chain A residue  664 VAL
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  802 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 6 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 50 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 71 optimal weight:    0.4980
   chunk 39 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 157 HIS
** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 ASN
A 258 ASN
A 469 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.157995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.124413 restraints weight = 7242.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.122714 restraints weight = 6109.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.123426 restraints weight = 5380.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.123671 restraints weight = 4892.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.123925 restraints weight = 4622.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.3371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   5726  Z= 0.198
  Angle     :  0.707   8.387   7788  Z= 0.356
  Chirality :  0.047   0.159    923
  Planarity :  0.004   0.035    982
  Dihedral  :  5.226  49.189    750
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 22.29 %
    Favored  : 74.04 %
  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: -2.36 (0.30), residues: 708
  helix: -0.12 (0.35), residues: 224
  sheet: -3.23 (0.52), residues: 83
  loop : -2.10 (0.28), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 275 
 TYR   0.017   0.002   TYR A 534 
 PHE   0.018   0.002   PHE A 385 
 TRP   0.016   0.001   TRP A 159 
 HIS   0.006   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 5721)
  covalent geometry    : angle       0.70242 ( 7778)
  SS BOND              : bond        0.00598 (    5)
  SS BOND              : angle       2.39713 (   10)
  hydrogen bonds       : bond        0.08210 (  147)
  hydrogen bonds       : angle       4.93449 (  426)

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

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

  1416 Ramachandran restraints generated.
    708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1416 Ramachandran restraints generated.
    708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 74
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.4949 (OUTLIER) cc_final: 0.4605 (mt)
REVERT: A   66 MET cc_start: 0.7722 (mmm) cc_final: 0.7393 (mmt)
REVERT: A   74 GLU cc_start: 0.7392 (pm20) cc_final: 0.6733 (pp20)
REVERT: A  105 LYS cc_start: 0.7968 (ptpp) cc_final: 0.7618 (mtmm)
REVERT: A  132 GLN cc_start: 0.8282 (mt0) cc_final: 0.8078 (mt0)
REVERT: A  517 GLN cc_start: 0.6852 (OUTLIER) cc_final: 0.6633 (tt0)
REVERT: A  712 LEU cc_start: 0.8300 (tt) cc_final: 0.7935 (mt)
REVERT: A  752 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8488 (mp)
  outliers start: 23
  outliers final: 14
  residues processed: 92
  average time/residue: 0.0431
  time to fit residues: 5.9231
Evaluate side-chains
  73 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 56
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  194 ASP
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  281 ASP
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  517 GLN
Chi-restraints excluded: chain A residue  664 VAL
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  782 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 26 optimal weight:    0.0570
   chunk 56 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0980
   overall best weight:    0.4098

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

Flipped N/Q/H residues before XYZ refinement:
** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 171 HIS
A 175 ASN
** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.160885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.127310 restraints weight = 7201.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.125518 restraints weight = 5853.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.126471 restraints weight = 5234.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.126822 restraints weight = 4541.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.127163 restraints weight = 4335.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.3693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5726  Z= 0.113
  Angle     :  0.599   9.549   7788  Z= 0.295
  Chirality :  0.043   0.153    923
  Planarity :  0.004   0.032    982
  Dihedral  :  4.438  37.266    748
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 24.20 %
    Favored  : 73.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.89 (0.31), residues: 708
  helix:  0.47 (0.37), residues: 218
  sheet: -2.72 (0.55), residues: 85
  loop : -1.97 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 542 
 TYR   0.014   0.001   TYR A 725 
 PHE   0.013   0.001   PHE A 547 
 TRP   0.009   0.001   TRP A 159 
 HIS   0.006   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 5721)
  covalent geometry    : angle       0.59541 ( 7778)
  SS BOND              : bond        0.00237 (    5)
  SS BOND              : angle       1.99025 (   10)
  hydrogen bonds       : bond        0.05364 (  147)
  hydrogen bonds       : angle       4.53681 (  426)

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

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

  1416 Ramachandran restraints generated.
    708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1416 Ramachandran restraints generated.
    708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.4827 (OUTLIER) cc_final: 0.4492 (mt)
REVERT: A   74 GLU cc_start: 0.7096 (pm20) cc_final: 0.6622 (pp20)
REVERT: A  105 LYS cc_start: 0.7923 (ptpp) cc_final: 0.7600 (mtmm)
REVERT: A  275 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7833 (ttp-110)
  outliers start: 12
  outliers final: 7
  residues processed: 80
  average time/residue: 0.0528
  time to fit residues: 6.2343
Evaluate side-chains
  68 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  275 ARG
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  707 THR
Chi-restraints excluded: chain A residue  782 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 171 HIS
A 175 ASN
A 258 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.148867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.112918 restraints weight = 7369.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.111535 restraints weight = 5795.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.112607 restraints weight = 5335.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.113095 restraints weight = 4692.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.113227 restraints weight = 4362.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.4025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   5726  Z= 0.181
  Angle     :  0.659   6.728   7788  Z= 0.332
  Chirality :  0.046   0.159    923
  Planarity :  0.004   0.031    982
  Dihedral  :  4.438  21.621    745
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 22.77 %
    Favored  : 74.20 %
  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: -2.02 (0.30), residues: 708
  helix:  0.32 (0.36), residues: 218
  sheet: -2.89 (0.51), residues: 88
  loop : -1.98 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 135 
 TYR   0.015   0.002   TYR A 725 
 PHE   0.015   0.001   PHE A 808 
 TRP   0.014   0.001   TRP A 159 
 HIS   0.006   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 5721)
  covalent geometry    : angle       0.65464 ( 7778)
  SS BOND              : bond        0.00543 (    5)
  SS BOND              : angle       2.25659 (   10)
  hydrogen bonds       : bond        0.07557 (  147)
  hydrogen bonds       : angle       4.71954 (  426)

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

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

  1416 Ramachandran restraints generated.
    708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1416 Ramachandran restraints generated.
    708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 61
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A   66 MET cc_start: 0.7568 (mmm) cc_final: 0.7193 (mmt)
REVERT: A  105 LYS cc_start: 0.8014 (ptpp) cc_final: 0.7706 (mtmm)
REVERT: A  154 GLN cc_start: 0.7014 (tt0) cc_final: 0.6622 (tp-100)
REVERT: A  678 CYS cc_start: 0.8150 (t) cc_final: 0.7786 (t)
REVERT: A  712 LEU cc_start: 0.8244 (tt) cc_final: 0.7956 (mt)
REVERT: A  752 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8418 (mp)
REVERT: A  754 PHE cc_start: 0.8092 (t80) cc_final: 0.7616 (t80)
  outliers start: 19
  outliers final: 10
  residues processed: 76
  average time/residue: 0.0590
  time to fit residues: 6.5376
Evaluate side-chains
  67 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  664 VAL
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  755 THR
Chi-restraints excluded: chain A residue  782 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 14 optimal weight:    0.0870
   chunk 2 optimal weight:   10.0000
   chunk 71 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0470
   chunk 70 optimal weight:    0.0060
   chunk 60 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.3272

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

Flipped N/Q/H residues before XYZ refinement:
** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 171 HIS
A 175 ASN
A 258 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.160342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.126511 restraints weight = 7275.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.124582 restraints weight = 5729.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.125678 restraints weight = 5341.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.125958 restraints weight = 4697.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.126543 restraints weight = 4362.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.4223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5726  Z= 0.104
  Angle     :  0.582  11.021   7788  Z= 0.284
  Chirality :  0.042   0.133    923
  Planarity :  0.003   0.030    982
  Dihedral  :  3.945  15.283    745
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 23.25 %
    Favored  : 74.20 %
  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: -1.67 (0.31), residues: 708
  helix:  0.98 (0.37), residues: 211
  sheet: -3.03 (0.57), residues: 68
  loop : -1.96 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 275 
 TYR   0.013   0.001   TYR A 725 
 PHE   0.013   0.001   PHE A 547 
 TRP   0.007   0.001   TRP A 159 
 HIS   0.006   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 5721)
  covalent geometry    : angle       0.57977 ( 7778)
  SS BOND              : bond        0.00221 (    5)
  SS BOND              : angle       1.60285 (   10)
  hydrogen bonds       : bond        0.04808 (  147)
  hydrogen bonds       : angle       4.40834 (  426)

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

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

  1416 Ramachandran restraints generated.
    708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1416 Ramachandran restraints generated.
    708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.224 
Fit side-chains
REVERT: A   66 MET cc_start: 0.7550 (mmm) cc_final: 0.7187 (mmt)
REVERT: A  105 LYS cc_start: 0.8011 (ptpp) cc_final: 0.7706 (mtmm)
REVERT: A  678 CYS cc_start: 0.7998 (t) cc_final: 0.7775 (t)
REVERT: A  752 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8568 (mp)
  outliers start: 16
  outliers final: 11
  residues processed: 74
  average time/residue: 0.0490
  time to fit residues: 5.6079
Evaluate side-chains
  68 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  707 THR
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  755 THR
Chi-restraints excluded: chain A residue  782 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 61 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 6 optimal weight:    4.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 171 HIS
A 175 ASN
A 258 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.148939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.111979 restraints weight = 7311.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.113500 restraints weight = 5834.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.114752 restraints weight = 5007.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.115325 restraints weight = 4546.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.115738 restraints weight = 4216.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.4331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5726  Z= 0.159
  Angle     :  0.646   9.550   7788  Z= 0.318
  Chirality :  0.045   0.144    923
  Planarity :  0.004   0.034    982
  Dihedral  :  4.186  18.010    745
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.77 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 23.73 %
    Favored  : 72.93 %
  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: -1.83 (0.31), residues: 708
  helix:  0.62 (0.36), residues: 218
  sheet: -2.73 (0.54), residues: 83
  loop : -1.99 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 275 
 TYR   0.015   0.002   TYR A 725 
 PHE   0.015   0.001   PHE A 808 
 TRP   0.011   0.001   TRP A 159 
 HIS   0.006   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 5721)
  covalent geometry    : angle       0.64285 ( 7778)
  SS BOND              : bond        0.00366 (    5)
  SS BOND              : angle       1.98220 (   10)
  hydrogen bonds       : bond        0.06809 (  147)
  hydrogen bonds       : angle       4.56993 (  426)

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

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

  1416 Ramachandran restraints generated.
    708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1416 Ramachandran restraints generated.
    708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 55
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A   66 MET cc_start: 0.7583 (mmm) cc_final: 0.7248 (mmt)
REVERT: A  137 ASP cc_start: 0.8578 (p0) cc_final: 0.8356 (p0)
REVERT: A  250 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8981 (tp)
REVERT: A  752 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8660 (mp)
  outliers start: 21
  outliers final: 14
  residues processed: 71
  average time/residue: 0.0515
  time to fit residues: 5.3864
Evaluate side-chains
  70 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 54
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  707 THR
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  755 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 38 optimal weight:    1.9990
   chunk 16 optimal weight:    0.2980
   chunk 15 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0670
   chunk 49 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 46 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
A 171 HIS
A 175 ASN
A 258 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.155808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.121296 restraints weight = 7261.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.119688 restraints weight = 5866.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.120324 restraints weight = 5185.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.120544 restraints weight = 4855.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.121381 restraints weight = 4479.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.4457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5726  Z= 0.118
  Angle     :  0.599  11.117   7788  Z= 0.290
  Chirality :  0.043   0.133    923
  Planarity :  0.003   0.032    982
  Dihedral  :  3.952  16.321    745
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 24.52 %
    Favored  : 73.09 %
  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: -1.70 (0.31), residues: 708
  helix:  0.91 (0.36), residues: 217
  sheet: -2.99 (0.60), residues: 58
  loop : -2.06 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 275 
 TYR   0.013   0.001   TYR A 725 
 PHE   0.013   0.001   PHE A 547 
 TRP   0.009   0.001   TRP A 159 
 HIS   0.005   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 5721)
  covalent geometry    : angle       0.59686 ( 7778)
  SS BOND              : bond        0.00220 (    5)
  SS BOND              : angle       1.67699 (   10)
  hydrogen bonds       : bond        0.05462 (  147)
  hydrogen bonds       : angle       4.41409 (  426)

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

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

  1416 Ramachandran restraints generated.
    708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1416 Ramachandran restraints generated.
    708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A   66 MET cc_start: 0.7645 (mmm) cc_final: 0.7328 (mmt)
REVERT: A  752 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8559 (mp)
  outliers start: 15
  outliers final: 12
  residues processed: 70
  average time/residue: 0.0470
  time to fit residues: 4.9807
Evaluate side-chains
  69 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  707 THR
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  755 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 58 optimal weight:    0.4980
   chunk 49 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 70 optimal weight:    0.3980
   chunk 17 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 171 HIS
A 258 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.155681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.121039 restraints weight = 7312.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.119830 restraints weight = 6008.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.121532 restraints weight = 5672.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.121904 restraints weight = 4855.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.122186 restraints weight = 4257.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.4529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5726  Z= 0.131
  Angle     :  0.594   8.209   7788  Z= 0.293
  Chirality :  0.043   0.134    923
  Planarity :  0.003   0.033    982
  Dihedral  :  3.976  16.078    745
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 24.04 %
    Favored  : 73.73 %
  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: -1.63 (0.31), residues: 708
  helix:  0.94 (0.36), residues: 217
  sheet: -2.54 (0.55), residues: 77
  loop : -2.00 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 275 
 TYR   0.013   0.001   TYR A 725 
 PHE   0.012   0.001   PHE A 547 
 TRP   0.006   0.001   TRP A 812 
 HIS   0.005   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 5721)
  covalent geometry    : angle       0.59048 ( 7778)
  SS BOND              : bond        0.00273 (    5)
  SS BOND              : angle       1.80014 (   10)
  hydrogen bonds       : bond        0.05930 (  147)
  hydrogen bonds       : angle       4.42136 (  426)

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

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

  1416 Ramachandran restraints generated.
    708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1416 Ramachandran restraints generated.
    708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 0.233 
Fit side-chains
REVERT: A   66 MET cc_start: 0.7599 (mmm) cc_final: 0.7283 (mmt)
REVERT: A  137 ASP cc_start: 0.8603 (p0) cc_final: 0.8366 (p0)
REVERT: A  231 ASP cc_start: 0.8115 (t0) cc_final: 0.7832 (t0)
REVERT: A  752 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8548 (mp)
  outliers start: 14
  outliers final: 13
  residues processed: 69
  average time/residue: 0.0476
  time to fit residues: 5.1103
Evaluate side-chains
  71 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  707 THR
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  755 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 67 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0470
   chunk 44 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 57 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 32 optimal weight:    0.1980
   overall best weight:    0.6278

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

Flipped N/Q/H residues before XYZ refinement:
A 171 HIS
A 175 ASN
A 258 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.155577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.120842 restraints weight = 7393.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.119675 restraints weight = 5787.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.120977 restraints weight = 5455.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.121387 restraints weight = 4904.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.121715 restraints weight = 4255.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.4601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5726  Z= 0.126
  Angle     :  0.600  11.177   7788  Z= 0.291
  Chirality :  0.043   0.134    923
  Planarity :  0.003   0.033    982
  Dihedral  :  3.937  16.425    745
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 23.89 %
    Favored  : 73.73 %
  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: -1.65 (0.31), residues: 708
  helix:  0.98 (0.36), residues: 217
  sheet: -3.03 (0.59), residues: 59
  loop : -2.02 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 275 
 TYR   0.013   0.001   TYR A 725 
 PHE   0.012   0.001   PHE A 547 
 TRP   0.006   0.001   TRP A 812 
 HIS   0.005   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 5721)
  covalent geometry    : angle       0.59704 ( 7778)
  SS BOND              : bond        0.00243 (    5)
  SS BOND              : angle       1.77514 (   10)
  hydrogen bonds       : bond        0.05738 (  147)
  hydrogen bonds       : angle       4.38057 (  426)

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

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

  1416 Ramachandran restraints generated.
    708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1416 Ramachandran restraints generated.
    708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A   66 MET cc_start: 0.7579 (mmm) cc_final: 0.7271 (mmt)
REVERT: A  231 ASP cc_start: 0.8109 (t0) cc_final: 0.7823 (t0)
REVERT: A  250 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8939 (tp)
REVERT: A  752 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8567 (mp)
  outliers start: 15
  outliers final: 13
  residues processed: 70
  average time/residue: 0.0446
  time to fit residues: 4.8282
Evaluate side-chains
  71 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  707 THR
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  755 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 45 optimal weight:    0.3980
   chunk 34 optimal weight:    0.5980
   chunk 67 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 48 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0370
   chunk 59 optimal weight:    4.9990
   overall best weight:    0.5058

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

Flipped N/Q/H residues before XYZ refinement:
A 171 HIS
A 175 ASN
A 258 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.152404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.118379 restraints weight = 7200.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.116717 restraints weight = 5752.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.118074 restraints weight = 5177.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.118268 restraints weight = 4410.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.118534 restraints weight = 4209.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.4654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5726  Z= 0.115
  Angle     :  0.572   7.926   7788  Z= 0.281
  Chirality :  0.043   0.135    923
  Planarity :  0.003   0.033    982
  Dihedral  :  3.845  15.243    745
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 23.89 %
    Favored  : 73.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.48 (0.31), residues: 708
  helix:  1.31 (0.36), residues: 210
  sheet: -2.90 (0.61), residues: 58
  loop : -1.99 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 275 
 TYR   0.012   0.001   TYR A 725 
 PHE   0.012   0.001   PHE A 547 
 TRP   0.006   0.001   TRP A 812 
 HIS   0.005   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 5721)
  covalent geometry    : angle       0.56948 ( 7778)
  SS BOND              : bond        0.00206 (    5)
  SS BOND              : angle       1.66913 (   10)
  hydrogen bonds       : bond        0.05304 (  147)
  hydrogen bonds       : angle       4.32160 (  426)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1070.78 seconds
wall clock time: 19 minutes 6.44 seconds (1146.44 seconds total)