Starting phenix.real_space_refine
on Thu Jun  5 22:38:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sva_25446/06_2025/7sva_25446.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sva_25446/06_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_25446/06_2025/7sva_25446.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sva_25446/06_2025/7sva_25446.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sva_25446/06_2025/7sva_25446.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sva_25446/06_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-5710/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: 4.67, per 1000 atoms: 0.72
  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: 1.64
  Conformation dependent library (CDL) restraints added in 689.0 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: 2.35
  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: 2.36

  Time building geometry restraints manager: 1.94 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     20.580
  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:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.790
-------------------------------------------------------------------------------
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= 0.141
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16783 (  245)
  hydrogen bonds       : angle       6.79600 (  708)
  covalent geometry    : bond        0.00287 ( 6675)
  covalent geometry    : angle       0.59544 ( 9084)

*********************** 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  : 0.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 57
  average time/residue: 0.3474
  time to fit residues: 23.7964
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  : 0.681 
-------------------------------------------------------------------------------
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 = 0.054727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.041043 restraints weight = 34231.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 4.33
r_work: 0.2834 rms_B_bonded: 4.85 restraints_weight: 0.5000
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
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= 0.155
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03332 (  245)
  hydrogen bonds       : angle       4.88271 (  708)
  covalent geometry    : bond        0.00358 ( 6675)
  covalent geometry    : angle       0.60390 ( 9084)

*********************** 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  : 0.745 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9284 (t0) cc_final: 0.8916 (p0)
REVERT: A  848 ASP cc_start: 0.8887 (t0) cc_final: 0.8605 (t0)
  outliers start: 3
  outliers final: 2
  residues processed: 34
  average time/residue: 0.2878
  time to fit residues: 12.6884
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  : 0.662 
-------------------------------------------------------------------------------
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:    0.0970
   chunk 32 optimal weight:   10.0000
   chunk 11 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 28 optimal weight:   10.0000
   chunk 59 optimal weight:    0.0050
   overall best weight:    0.8196

-------------------------------------------------------------------------------
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 = 0.3477 r_free = 0.3477 target = 0.055348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.041624 restraints weight = 34402.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.2992 rms_B_bonded: 4.44
r_work: 0.2860 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.1799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6675  Z= 0.095
  Angle     :  0.529   8.045   9084  Z= 0.267
  Chirality :  0.040   0.151   1017
  Planarity :  0.004   0.051   1131
  Dihedral  : 10.761  63.854   1033
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  7.53 %
    Favored  : 91.90 %
  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: -0.02 (0.32), residues: 780
  helix:  2.18 (0.36), residues: 244
  sheet: -0.62 (0.40), residues: 173
  loop : -1.25 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 732 
 HIS   0.002   0.001   HIS A 838 
 PHE   0.011   0.001   PHE A 211 
 TYR   0.007   0.001   TYR A 312 
 ARG   0.003   0.000   ARG A 562 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02856 (  245)
  hydrogen bonds       : angle       4.52707 (  708)
  covalent geometry    : bond        0.00219 ( 6675)
  covalent geometry    : angle       0.52900 ( 9084)

*********************** 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
  37 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9255 (t0) cc_final: 0.8865 (p0)
REVERT: A  848 ASP cc_start: 0.8942 (t0) cc_final: 0.8677 (t0)
  outliers start: 4
  outliers final: 2
  residues processed: 37
  average time/residue: 0.2562
  time to fit residues: 12.6169
Evaluate side-chains
  30 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 28
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  603 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 59 optimal weight:   20.0000
   chunk 60 optimal weight:    4.9990
   chunk 14 optimal weight:   10.0000
   chunk 79 optimal weight:   10.0000
   chunk 74 optimal weight:   10.0000
   chunk 4 optimal weight:    8.9990
   chunk 28 optimal weight:    3.9990
   chunk 32 optimal weight:    8.9990
   chunk 54 optimal weight:    7.9990
   chunk 22 optimal weight:    7.9990
   overall best weight:    6.1990

-------------------------------------------------------------------------------
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 = 0.3399 r_free = 0.3399 target = 0.053254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.039473 restraints weight = 35444.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 4.42
r_work: 0.2770 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.2587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.058   6675  Z= 0.294
  Angle     :  0.677   6.451   9084  Z= 0.346
  Chirality :  0.044   0.148   1017
  Planarity :  0.006   0.066   1131
  Dihedral  : 10.742  63.912   1029
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  9.26 %
    Favored  : 89.58 %
  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: -0.41 (0.31), residues: 780
  helix:  1.82 (0.35), residues: 240
  sheet: -0.94 (0.39), residues: 173
  loop : -1.36 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 732 
 HIS   0.007   0.001   HIS A 427 
 PHE   0.013   0.002   PHE A 874 
 TYR   0.012   0.002   TYR A 596 
 ARG   0.008   0.001   ARG A 789 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03711 (  245)
  hydrogen bonds       : angle       4.78077 (  708)
  covalent geometry    : bond        0.00662 ( 6675)
  covalent geometry    : angle       0.67749 ( 9084)

*********************** 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
  36 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 28
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9267 (t0) cc_final: 0.8936 (p0)
REVERT: A  630 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8700 (pp)
REVERT: A  848 ASP cc_start: 0.8920 (t0) cc_final: 0.8626 (t0)
  outliers start: 8
  outliers final: 3
  residues processed: 36
  average time/residue: 0.1954
  time to fit residues: 10.2136
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  : 0.800 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 14 optimal weight:    1.9990
   chunk 71 optimal weight:    9.9990
   chunk 73 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0970
   chunk 70 optimal weight:    7.9990
   chunk 13 optimal weight:    5.9990
   chunk 79 optimal weight:   10.0000
   overall best weight:    1.6186

-------------------------------------------------------------------------------
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 = 0.3436 r_free = 0.3436 target = 0.054307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.040648 restraints weight = 34938.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.2949 rms_B_bonded: 4.35
r_work: 0.2816 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6675  Z= 0.112
  Angle     :  0.540   6.450   9084  Z= 0.277
  Chirality :  0.041   0.148   1017
  Planarity :  0.004   0.046   1131
  Dihedral  : 10.487  63.867   1029
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 11.00 %
    Favored  : 88.42 %
  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: -0.18 (0.31), residues: 780
  helix:  2.11 (0.35), residues: 242
  sheet: -0.83 (0.39), residues: 173
  loop : -1.31 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 539 
 HIS   0.002   0.001   HIS A 881 
 PHE   0.010   0.001   PHE A 148 
 TYR   0.009   0.001   TYR A 893 
 ARG   0.004   0.000   ARG A 789 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02909 (  245)
  hydrogen bonds       : angle       4.44393 (  708)
  covalent geometry    : bond        0.00262 ( 6675)
  covalent geometry    : angle       0.53952 ( 9084)

*********************** 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
  33 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 29
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9268 (t0) cc_final: 0.8934 (p0)
REVERT: A  630 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8681 (pp)
REVERT: A  848 ASP cc_start: 0.8897 (t0) cc_final: 0.8638 (t0)
  outliers start: 4
  outliers final: 2
  residues processed: 33
  average time/residue: 0.2414
  time to fit residues: 11.3326
Evaluate side-chains
  32 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 29
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 73 optimal weight:    6.9990
   chunk 52 optimal weight:    9.9990
   chunk 65 optimal weight:    9.9990
   chunk 28 optimal weight:    8.9990
   chunk 10 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 54 optimal weight:   20.0000
   chunk 3 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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 = 0.053744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.040121 restraints weight = 34785.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.2933 rms_B_bonded: 4.35
r_work: 0.2801 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
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      :  0.004   0.040   6675  Z= 0.166
  Angle     :  0.560   7.229   9084  Z= 0.285
  Chirality :  0.041   0.149   1017
  Planarity :  0.005   0.045   1131
  Dihedral  : 10.424  63.912   1029
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 11.58 %
    Favored  : 87.41 %
  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: -0.16 (0.31), residues: 780
  helix:  2.13 (0.35), residues: 242
  sheet: -0.71 (0.40), residues: 163
  loop : -1.36 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 732 
 HIS   0.002   0.001   HIS A 894 
 PHE   0.008   0.001   PHE A 148 
 TYR   0.010   0.001   TYR A 596 
 ARG   0.004   0.000   ARG A 789 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03044 (  245)
  hydrogen bonds       : angle       4.40441 (  708)
  covalent geometry    : bond        0.00382 ( 6675)
  covalent geometry    : angle       0.56040 ( 9084)

*********************** 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: 7
    poor density    : 30
  time to evaluate  : 0.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9272 (t0) cc_final: 0.8953 (p0)
REVERT: A  630 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8637 (pp)
REVERT: A  848 ASP cc_start: 0.8903 (t0) cc_final: 0.8646 (t0)
  outliers start: 7
  outliers final: 4
  residues processed: 37
  average time/residue: 0.2120
  time to fit residues: 11.2605
Evaluate side-chains
  35 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 30
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  552 VAL
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 27 optimal weight:    8.9990
   chunk 77 optimal weight:    8.9990
   chunk 15 optimal weight:    8.9990
   chunk 1 optimal weight:    6.9990
   chunk 9 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 72 optimal weight:    7.9990
   chunk 55 optimal weight:    5.9990
   chunk 79 optimal weight:   10.0000
   chunk 51 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   overall best weight:    4.9988

-------------------------------------------------------------------------------
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 = 0.3398 r_free = 0.3398 target = 0.053278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.039812 restraints weight = 35112.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.2910 rms_B_bonded: 4.37
r_work: 0.2778 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8640
moved from start:          0.2890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   6675  Z= 0.236
  Angle     :  0.610   7.043   9084  Z= 0.311
  Chirality :  0.042   0.145   1017
  Planarity :  0.005   0.044   1131
  Dihedral  : 10.567  64.002   1029
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 12.16 %
    Favored  : 86.98 %
  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: -0.34 (0.31), residues: 780
  helix:  1.95 (0.34), residues: 242
  sheet: -0.71 (0.40), residues: 166
  loop : -1.50 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 732 
 HIS   0.003   0.001   HIS A 250 
 PHE   0.009   0.002   PHE A 874 
 TYR   0.011   0.001   TYR A 596 
 ARG   0.006   0.001   ARG A 789 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03345 (  245)
  hydrogen bonds       : angle       4.53896 (  708)
  covalent geometry    : bond        0.00533 ( 6675)
  covalent geometry    : angle       0.61034 ( 9084)

*********************** 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
  35 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 29
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9263 (t0) cc_final: 0.8964 (p0)
REVERT: A  630 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8671 (pp)
REVERT: A  848 ASP cc_start: 0.8925 (t0) cc_final: 0.8657 (t0)
  outliers start: 6
  outliers final: 3
  residues processed: 34
  average time/residue: 0.2165
  time to fit residues: 10.4149
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  : 0.783 
-------------------------------------------------------------------------------
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  823 ASN
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:    6.9990
   chunk 42 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 56 optimal weight:    1.9990
   chunk 38 optimal weight:    6.9990
   chunk 54 optimal weight:    0.0870
   chunk 17 optimal weight:    7.9990
   chunk 21 optimal weight:    9.9990
   chunk 53 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   overall best weight:    3.2166

-------------------------------------------------------------------------------
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 = 0.3410 r_free = 0.3410 target = 0.053624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.040250 restraints weight = 35127.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.2931 rms_B_bonded: 4.34
r_work: 0.2798 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8628
moved from start:          0.2901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6675  Z= 0.163
  Angle     :  0.564   8.781   9084  Z= 0.286
  Chirality :  0.041   0.204   1017
  Planarity :  0.004   0.044   1131
  Dihedral  : 10.448  63.943   1029
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 13.02 %
    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: -0.20 (0.31), residues: 780
  helix:  2.07 (0.34), residues: 242
  sheet: -0.67 (0.40), residues: 170
  loop : -1.41 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 732 
 HIS   0.002   0.001   HIS A 894 
 PHE   0.009   0.001   PHE A 148 
 TYR   0.010   0.001   TYR A 596 
 ARG   0.004   0.000   ARG A 789 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03037 (  245)
  hydrogen bonds       : angle       4.40184 (  708)
  covalent geometry    : bond        0.00376 ( 6675)
  covalent geometry    : angle       0.56364 ( 9084)

*********************** 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
  32 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 28
  time to evaluate  : 0.669 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9253 (t0) cc_final: 0.8947 (p0)
REVERT: A  630 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8681 (pp)
  outliers start: 4
  outliers final: 3
  residues processed: 32
  average time/residue: 0.2256
  time to fit residues: 10.1601
Evaluate side-chains
  33 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 29
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  552 VAL
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 24 optimal weight:   20.0000
   chunk 44 optimal weight:    5.9990
   chunk 72 optimal weight:    7.9990
   chunk 45 optimal weight:   10.0000
   chunk 31 optimal weight:    9.9990
   chunk 12 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 13 optimal weight:    0.8980
   chunk 66 optimal weight:    6.9990
   overall best weight:    2.7788

-------------------------------------------------------------------------------
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 = 0.3416 r_free = 0.3416 target = 0.053733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.040365 restraints weight = 35095.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 4.35
r_work: 0.2805 rms_B_bonded: 4.89 restraints_weight: 0.5000
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.2944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6675  Z= 0.149
  Angle     :  0.554   7.929   9084  Z= 0.280
  Chirality :  0.041   0.190   1017
  Planarity :  0.004   0.043   1131
  Dihedral  : 10.378  63.931   1029
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 13.17 %
    Favored  : 86.25 %
  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: -0.12 (0.31), residues: 780
  helix:  2.18 (0.35), residues: 241
  sheet: -0.61 (0.40), residues: 170
  loop : -1.39 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 732 
 HIS   0.002   0.001   HIS A 894 
 PHE   0.009   0.001   PHE A 255 
 TYR   0.010   0.001   TYR A 596 
 ARG   0.003   0.000   ARG A 789 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02921 (  245)
  hydrogen bonds       : angle       4.32741 (  708)
  covalent geometry    : bond        0.00344 ( 6675)
  covalent geometry    : angle       0.55403 ( 9084)

*********************** 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
  32 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 28
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9259 (t0) cc_final: 0.8948 (p0)
REVERT: A  630 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8633 (pp)
  outliers start: 4
  outliers final: 3
  residues processed: 32
  average time/residue: 0.2229
  time to fit residues: 10.0256
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  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  552 VAL
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:    5.9990
   chunk 27 optimal weight:    0.3980
   chunk 34 optimal weight:    5.9990
   chunk 59 optimal weight:   20.0000
   chunk 76 optimal weight:    6.9990
   chunk 40 optimal weight:    8.9990
   chunk 55 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    2.6788

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

Flipped N/Q/H residues before XYZ refinement:
** A 749 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 = 0.3418 r_free = 0.3418 target = 0.053837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.040362 restraints weight = 35423.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.2941 rms_B_bonded: 4.40
r_work: 0.2807 rms_B_bonded: 4.89 restraints_weight: 0.5000
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.2986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6675  Z= 0.145
  Angle     :  0.550   7.470   9084  Z= 0.278
  Chirality :  0.041   0.181   1017
  Planarity :  0.004   0.043   1131
  Dihedral  : 10.343  63.928   1029
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 13.02 %
    Favored  : 86.25 %
  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: -0.08 (0.31), residues: 780
  helix:  2.22 (0.35), residues: 241
  sheet: -0.63 (0.39), residues: 175
  loop : -1.35 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 732 
 HIS   0.002   0.001   HIS A 894 
 PHE   0.008   0.001   PHE A 255 
 TYR   0.011   0.001   TYR A 596 
 ARG   0.003   0.000   ARG A 789 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02875 (  245)
  hydrogen bonds       : angle       4.29763 (  708)
  covalent geometry    : bond        0.00337 ( 6675)
  covalent geometry    : angle       0.55036 ( 9084)

********************** 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: 5
    poor density    : 31
  time to evaluate  : 0.708 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9277 (t0) cc_final: 0.8972 (p0)
REVERT: A  630 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8567 (pp)
  outliers start: 5
  outliers final: 4
  residues processed: 36
  average time/residue: 0.2154
  time to fit residues: 11.3834
Evaluate side-chains
  36 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  552 VAL
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  945 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 75 optimal weight:    2.9990
   chunk 49 optimal weight:    8.9990
   chunk 17 optimal weight:    4.9990
   chunk 58 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0770
   chunk 8 optimal weight:    5.9990
   chunk 38 optimal weight:    8.9990
   chunk 77 optimal weight:    0.9990
   overall best weight:    1.4146

-------------------------------------------------------------------------------
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 = 0.3439 r_free = 0.3439 target = 0.054362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.040965 restraints weight = 35541.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 4.42
r_work: 0.2831 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.2976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6675  Z= 0.104
  Angle     :  0.526   8.202   9084  Z= 0.264
  Chirality :  0.040   0.171   1017
  Planarity :  0.004   0.042   1131
  Dihedral  : 10.278  63.890   1029
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 13.17 %
    Favored  : 86.25 %
  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:  0.05 (0.31), residues: 780
  helix:  2.35 (0.35), residues: 241
  sheet: -0.56 (0.40), residues: 167
  loop : -1.28 (0.32), residues: 372

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 211 
 TYR   0.009   0.001   TYR A 312 
 ARG   0.002   0.000   ARG A 789 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02606 (  245)
  hydrogen bonds       : angle       4.16067 (  708)
  covalent geometry    : bond        0.00246 ( 6675)
  covalent geometry    : angle       0.52569 ( 9084)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3517.98 seconds
wall clock time: 61 minutes 14.75 seconds (3674.75 seconds total)