Starting phenix.real_space_refine
on Tue Feb 11 23:27:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sva_25446/02_2025/7sva_25446.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sva_25446/02_2025/7sva_25446.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sva_25446/02_2025/7sva_25446.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sva_25446/02_2025/7sva_25446.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sva_25446/02_2025/7sva_25446.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sva_25446/02_2025/7sva_25446.cif"
  }
  resolution = 3.26
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 93 atoms to isotropic.
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: 6
    Type Number    sf(0)   Gaussians
     P      11      5.49       5
     Mg      1      5.21       5
     S      37      5.16       5
     C    4090      2.51       5
     N    1159      2.21       5
     O    1217      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6515
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6290
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 792, 6290
          Classifications: {'peptide': 792}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 747}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 224
          Classifications: {'DNA': 1, 'RNA': 10}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 1}
          Link IDs: {'rna2p': 4, 'rna3p': 6}
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'  C:plan': 1, '  C:plan2': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.53, per 1000 atoms: 0.70
  Number of scatterers: 6515
  At special positions: 0
  Unit cell: (77.542, 95.088, 113.766, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      37     16.00
     P      11     15.00
     Mg      1     11.99
     O    1217      8.00
     N    1159      7.00
     C    4090      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.75
  Conformation dependent library (CDL) restraints added in 710.5 milliseconds
  

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1494

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 8 sheets defined
      31.4% alpha, 17.7% beta
      0 base pairs and 4 stacking pairs defined.
    Time for finding SS restraints: 2.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 170 through 186
    Processing helix  chain 'A' and resid 248 through 257
      removed outlier: 3.690A  pdb=" N   LEU A 252 " --> pdb=" O   ASN A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 283
      removed outlier: 5.121A  pdb=" N   LEU A 278 " --> pdb=" O   VAL A 274 " (cutoff:3.500A)
      removed outlier: 4.677A  pdb=" N   SER A 279 " --> pdb=" O   LEU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 348
    Processing helix  chain 'A' and resid 357 through 369
    Processing helix  chain 'A' and resid 460 through 472
      removed outlier: 4.205A  pdb=" N   THR A 465 " --> pdb=" O   GLU A 461 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ALA A 466 " --> pdb=" O   LYS A 462 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LEU A 467 " --> pdb=" O   GLN A 463 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   VAL A 470 " --> pdb=" O   ALA A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 490
      removed outlier: 3.731A  pdb=" N   ALA A 490 " --> pdb=" O   VAL A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 501
    Processing helix  chain 'A' and resid 565 through 584
    Processing helix  chain 'A' and resid 602 through 617
    Processing helix  chain 'A' and resid 637 through 648
    Processing helix  chain 'A' and resid 658 through 663
    Processing helix  chain 'A' and resid 665 through 679
      removed outlier: 3.671A  pdb=" N   VAL A 678 " --> pdb=" O   LEU A 674 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 692
    Processing helix  chain 'A' and resid 770 through 784
      removed outlier: 3.703A  pdb=" N   ASP A 774 " --> pdb=" O   GLY A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 801 through 821
      removed outlier: 3.955A  pdb=" N   ILE A 813 " --> pdb=" O   GLU A 809 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLU A 821 " --> pdb=" O   CYS A 817 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 903 through 915
      removed outlier: 3.541A  pdb=" N   CYS A 915 " --> pdb=" O   THR A 911 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 928 through 941
    Processing helix  chain 'A' and resid 942 through 944
      No H-bonds generated for 'chain 'A' and resid 942 through 944'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 738 through 745
      removed outlier: 3.751A  pdb=" N   ALA A 724 " --> pdb=" O   CYS A 743 " (cutoff:3.500A)
      removed outlier: 5.107A  pdb=" N   ILE A 705 " --> pdb=" O   SER A 729 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   VAL A 710 " --> pdb=" O   ALA A 795 " (cutoff:3.500A)
      removed outlier: 7.555A  pdb=" N   ILE A 790 " --> pdb=" O   THR A 829 " (cutoff:3.500A)
      removed outlier: 8.066A  pdb=" N   ILE A 831 " --> pdb=" O   ILE A 790 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   PHE A 792 " --> pdb=" O   ILE A 831 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   VAL A 833 " --> pdb=" O   PHE A 792 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   ARG A 794 " --> pdb=" O   VAL A 833 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 315 through 318
      removed outlier: 3.794A  pdb=" N   LEU A 322 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   ASN A 503 " --> pdb=" O   ASP A 151 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 195 through 197
      removed outlier: 7.179A  pdb=" N   GLN A 159 " --> pdb=" O   VAL A 244 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE A 241 " --> pdb=" O   LYS A 214 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   LYS A 214 " --> pdb=" O   ILE A 241 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 291
      removed outlier: 4.031A  pdb=" N   PHE A 311 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 384 through 387
      removed outlier: 3.600A  pdb=" N   VAL A 373 " --> pdb=" O   TYR A 385 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   VAL A 371 " --> pdb=" O   VAL A 387 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 394
      removed outlier: 4.665A  pdb=" N   GLY A 389 " --> pdb=" O   GLN A 432 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   GLN A 432 " --> pdb=" O   GLY A 389 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   THR A 391 " --> pdb=" O   CYS A 430 " (cutoff:3.500A)
      removed outlier: 5.258A  pdb=" N   CYS A 430 " --> pdb=" O   THR A 391 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 531 through 532
      removed outlier: 3.542A  pdb=" N   VAL A 686 " --> pdb=" O   LYS A 522 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 596 through 597
      removed outlier: 4.187A  pdb=" N   TYR A 596 " --> pdb=" O   CYS A 557 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ALA A 556 " --> pdb=" O   LEU A 627 " (cutoff:3.500A)
      removed outlier: 8.131A  pdb=" N   ILE A 629 " --> pdb=" O   ALA A 556 " (cutoff:3.500A)
      removed outlier: 7.108A  pdb=" N   VAL A 558 " --> pdb=" O   ILE A 629 " (cutoff:3.500A)
      removed outlier: 7.197A  pdb=" N   CYS A 656 " --> pdb=" O   LEU A 626 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   ALA A 628 " --> pdb=" O   CYS A 656 " (cutoff:3.500A)

    245 hydrogen bonds defined for protein.
    708 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      4 stacking parallelities
  Total time for adding SS restraints: 2.29

  Time building geometry restraints manager: 2.00 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2082
        1.34 -     1.46: 1074
        1.46 -     1.58: 3446
        1.58 -     1.70: 21
        1.70 -     1.81: 52
  Bond restraints: 6675
  Sorted by residual:
  bond pdb=" N   SER A 720 "
       pdb=" CA  SER A 720 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.032 1.29e-02 6.01e+03 6.04e+00
  bond pdb=" N   GLU A 718 "
       pdb=" CA  GLU A 718 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.20e-02 6.94e+03 4.96e+00
  bond pdb=" N   ARG A 780 "
       pdb=" CA  ARG A 780 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.026 1.19e-02 7.06e+03 4.96e+00
  bond pdb=" N   SER A 719 "
       pdb=" CA  SER A 719 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 1.29e-02 6.01e+03 4.95e+00
  bond pdb=" N   ASN A 715 "
       pdb=" CA  ASN A 715 "
    ideal  model  delta    sigma   weight residual
    1.457  1.484 -0.027 1.29e-02 6.01e+03 4.27e+00
  ... (remaining 6670 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.22: 8950
        2.22 -     4.43: 119
        4.43 -     6.65: 10
        6.65 -     8.86: 3
        8.86 -    11.08: 2
  Bond angle restraints: 9084
  Sorted by residual:
  angle pdb=" N   TRP A 732 "
        pdb=" CA  TRP A 732 "
        pdb=" C   TRP A 732 "
      ideal   model   delta    sigma   weight residual
     109.81  119.53   -9.72 2.21e+00 2.05e-01 1.93e+01
  angle pdb=" C   LYS A 457 "
        pdb=" CA  LYS A 457 "
        pdb=" CB  LYS A 457 "
      ideal   model   delta    sigma   weight residual
     116.34  110.51    5.83 1.40e+00 5.10e-01 1.74e+01
  angle pdb=" CA  LEU A 368 "
        pdb=" CB  LEU A 368 "
        pdb=" CG  LEU A 368 "
      ideal   model   delta    sigma   weight residual
     116.30  127.38  -11.08 3.50e+00 8.16e-02 1.00e+01
  angle pdb=" CA  GLU A 718 "
        pdb=" C   GLU A 718 "
        pdb=" O   GLU A 718 "
      ideal   model   delta    sigma   weight residual
     120.90  117.91    2.99 1.07e+00 8.73e-01 7.81e+00
  angle pdb=" CA  GLU A 717 "
        pdb=" C   GLU A 717 "
        pdb=" O   GLU A 717 "
      ideal   model   delta    sigma   weight residual
     122.32  118.31    4.01 1.51e+00 4.39e-01 7.07e+00
  ... (remaining 9079 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.86: 3542
       16.86 -    33.72: 407
       33.72 -    50.58: 86
       50.58 -    67.44: 36
       67.44 -    84.30: 10
  Dihedral angle restraints: 4081
    sinusoidal: 1771
      harmonic: 2310
  Sorted by residual:
  dihedral pdb=" CA  GLY A 856 "
           pdb=" C   GLY A 856 "
           pdb=" N   ASN A 857 "
           pdb=" CA  ASN A 857 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.44  -19.56     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  TRP A 732 "
           pdb=" C   TRP A 732 "
           pdb=" N   PRO A 733 "
           pdb=" CA  PRO A 733 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.75  -18.25     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  ASN A 548 "
           pdb=" C   ASN A 548 "
           pdb=" N   GLY A 549 "
           pdb=" CA  GLY A 549 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.08   17.92     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 4078 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 859
       0.056 -    0.112: 143
       0.112 -    0.167: 14
       0.167 -    0.223: 0
       0.223 -    0.279: 1
  Chirality restraints: 1017
  Sorted by residual:
  chirality pdb=" CA  TRP A 732 "
            pdb=" N   TRP A 732 "
            pdb=" C   TRP A 732 "
            pdb=" CB  TRP A 732 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.94e+00
  chirality pdb=" CB  THR A 154 "
            pdb=" CA  THR A 154 "
            pdb=" OG1 THR A 154 "
            pdb=" CG2 THR A 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.75e-01
  chirality pdb=" CB  ILE A 701 "
            pdb=" CA  ILE A 701 "
            pdb=" CG1 ILE A 701 "
            pdb=" CG2 ILE A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.15 2.00e-01 2.50e+01 5.53e-01
  ... (remaining 1014 not shown)

  Planarity restraints: 1131
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 732 "   -0.032 2.00e-02 2.50e+03   2.88e-02 2.07e+01
        pdb=" CG  TRP A 732 "    0.077 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 732 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 732 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 732 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 732 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 732 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 732 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 732 "   -0.010 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 732 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 695 "   -0.060 5.00e-02 4.00e+02   8.95e-02 1.28e+01
        pdb=" N   PRO A 696 "    0.155 5.00e-02 4.00e+02
        pdb=" CA  PRO A 696 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 696 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 732 "   -0.036 5.00e-02 4.00e+02   5.51e-02 4.85e+00
        pdb=" N   PRO A 733 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 733 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 733 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1128 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 76
        2.64 -     3.21: 5713
        3.21 -     3.77: 10012
        3.77 -     4.34: 13415
        4.34 -     4.90: 22923
  Nonbonded interactions: 52139
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 709 "
            pdb="MG    MG A1001 "
     model   vdw
     2.078 2.170
  nonbonded pdb=" OD1 ASP A 709 "
            pdb="MG    MG A1001 "
     model   vdw
     2.097 2.170
  nonbonded pdb=" O   ARG A 643 "
            pdb=" OG1 THR A 647 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" OG1 THR A 829 "
            pdb=" OD1 ASN A 900 "
     model   vdw
     2.177 3.040
  nonbonded pdb=" OE1 GLU A 646 "
            pdb=" OH  TYR A 944 "
     model   vdw
     2.192 3.040
  ... (remaining 52134 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     20.090
  Find NCS groups from input model:        0.080
  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:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7072
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6675  Z= 0.190
  Angle     :  0.595  11.079   9084  Z= 0.316
  Chirality :  0.041   0.279   1017
  Planarity :  0.005   0.089   1131
  Dihedral  : 15.797  84.303   2587
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  0.29 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.32), residues: 780
  helix:  1.87 (0.35), residues: 239
  sheet: -1.04 (0.40), residues: 179
  loop : -1.39 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.077   0.003   TRP A 732 
 HIS   0.001   0.000   HIS A 427 
 PHE   0.011   0.001   PHE A 802 
 TYR   0.007   0.001   TYR A 312 
 ARG   0.006   0.000   ARG A 300 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 57
  average time/residue: 0.3686
  time to fit residues: 25.2352
Evaluate side-chains
  26 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  717 GLU
Chi-restraints excluded: chain A residue  719 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    9.9990
   chunk 60 optimal weight:    9.9990
   chunk 33 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 32 optimal weight:    8.9990
   chunk 62 optimal weight:    9.9990
   chunk 24 optimal weight:    0.0370
   chunk 38 optimal weight:    7.9990
   chunk 46 optimal weight:   10.0000
   chunk 72 optimal weight:    0.0270
   overall best weight:    2.6122

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

Flipped N/Q/H residues before XYZ refinement:
** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 325 ASN
A 489 ASN
A 677 ASN
A 715 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.054689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.040927 restraints weight = 34028.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.2964 rms_B_bonded: 4.37
r_work: 0.2834 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.1587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6675  Z= 0.236
  Angle     :  0.604  10.953   9084  Z= 0.304
  Chirality :  0.042   0.156   1017
  Planarity :  0.005   0.059   1131
  Dihedral  : 10.992  63.918   1033
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  6.08 %
    Favored  : 93.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.32), residues: 780
  helix:  2.03 (0.36), residues: 244
  sheet: -0.83 (0.40), residues: 177
  loop : -1.35 (0.34), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 732 
 HIS   0.003   0.001   HIS A 427 
 PHE   0.013   0.001   PHE A 211 
 TYR   0.010   0.001   TYR A 596 
 ARG   0.005   0.001   ARG A 382 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 32
  time to evaluate  : 0.800 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9292 (t0) cc_final: 0.8922 (p0)
REVERT: A  848 ASP cc_start: 0.8889 (t0) cc_final: 0.8608 (t0)
  outliers start: 3
  outliers final: 2
  residues processed: 34
  average time/residue: 0.3008
  time to fit residues: 13.3213
Evaluate side-chains
  29 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 27
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  717 GLU
Chi-restraints excluded: chain A residue  719 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 48 optimal weight:   10.0000
   chunk 62 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 11 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 16 optimal weight:    7.9990
   chunk 28 optimal weight:   10.0000
   chunk 59 optimal weight:    0.6980
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.054862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.041237 restraints weight = 34766.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 4.30
r_work: 0.2836 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6675  Z= 0.185
  Angle     :  0.537   7.876   9084  Z= 0.272
  Chirality :  0.040   0.151   1017
  Planarity :  0.005   0.050   1131
  Dihedral  : 10.764  63.849   1033
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  7.96 %
    Favored  : 91.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.32), residues: 780
  helix:  2.15 (0.36), residues: 244
  sheet: -0.66 (0.41), residues: 168
  loop : -1.24 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 732 
 HIS   0.002   0.001   HIS A 427 
 PHE   0.010   0.001   PHE A 211 
 TYR   0.009   0.001   TYR A 596 
 ARG   0.004   0.000   ARG A 789 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9270 (t0) cc_final: 0.8896 (p0)
REVERT: A  848 ASP cc_start: 0.8911 (t0) cc_final: 0.8628 (t0)
  outliers start: 4
  outliers final: 3
  residues processed: 36
  average time/residue: 0.2650
  time to fit residues: 12.7005
Evaluate side-chains
  31 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 28
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  717 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 53 optimal weight:    0.6980
   chunk 59 optimal weight:    5.9990
   chunk 60 optimal weight:    6.9990
   chunk 14 optimal weight:    9.9990
   chunk 79 optimal weight:   10.0000
   chunk 74 optimal weight:    9.9990
   chunk 4 optimal weight:   10.0000
   chunk 28 optimal weight:   20.0000
   chunk 32 optimal weight:    0.9980
   chunk 54 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   overall best weight:    4.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 427 HIS
A 823 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.053716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.040070 restraints weight = 35453.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.2926 rms_B_bonded: 4.34
r_work: 0.2794 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   6675  Z= 0.313
  Angle     :  0.591   6.124   9084  Z= 0.302
  Chirality :  0.042   0.150   1017
  Planarity :  0.005   0.049   1131
  Dihedral  : 10.789  63.914   1032
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  9.84 %
    Favored  : 88.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.31), residues: 780
  helix:  2.02 (0.35), residues: 243
  sheet: -0.82 (0.39), residues: 173
  loop : -1.28 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 732 
 HIS   0.004   0.001   HIS A 427 
 PHE   0.010   0.001   PHE A 874 
 TYR   0.010   0.001   TYR A 596 
 ARG   0.006   0.001   ARG A 789 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9259 (t0) cc_final: 0.8924 (p0)
REVERT: A  630 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8669 (pp)
REVERT: A  848 ASP cc_start: 0.8936 (t0) cc_final: 0.8660 (t0)
  outliers start: 9
  outliers final: 3
  residues processed: 37
  average time/residue: 0.1779
  time to fit residues: 9.4910
Evaluate side-chains
  32 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 28
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  945 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 6 optimal weight:   20.0000
   chunk 14 optimal weight:    3.9990
   chunk 71 optimal weight:   10.0000
   chunk 73 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 36 optimal weight:    9.9990
   chunk 70 optimal weight:    7.9990
   chunk 13 optimal weight:    6.9990
   chunk 79 optimal weight:   10.0000
   overall best weight:    4.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.053388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.039754 restraints weight = 35305.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.2917 rms_B_bonded: 4.40
r_work: 0.2785 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.2663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6675  Z= 0.332
  Angle     :  0.599   6.432   9084  Z= 0.308
  Chirality :  0.042   0.149   1017
  Planarity :  0.005   0.046   1131
  Dihedral  : 10.597  63.951   1029
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 11.14 %
    Favored  : 87.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.31), residues: 780
  helix:  1.94 (0.34), residues: 243
  sheet: -0.93 (0.40), residues: 168
  loop : -1.35 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 539 
 HIS   0.002   0.001   HIS A 894 
 PHE   0.009   0.001   PHE A 148 
 TYR   0.011   0.001   TYR A 596 
 ARG   0.006   0.001   ARG A 789 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 0.794 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9290 (t0) cc_final: 0.8974 (p0)
REVERT: A  630 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8666 (pp)
REVERT: A  848 ASP cc_start: 0.8932 (t0) cc_final: 0.8660 (t0)
  outliers start: 7
  outliers final: 4
  residues processed: 34
  average time/residue: 0.2234
  time to fit residues: 10.7460
Evaluate side-chains
  33 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 28
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  823 ASN
Chi-restraints excluded: chain A residue  945 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 73 optimal weight:    5.9990
   chunk 52 optimal weight:    9.9990
   chunk 65 optimal weight:    8.9990
   chunk 28 optimal weight:    8.9990
   chunk 10 optimal weight:   20.0000
   chunk 44 optimal weight:    5.9990
   chunk 54 optimal weight:   20.0000
   chunk 3 optimal weight:    7.9990
   chunk 37 optimal weight:    9.9990
   chunk 41 optimal weight:   10.0000
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 677 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.052952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.039467 restraints weight = 35173.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.2896 rms_B_bonded: 4.33
r_work: 0.2763 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
moved from start:          0.3076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056   6675  Z= 0.442
  Angle     :  0.673   7.106   9084  Z= 0.344
  Chirality :  0.044   0.144   1017
  Planarity :  0.006   0.051   1131
  Dihedral  : 10.862  63.986   1029
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 12.45 %
    Favored  : 86.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.30), residues: 780
  helix:  1.64 (0.34), residues: 243
  sheet: -0.85 (0.40), residues: 165
  loop : -1.64 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 732 
 HIS   0.004   0.001   HIS A 250 
 PHE   0.010   0.002   PHE A 255 
 TYR   0.013   0.002   TYR A 596 
 ARG   0.007   0.001   ARG A 789 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 29
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9284 (t0) cc_final: 0.8978 (p0)
REVERT: A  630 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8678 (pp)
REVERT: A  852 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.8078 (p)
  outliers start: 8
  outliers final: 4
  residues processed: 36
  average time/residue: 0.2298
  time to fit residues: 11.3424
Evaluate side-chains
  33 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 27
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  678 VAL
Chi-restraints excluded: chain A residue  823 ASN
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain A residue  945 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 27 optimal weight:   20.0000
   chunk 77 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 1 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 72 optimal weight:    4.9990
   chunk 55 optimal weight:    9.9990
   chunk 79 optimal weight:   10.0000
   chunk 51 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.053279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.039920 restraints weight = 35360.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.2912 rms_B_bonded: 4.35
r_work: 0.2780 rms_B_bonded: 4.90 restraints_weight: 0.5000
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.3045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   6675  Z= 0.308
  Angle     :  0.591   6.645   9084  Z= 0.303
  Chirality :  0.042   0.185   1017
  Planarity :  0.005   0.050   1131
  Dihedral  : 10.683  63.944   1029
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 13.17 %
    Favored  : 85.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.31), residues: 780
  helix:  1.88 (0.34), residues: 241
  sheet: -0.80 (0.40), residues: 166
  loop : -1.59 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 732 
 HIS   0.003   0.001   HIS A 881 
 PHE   0.010   0.001   PHE A 148 
 TYR   0.014   0.001   TYR A 596 
 ARG   0.013   0.001   ARG A 246 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 27
  time to evaluate  : 0.727 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9267 (t0) cc_final: 0.8965 (p0)
REVERT: A  630 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8693 (pp)
  outliers start: 7
  outliers final: 4
  residues processed: 33
  average time/residue: 0.1985
  time to fit residues: 9.5832
Evaluate side-chains
  32 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 27
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  673 SER
Chi-restraints excluded: chain A residue  678 VAL
Chi-restraints excluded: chain A residue  945 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 42 optimal weight:   10.0000
   chunk 28 optimal weight:    6.9990
   chunk 56 optimal weight:    0.4980
   chunk 38 optimal weight:    6.9990
   chunk 54 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 33 optimal weight:    0.6980
   overall best weight:    2.0386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.053846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.040367 restraints weight = 35295.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.2937 rms_B_bonded: 4.37
r_work: 0.2805 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.2989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6675  Z= 0.192
  Angle     :  0.547   9.166   9084  Z= 0.277
  Chirality :  0.041   0.175   1017
  Planarity :  0.004   0.043   1131
  Dihedral  : 10.469  63.889   1029
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 13.75 %
    Favored  : 85.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.31), residues: 780
  helix:  2.13 (0.35), residues: 241
  sheet: -0.66 (0.40), residues: 170
  loop : -1.44 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 897 
 HIS   0.002   0.001   HIS A 838 
 PHE   0.009   0.001   PHE A 148 
 TYR   0.010   0.001   TYR A 596 
 ARG   0.010   0.000   ARG A 246 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 29
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9287 (t0) cc_final: 0.8988 (p0)
REVERT: A  630 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8647 (pp)
REVERT: A  771 MET cc_start: 0.8449 (mtt) cc_final: 0.8234 (mtt)
  outliers start: 5
  outliers final: 1
  residues processed: 34
  average time/residue: 0.2250
  time to fit residues: 10.6743
Evaluate side-chains
  31 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 29
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  630 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 43 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 72 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 31 optimal weight:   10.0000
   chunk 12 optimal weight:    0.0470
   chunk 27 optimal weight:   20.0000
   chunk 13 optimal weight:    0.8980
   chunk 66 optimal weight:    0.3980
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
A 749 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.054842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.041295 restraints weight = 35020.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 4.43
r_work: 0.2852 rms_B_bonded: 4.96 restraints_weight: 0.5000
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.2967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6675  Z= 0.140
  Angle     :  0.539   7.875   9084  Z= 0.271
  Chirality :  0.041   0.168   1017
  Planarity :  0.004   0.042   1131
  Dihedral  : 10.304  63.852   1029
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 14.47 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.31), residues: 780
  helix:  2.29 (0.35), residues: 241
  sheet: -0.69 (0.39), residues: 174
  loop : -1.33 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 308 
 HIS   0.002   0.000   HIS A 838 
 PHE   0.010   0.001   PHE A 211 
 TYR   0.011   0.001   TYR A 893 
 ARG   0.011   0.000   ARG A 246 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.818 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9287 (t0) cc_final: 0.8952 (p0)
REVERT: A  246 ARG cc_start: 0.8022 (ttm110) cc_final: 0.7492 (ttm170)
REVERT: A  502 MET cc_start: 0.9122 (mmm) cc_final: 0.8601 (mmm)
REVERT: A  630 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8602 (pp)
  outliers start: 3
  outliers final: 2
  residues processed: 38
  average time/residue: 0.2641
  time to fit residues: 13.4912
Evaluate side-chains
  33 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 30
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  945 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 74 optimal weight:    7.9990
   chunk 27 optimal weight:    9.9990
   chunk 34 optimal weight:    5.9990
   chunk 59 optimal weight:   20.0000
   chunk 76 optimal weight:    0.8980
   chunk 40 optimal weight:    8.9990
   chunk 55 optimal weight:    5.9990
   chunk 62 optimal weight:    9.9990
   chunk 9 optimal weight:    8.9990
   chunk 31 optimal weight:    9.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    4.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 838 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.053448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.040168 restraints weight = 35733.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.2926 rms_B_bonded: 4.35
r_work: 0.2794 rms_B_bonded: 4.82 restraints_weight: 0.5000
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.3095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6675  Z= 0.316
  Angle     :  0.622   7.381   9084  Z= 0.314
  Chirality :  0.042   0.161   1017
  Planarity :  0.005   0.043   1131
  Dihedral  : 10.406  63.972   1029
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 14.76 %
    Favored  : 84.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.31), residues: 780
  helix:  2.20 (0.35), residues: 241
  sheet: -0.49 (0.40), residues: 166
  loop : -1.42 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 732 
 HIS   0.003   0.001   HIS A 894 
 PHE   0.009   0.001   PHE A 779 
 TYR   0.014   0.001   TYR A 596 
 ARG   0.010   0.001   ARG A 246 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9247 (t0) cc_final: 0.8942 (p0)
REVERT: A  630 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8593 (pp)
  outliers start: 3
  outliers final: 2
  residues processed: 36
  average time/residue: 0.2688
  time to fit residues: 12.9147
Evaluate side-chains
  34 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  945 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 75 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 58 optimal weight:    6.9990
   chunk 39 optimal weight:    0.6980
   chunk 32 optimal weight:    5.9990
   chunk 68 optimal weight:    0.3980
   chunk 8 optimal weight:    9.9990
   chunk 38 optimal weight:    7.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    1.5984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.054166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.040781 restraints weight = 35726.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 4.39
r_work: 0.2828 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.3063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6675  Z= 0.174
  Angle     :  0.573   9.526   9084  Z= 0.289
  Chirality :  0.041   0.162   1017
  Planarity :  0.005   0.064   1131
  Dihedral  : 10.320  63.898   1029
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 14.76 %
    Favored  : 84.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.31), residues: 780
  helix:  2.29 (0.35), residues: 241
  sheet: -0.51 (0.40), residues: 175
  loop : -1.37 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 897 
 HIS   0.002   0.001   HIS A 838 
 PHE   0.009   0.001   PHE A 148 
 TYR   0.010   0.001   TYR A 596 
 ARG   0.011   0.000   ARG A 246 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3591.31 seconds
wall clock time: 64 minutes 28.92 seconds (3868.92 seconds total)