Starting phenix.real_space_refine
on Sat May 10 07:51:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wvw_37874/05_2025/8wvw_37874.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wvw_37874/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wvw_37874/05_2025/8wvw_37874.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wvw_37874/05_2025/8wvw_37874.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wvw_37874/05_2025/8wvw_37874.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wvw_37874/05_2025/8wvw_37874.cif"
  }
  resolution = 3.53
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'GLU:plan': 1, 'TRP:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 35
  Time building chain proxies: 4.97, per 1000 atoms: 0.89
  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: 1.36
  Conformation dependent library (CDL) restraints added in 863.2 milliseconds
  

  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: 0.65
  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: 1.79

  Time building geometry restraints manager: 1.62 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:             3.360
  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:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.860
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.570
-------------------------------------------------------------------------------
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 : 18.80
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.010   0.001   TRP A 812 
 HIS   0.010   0.001   HIS A 293 
 PHE   0.031   0.002   PHE A 547 
 TYR   0.033   0.003   TYR A 468 
 ARG   0.003   0.000   ARG A 542 

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

*********************** 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  : 0.616 
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: 0.1453
  time to fit residues: 21.1925
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  : 0.664 
-------------------------------------------------------------------------------
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 60 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 29 optimal weight:    0.5980
   chunk 56 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   chunk 42 optimal weight:    0.5980
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
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 = 0.3798 r_free = 0.3798 target = 0.167517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.132191 restraints weight = 7280.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.133086 restraints weight = 5880.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.133635 restraints weight = 4541.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5726  Z= 0.142
  Angle     :  0.674   7.153   7788  Z= 0.340
  Chirality :  0.045   0.133    923
  Planarity :  0.005   0.047    982
  Dihedral  :  5.355  55.743    755
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 23.25 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.30 (0.30), residues: 708
  helix: -0.06 (0.36), residues: 213
  sheet: -2.80 (0.61), residues: 75
  loop : -2.15 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 159 
 HIS   0.008   0.002   HIS A 293 
 PHE   0.020   0.001   PHE A 696 
 TYR   0.016   0.002   TYR A 725 
 ARG   0.005   0.001   ARG A 542 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06634 (  147)
  hydrogen bonds       : angle       5.10561 (  426)
  SS BOND              : bond        0.00333 (    5)
  SS BOND              : angle       1.88475 (   10)
  covalent geometry    : bond        0.00328 ( 5721)
  covalent geometry    : angle       0.67151 ( 7778)

*********************** 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
  92 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.616 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.4943 (OUTLIER) cc_final: 0.4738 (mt)
REVERT: A   99 LYS cc_start: 0.7668 (ttpt) cc_final: 0.7160 (tptt)
REVERT: A  105 LYS cc_start: 0.7909 (ptpp) cc_final: 0.7584 (mtmm)
REVERT: A  132 GLN cc_start: 0.7921 (mt0) cc_final: 0.7578 (mt0)
REVERT: A  589 ILE cc_start: 0.8217 (mm) cc_final: 0.8015 (mt)
  outliers start: 19
  outliers final: 8
  residues processed: 88
  average time/residue: 0.1377
  time to fit residues: 17.2437
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  : 0.584 
-------------------------------------------------------------------------------
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  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 37 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0980
   chunk 55 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 40 optimal weight:    0.2980
   chunk 23 optimal weight:    0.1980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A 157 HIS
A 171 HIS
A 175 ASN
** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 469 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.164606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.130688 restraints weight = 7272.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.129697 restraints weight = 6081.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.130726 restraints weight = 5918.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.2936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5726  Z= 0.119
  Angle     :  0.595   5.849   7788  Z= 0.296
  Chirality :  0.043   0.131    923
  Planarity :  0.004   0.034    982
  Dihedral  :  4.782  44.989    750
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 22.77 %
    Favored  : 74.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.02 (0.31), residues: 708
  helix:  0.26 (0.36), residues: 226
  sheet: -2.87 (0.59), residues: 76
  loop : -2.05 (0.28), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 159 
 HIS   0.007   0.001   HIS A 293 
 PHE   0.010   0.001   PHE A 547 
 TYR   0.013   0.001   TYR A 534 
 ARG   0.004   0.000   ARG A 275 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05630 (  147)
  hydrogen bonds       : angle       4.62033 (  426)
  SS BOND              : bond        0.00410 (    5)
  SS BOND              : angle       1.94249 (   10)
  covalent geometry    : bond        0.00268 ( 5721)
  covalent geometry    : angle       0.59084 ( 7778)

*********************** 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
  81 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.592 
Fit side-chains
REVERT: A   66 MET cc_start: 0.7602 (mmm) cc_final: 0.7280 (mmt)
REVERT: A   99 LYS cc_start: 0.7941 (ttpt) cc_final: 0.7350 (tptt)
REVERT: A  105 LYS cc_start: 0.7942 (ptpp) cc_final: 0.7637 (mtmm)
REVERT: A  132 GLN cc_start: 0.8127 (mt0) cc_final: 0.7804 (mt0)
  outliers start: 17
  outliers final: 10
  residues processed: 77
  average time/residue: 0.1159
  time to fit residues: 13.2222
Evaluate side-chains
  67 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
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  213 ILE
Chi-restraints excluded: chain A residue  217 SER
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  664 VAL
Chi-restraints excluded: chain A residue  782 MET
Chi-restraints excluded: chain A residue  802 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 71 optimal weight:    0.4980
   chunk 30 optimal weight:    2.9990
   chunk 28 optimal weight:    0.4980
   chunk 36 optimal weight:    2.9990
   chunk 47 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3724 r_free = 0.3724 target = 0.160513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.125482 restraints weight = 7368.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.124884 restraints weight = 5659.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.125600 restraints weight = 4876.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.3570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5726  Z= 0.156
  Angle     :  0.649  10.922   7788  Z= 0.321
  Chirality :  0.045   0.175    923
  Planarity :  0.004   0.028    982
  Dihedral  :  4.347  22.172    746
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 22.45 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.03 (0.30), residues: 708
  helix:  0.35 (0.36), residues: 218
  sheet: -3.22 (0.54), residues: 74
  loop : -1.99 (0.28), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 159 
 HIS   0.006   0.001   HIS A 293 
 PHE   0.014   0.001   PHE A 808 
 TYR   0.014   0.002   TYR A 725 
 ARG   0.002   0.000   ARG A 135 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07013 (  147)
  hydrogen bonds       : angle       4.70262 (  426)
  SS BOND              : bond        0.00457 (    5)
  SS BOND              : angle       1.70902 (   10)
  covalent geometry    : bond        0.00378 ( 5721)
  covalent geometry    : angle       0.64681 ( 7778)

*********************** 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
  87 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 64
  time to evaluate  : 0.680 
Fit side-chains
REVERT: A   74 GLU cc_start: 0.7376 (pm20) cc_final: 0.6733 (pp20)
REVERT: A  105 LYS cc_start: 0.8002 (ptpp) cc_final: 0.7665 (mtmm)
REVERT: A  712 LEU cc_start: 0.8216 (tt) cc_final: 0.7926 (mt)
REVERT: A  752 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8476 (mp)
  outliers start: 23
  outliers final: 14
  residues processed: 83
  average time/residue: 0.1438
  time to fit residues: 17.1393
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  : 0.667 
-------------------------------------------------------------------------------
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  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  451 LEU
Chi-restraints excluded: chain A residue  664 VAL
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  782 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 64 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.3665 r_free = 0.3665 target = 0.155598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.120394 restraints weight = 7220.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.119069 restraints weight = 6133.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.120729 restraints weight = 5695.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.3909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5726  Z= 0.143
  Angle     :  0.620   7.374   7788  Z= 0.309
  Chirality :  0.044   0.138    923
  Planarity :  0.004   0.029    982
  Dihedral  :  4.138  19.552    745
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 22.77 %
    Favored  : 74.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (0.31), residues: 708
  helix:  0.47 (0.36), residues: 218
  sheet: -2.68 (0.55), residues: 85
  loop : -1.90 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 159 
 HIS   0.007   0.001   HIS A 256 
 PHE   0.012   0.001   PHE A 808 
 TYR   0.015   0.001   TYR A 725 
 ARG   0.004   0.000   ARG A 275 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06359 (  147)
  hydrogen bonds       : angle       4.57915 (  426)
  SS BOND              : bond        0.00332 (    5)
  SS BOND              : angle       2.05534 (   10)
  covalent geometry    : bond        0.00347 ( 5721)
  covalent geometry    : angle       0.61616 ( 7778)

*********************** 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
  77 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.653 
Fit side-chains
REVERT: A   74 GLU cc_start: 0.7191 (pm20) cc_final: 0.6724 (pp20)
REVERT: A  105 LYS cc_start: 0.7945 (ptpp) cc_final: 0.7657 (mtmm)
REVERT: A  678 CYS cc_start: 0.8115 (t) cc_final: 0.7707 (t)
REVERT: A  752 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8533 (mp)
  outliers start: 17
  outliers final: 13
  residues processed: 72
  average time/residue: 0.1194
  time to fit residues: 12.9326
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  : 0.653 
-------------------------------------------------------------------------------
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  213 ILE
Chi-restraints excluded: chain A residue  227 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  451 LEU
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  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 25 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0050
   chunk 55 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 24 optimal weight:    0.3980
   chunk 0 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.6798

-------------------------------------------------------------------------------
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 = 0.3632 r_free = 0.3632 target = 0.153016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.117372 restraints weight = 7168.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.115452 restraints weight = 6447.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.117561 restraints weight = 5722.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.4099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5726  Z= 0.131
  Angle     :  0.608  10.880   7788  Z= 0.298
  Chirality :  0.043   0.134    923
  Planarity :  0.003   0.031    982
  Dihedral  :  4.045  17.454    745
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 22.13 %
    Favored  : 74.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.31), residues: 708
  helix:  0.63 (0.36), residues: 217
  sheet: -2.64 (0.54), residues: 86
  loop : -1.88 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 159 
 HIS   0.006   0.001   HIS A 293 
 PHE   0.012   0.001   PHE A  80 
 TYR   0.014   0.001   TYR A 725 
 ARG   0.002   0.000   ARG A 275 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06028 (  147)
  hydrogen bonds       : angle       4.51366 (  426)
  SS BOND              : bond        0.00301 (    5)
  SS BOND              : angle       1.89864 (   10)
  covalent geometry    : bond        0.00317 ( 5721)
  covalent geometry    : angle       0.60467 ( 7778)

*********************** 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
  79 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 57
  time to evaluate  : 0.701 
Fit side-chains
REVERT: A   66 MET cc_start: 0.7609 (mmm) cc_final: 0.7236 (mmt)
REVERT: A   74 GLU cc_start: 0.7262 (pm20) cc_final: 0.6817 (pp20)
REVERT: A  105 LYS cc_start: 0.7979 (ptpp) cc_final: 0.7677 (mtmm)
REVERT: A  678 CYS cc_start: 0.8074 (t) cc_final: 0.7742 (t)
REVERT: A  752 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8568 (mp)
  outliers start: 22
  outliers final: 17
  residues processed: 75
  average time/residue: 0.1156
  time to fit residues: 13.2647
Evaluate side-chains
  71 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 53
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  110 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  227 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  451 LEU
Chi-restraints excluded: chain A residue  664 VAL
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
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 34 optimal weight:    1.9990
   chunk 9 optimal weight:    0.4980
   chunk 32 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 26 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 64 optimal weight:    0.3980
   chunk 68 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0670
   chunk 57 optimal weight:    0.9980
   chunk 7 optimal weight:    7.9990
   overall best weight:    0.4918

-------------------------------------------------------------------------------
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 = 0.3717 r_free = 0.3717 target = 0.160313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.127135 restraints weight = 7269.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.125536 restraints weight = 5695.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.126351 restraints weight = 5346.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.4244

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= 0.115
  Angle     :  0.577   8.961   7788  Z= 0.286
  Chirality :  0.043   0.135    923
  Planarity :  0.003   0.032    982
  Dihedral  :  3.872  15.921    745
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 22.29 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.31), residues: 708
  helix:  0.85 (0.36), residues: 218
  sheet: -2.85 (0.56), residues: 73
  loop : -1.91 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 159 
 HIS   0.005   0.001   HIS A 256 
 PHE   0.010   0.001   PHE A  80 
 TYR   0.013   0.001   TYR A 725 
 ARG   0.001   0.000   ARG A 135 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05346 (  147)
  hydrogen bonds       : angle       4.40991 (  426)
  SS BOND              : bond        0.00264 (    5)
  SS BOND              : angle       1.72640 (   10)
  covalent geometry    : bond        0.00271 ( 5721)
  covalent geometry    : angle       0.57411 ( 7778)

*********************** 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
  80 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 61
  time to evaluate  : 0.641 
Fit side-chains
REVERT: A   74 GLU cc_start: 0.7210 (pm20) cc_final: 0.6805 (pp20)
REVERT: A  678 CYS cc_start: 0.7980 (t) cc_final: 0.7771 (t)
REVERT: A  752 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8556 (mp)
  outliers start: 19
  outliers final: 13
  residues processed: 76
  average time/residue: 0.1171
  time to fit residues: 13.3982
Evaluate side-chains
  68 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  194 ASP
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  227 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  451 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  782 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 3 optimal weight:    6.9990
   chunk 29 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 ** 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 = 0.3660 r_free = 0.3660 target = 0.155564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.121384 restraints weight = 7286.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.119651 restraints weight = 6121.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.120888 restraints weight = 5660.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.4345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   5726  Z= 0.159
  Angle     :  0.646  11.069   7788  Z= 0.317
  Chirality :  0.044   0.143    923
  Planarity :  0.004   0.033    982
  Dihedral  :  4.099  17.650    745
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 23.25 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.31), residues: 708
  helix:  0.57 (0.36), residues: 224
  sheet: -2.65 (0.53), residues: 88
  loop : -1.98 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 159 
 HIS   0.005   0.001   HIS A 293 
 PHE   0.018   0.001   PHE A 547 
 TYR   0.014   0.002   TYR A 725 
 ARG   0.002   0.000   ARG A 135 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06676 (  147)
  hydrogen bonds       : angle       4.53337 (  426)
  SS BOND              : bond        0.00369 (    5)
  SS BOND              : angle       2.02139 (   10)
  covalent geometry    : bond        0.00394 ( 5721)
  covalent geometry    : angle       0.64283 ( 7778)

*********************** 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
  79 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 61
  time to evaluate  : 0.670 
Fit side-chains
REVERT: A   66 MET cc_start: 0.7572 (mmm) cc_final: 0.7164 (mmt)
REVERT: A  137 ASP cc_start: 0.8607 (p0) cc_final: 0.8402 (p0)
REVERT: A  231 ASP cc_start: 0.8116 (t0) cc_final: 0.7913 (t0)
REVERT: A  752 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8569 (mp)
  outliers start: 18
  outliers final: 15
  residues processed: 74
  average time/residue: 0.1280
  time to fit residues: 13.7839
Evaluate side-chains
  73 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  110 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  227 LEU
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 27 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    0.0670
   chunk 68 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0270
   overall best weight:    0.4576

-------------------------------------------------------------------------------
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 ** 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 = 0.3677 r_free = 0.3677 target = 0.157507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.121821 restraints weight = 7276.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.121504 restraints weight = 5671.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.122467 restraints weight = 4882.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.4466

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= 0.112
  Angle     :  0.575   8.445   7788  Z= 0.285
  Chirality :  0.043   0.205    923
  Planarity :  0.003   0.032    982
  Dihedral  :  3.856  15.547    745
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 23.73 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.31), residues: 708
  helix:  0.97 (0.36), residues: 219
  sheet: -2.84 (0.59), residues: 63
  loop : -1.97 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 812 
 HIS   0.005   0.001   HIS A 293 
 PHE   0.018   0.001   PHE A 547 
 TYR   0.016   0.001   TYR A 725 
 ARG   0.001   0.000   ARG A 542 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05202 (  147)
  hydrogen bonds       : angle       4.37180 (  426)
  SS BOND              : bond        0.00281 (    5)
  SS BOND              : angle       1.70986 (   10)
  covalent geometry    : bond        0.00259 ( 5721)
  covalent geometry    : angle       0.57159 ( 7778)

*********************** 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
  76 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.628 
Fit side-chains
REVERT: A  752 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8571 (mp)
  outliers start: 16
  outliers final: 14
  residues processed: 72
  average time/residue: 0.1110
  time to fit residues: 12.1900
Evaluate side-chains
  74 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  110 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  227 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  451 LEU
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  668 LEU
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 6 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 65 optimal weight:    0.5980
   chunk 21 optimal weight:    0.2980
   chunk 56 optimal weight:    0.9990
   chunk 11 optimal weight:    0.3980
   chunk 50 optimal weight:    0.5980
   chunk 68 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 ** 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 = 0.3691 r_free = 0.3691 target = 0.158727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.125512 restraints weight = 7364.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.123835 restraints weight = 5937.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.124596 restraints weight = 5291.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.4548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5726  Z= 0.117
  Angle     :  0.588  10.052   7788  Z= 0.287
  Chirality :  0.043   0.185    923
  Planarity :  0.003   0.032    982
  Dihedral  :  3.803  14.708    745
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 24.52 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (0.31), residues: 708
  helix:  1.01 (0.36), residues: 219
  sheet: -2.86 (0.60), residues: 64
  loop : -1.97 (0.28), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 812 
 HIS   0.005   0.001   HIS A 293 
 PHE   0.010   0.001   PHE A 547 
 TYR   0.014   0.001   TYR A 725 
 ARG   0.001   0.000   ARG A 542 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05329 (  147)
  hydrogen bonds       : angle       4.36869 (  426)
  SS BOND              : bond        0.00235 (    5)
  SS BOND              : angle       1.71545 (   10)
  covalent geometry    : bond        0.00275 ( 5721)
  covalent geometry    : angle       0.58558 ( 7778)

********************** 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
  73 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.693 
Fit side-chains
REVERT: A  752 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8590 (mp)
  outliers start: 13
  outliers final: 12
  residues processed: 69
  average time/residue: 0.1143
  time to fit residues: 11.9866
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  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  110 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  227 LEU
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  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 18 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0060
   chunk 23 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.9400

-------------------------------------------------------------------------------
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 = 0.3646 r_free = 0.3646 target = 0.153938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.117514 restraints weight = 7347.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.117130 restraints weight = 5728.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.118554 restraints weight = 4898.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.4608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5726  Z= 0.164
  Angle     :  0.640   8.585   7788  Z= 0.318
  Chirality :  0.045   0.192    923
  Planarity :  0.004   0.034    982
  Dihedral  :  4.166  18.551    745
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 24.20 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.31), residues: 708
  helix:  0.61 (0.35), residues: 224
  sheet: -2.50 (0.54), residues: 81
  loop : -2.03 (0.29), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 812 
 HIS   0.005   0.001   HIS A 293 
 PHE   0.017   0.001   PHE A 547 
 TYR   0.015   0.002   TYR A 725 
 ARG   0.002   0.000   ARG A 135 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06879 (  147)
  hydrogen bonds       : angle       4.49933 (  426)
  SS BOND              : bond        0.00383 (    5)
  SS BOND              : angle       2.01095 (   10)
  covalent geometry    : bond        0.00405 ( 5721)
  covalent geometry    : angle       0.63614 ( 7778)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2068.46 seconds
wall clock time: 37 minutes 12.48 seconds (2232.48 seconds total)