Starting phenix.real_space_refine
on Tue Feb  3 20:18:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sva_25446/02_2026/7sva_25446.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sva_25446/02_2026/7sva_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_2026/7sva_25446.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sva_25446/02_2026/7sva_25446.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sva_25446/02_2026/7sva_25446.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sva_25446/02_2026/7sva_25446.cif"
  }
  resolution = 3.26
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: 1.60, per 1000 atoms: 0.25
  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: 0.66
  Conformation dependent library (CDL) restraints added in 247.2 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: 0.72
  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: 1.18

  Time building geometry restraints manager: 0.86 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:             3.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     8.280
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.500
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.006   0.000   ARG A 300 
 TYR   0.007   0.001   TYR A 312 
 PHE   0.011   0.001   PHE A 802 
 TRP   0.077   0.003   TRP A 732 
 HIS   0.001   0.000   HIS A 427 

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

*********************** 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  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 57
  average time/residue: 0.1532
  time to fit residues: 10.4546
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  : 0.199 
-------------------------------------------------------------------------------
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 49 optimal weight:    7.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    6.9990
   chunk 74 optimal weight:    9.9990
   overall best weight:    3.3988

-------------------------------------------------------------------------------
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 453 GLN
A 489 ASN
A 677 ASN
A 715 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.054360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.040576 restraints weight = 34704.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.2948 rms_B_bonded: 4.39
r_work: 0.2816 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6675  Z= 0.182
  Angle     :  0.621  10.803   9084  Z= 0.313
  Chirality :  0.043   0.162   1017
  Planarity :  0.005   0.059   1131
  Dihedral  : 11.038  64.492   1033
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  6.80 %
    Favored  : 92.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.32), residues: 780
  helix:  1.99 (0.36), residues: 242
  sheet: -0.86 (0.40), residues: 172
  loop : -1.30 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 474 
 TYR   0.012   0.001   TYR A 596 
 PHE   0.013   0.001   PHE A 874 
 TRP   0.027   0.002   TRP A 732 
 HIS   0.004   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 6675)
  covalent geometry    : angle       0.62073 ( 9084)
  hydrogen bonds       : bond        0.03508 (  245)
  hydrogen bonds       : angle       4.93495 (  708)

*********************** 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
  34 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 32
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9285 (t0) cc_final: 0.8925 (p0)
REVERT: A  848 ASP cc_start: 0.8883 (t0) cc_final: 0.8593 (t0)
  outliers start: 2
  outliers final: 2
  residues processed: 34
  average time/residue: 0.1254
  time to fit residues: 5.3756
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  : 0.160 
-------------------------------------------------------------------------------
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 41 optimal weight:    9.9990
   chunk 35 optimal weight:    8.9990
   chunk 29 optimal weight:    9.9990
   chunk 76 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 11 optimal weight:    8.9990
   chunk 74 optimal weight:    7.9990
   chunk 23 optimal weight:    6.9990
   chunk 13 optimal weight:    7.9990
   chunk 58 optimal weight:    9.9990
   overall best weight:    4.7990

-------------------------------------------------------------------------------
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 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 = 0.3409 r_free = 0.3409 target = 0.053511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.039799 restraints weight = 34711.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.2917 rms_B_bonded: 4.34
r_work: 0.2784 rms_B_bonded: 4.90 restraints_weight: 0.5000
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8641
moved from start:          0.2431

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= 0.234
  Angle     :  0.628   7.368   9084  Z= 0.321
  Chirality :  0.043   0.150   1017
  Planarity :  0.005   0.052   1131
  Dihedral  : 11.011  64.035   1033
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  8.68 %
    Favored  : 90.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.31), residues: 780
  helix:  1.98 (0.35), residues: 240
  sheet: -0.99 (0.39), residues: 173
  loop : -1.39 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 789 
 TYR   0.012   0.002   TYR A 596 
 PHE   0.013   0.002   PHE A 874 
 TRP   0.018   0.002   TRP A 732 
 HIS   0.005   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 ( 6675)
  covalent geometry    : angle       0.62815 ( 9084)
  hydrogen bonds       : bond        0.03621 (  245)
  hydrogen bonds       : angle       4.79133 (  708)

*********************** 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: 5
    poor density    : 31
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9286 (t0) cc_final: 0.8925 (p0)
REVERT: A  630 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8704 (pp)
REVERT: A  848 ASP cc_start: 0.8900 (t0) cc_final: 0.8623 (t0)
  outliers start: 5
  outliers final: 4
  residues processed: 36
  average time/residue: 0.0708
  time to fit residues: 3.4506
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  : 0.225 
-------------------------------------------------------------------------------
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  630 LEU
Chi-restraints excluded: chain A residue  717 GLU
Chi-restraints excluded: chain A residue  719 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 42 optimal weight:    8.9990
   chunk 11 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 40 optimal weight:   10.0000
   chunk 17 optimal weight:    7.9990
   chunk 79 optimal weight:   10.0000
   chunk 55 optimal weight:   10.0000
   overall best weight:    4.1990

-------------------------------------------------------------------------------
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 = 0.3406 r_free = 0.3406 target = 0.053476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.039821 restraints weight = 35099.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.2915 rms_B_bonded: 4.33
r_work: 0.2784 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          0.2636

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= 0.205
  Angle     :  0.585   6.639   9084  Z= 0.299
  Chirality :  0.042   0.150   1017
  Planarity :  0.005   0.048   1131
  Dihedral  : 10.951  63.959   1033
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 10.56 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.31), residues: 780
  helix:  1.92 (0.34), residues: 242
  sheet: -0.95 (0.40), residues: 168
  loop : -1.43 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 789 
 TYR   0.010   0.001   TYR A 596 
 PHE   0.011   0.001   PHE A 148 
 TRP   0.009   0.001   TRP A 732 
 HIS   0.003   0.001   HIS A 894 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 6675)
  covalent geometry    : angle       0.58527 ( 9084)
  hydrogen bonds       : bond        0.03319 (  245)
  hydrogen bonds       : angle       4.66044 (  708)

*********************** 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
  39 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 28
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9263 (t0) cc_final: 0.8922 (p0)
REVERT: A  630 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8667 (pp)
REVERT: A  848 ASP cc_start: 0.8915 (t0) cc_final: 0.8639 (t0)
  outliers start: 11
  outliers final: 6
  residues processed: 38
  average time/residue: 0.0654
  time to fit residues: 3.6759
Evaluate side-chains
  36 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 29
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
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  717 GLU
Chi-restraints excluded: chain A residue  719 SER
Chi-restraints excluded: chain A residue  823 ASN
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 30 optimal weight:    8.9990
   chunk 43 optimal weight:    0.9990
   chunk 35 optimal weight:    8.9990
   chunk 67 optimal weight:    6.9990
   chunk 3 optimal weight:    9.9990
   chunk 17 optimal weight:    5.9990
   chunk 2 optimal weight:    0.7980
   chunk 23 optimal weight:    7.9990
   chunk 9 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   overall best weight:    3.3588

-------------------------------------------------------------------------------
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 = 0.3410 r_free = 0.3410 target = 0.053597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.040018 restraints weight = 35872.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.2922 rms_B_bonded: 4.39
r_work: 0.2790 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.2734

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= 0.173
  Angle     :  0.566   6.484   9084  Z= 0.291
  Chirality :  0.041   0.148   1017
  Planarity :  0.005   0.046   1131
  Dihedral  : 10.836  63.912   1033
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 12.01 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.31), residues: 780
  helix:  2.02 (0.34), residues: 242
  sheet: -0.99 (0.40), residues: 168
  loop : -1.39 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 789 
 TYR   0.012   0.001   TYR A 893 
 PHE   0.009   0.001   PHE A 148 
 TRP   0.007   0.001   TRP A 539 
 HIS   0.002   0.001   HIS A 838 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 6675)
  covalent geometry    : angle       0.56613 ( 9084)
  hydrogen bonds       : bond        0.03168 (  245)
  hydrogen bonds       : angle       4.54445 (  708)

*********************** 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
  40 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9291 (t0) cc_final: 0.8942 (p0)
REVERT: A  630 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8666 (pp)
REVERT: A  848 ASP cc_start: 0.8914 (t0) cc_final: 0.8647 (t0)
  outliers start: 9
  outliers final: 6
  residues processed: 40
  average time/residue: 0.0792
  time to fit residues: 4.3306
Evaluate side-chains
  36 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 29
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
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  717 GLU
Chi-restraints excluded: chain A residue  719 SER
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 50 optimal weight:    4.9990
   chunk 79 optimal weight:   10.0000
   chunk 5 optimal weight:   20.0000
   chunk 45 optimal weight:    6.9990
   chunk 22 optimal weight:    6.9990
   chunk 39 optimal weight:    0.7980
   chunk 54 optimal weight:    6.9990
   chunk 63 optimal weight:    7.9990
   chunk 20 optimal weight:   10.0000
   chunk 36 optimal weight:    0.1980
   chunk 70 optimal weight:    6.9990
   overall best weight:    3.9986

-------------------------------------------------------------------------------
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 = 0.3404 r_free = 0.3404 target = 0.053475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.039906 restraints weight = 35801.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.2919 rms_B_bonded: 4.42
r_work: 0.2787 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.2872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6675  Z= 0.196
  Angle     :  0.579   6.472   9084  Z= 0.297
  Chirality :  0.042   0.149   1017
  Planarity :  0.005   0.045   1131
  Dihedral  : 10.850  63.939   1033
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 13.02 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.31), residues: 780
  helix:  1.98 (0.34), residues: 242
  sheet: -0.78 (0.40), residues: 166
  loop : -1.48 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 789 
 TYR   0.011   0.001   TYR A 596 
 PHE   0.009   0.001   PHE A 148 
 TRP   0.007   0.001   TRP A 732 
 HIS   0.003   0.001   HIS A 894 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 6675)
  covalent geometry    : angle       0.57925 ( 9084)
  hydrogen bonds       : bond        0.03224 (  245)
  hydrogen bonds       : angle       4.53934 (  708)

*********************** 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
  38 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 29
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9286 (t0) cc_final: 0.8963 (p0)
REVERT: A  254 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8182 (mt-10)
REVERT: A  630 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8675 (pp)
  outliers start: 9
  outliers final: 6
  residues processed: 38
  average time/residue: 0.0838
  time to fit residues: 4.4026
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  : 0.189 
-------------------------------------------------------------------------------
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  717 GLU
Chi-restraints excluded: chain A residue  719 SER
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 30 optimal weight:    8.9990
   chunk 70 optimal weight:   10.0000
   chunk 25 optimal weight:    8.9990
   chunk 66 optimal weight:    3.9990
   chunk 78 optimal weight:   10.0000
   chunk 7 optimal weight:    7.9990
   chunk 0 optimal weight:    7.9990
   chunk 76 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   overall best weight:    3.3386

-------------------------------------------------------------------------------
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 = 0.3409 r_free = 0.3409 target = 0.053643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.040117 restraints weight = 35295.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.2926 rms_B_bonded: 4.36
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:          0.2930

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= 0.171
  Angle     :  0.565   6.407   9084  Z= 0.289
  Chirality :  0.042   0.189   1017
  Planarity :  0.005   0.044   1131
  Dihedral  : 10.791  63.921   1033
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 13.60 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.31), residues: 780
  helix:  2.03 (0.34), residues: 241
  sheet: -0.77 (0.40), residues: 171
  loop : -1.40 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 789 
 TYR   0.012   0.001   TYR A 596 
 PHE   0.009   0.001   PHE A 148 
 TRP   0.006   0.001   TRP A 732 
 HIS   0.003   0.001   HIS A 838 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 6675)
  covalent geometry    : angle       0.56493 ( 9084)
  hydrogen bonds       : bond        0.03151 (  245)
  hydrogen bonds       : angle       4.49160 (  708)

*********************** 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
  41 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 30
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9274 (t0) cc_final: 0.8962 (p0)
REVERT: A  259 LYS cc_start: 0.8611 (mtmm) cc_final: 0.8355 (pttp)
REVERT: A  630 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8676 (pp)
REVERT: A  848 ASP cc_start: 0.8918 (t0) cc_final: 0.8638 (t0)
  outliers start: 11
  outliers final: 7
  residues processed: 40
  average time/residue: 0.0835
  time to fit residues: 4.6030
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  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 VAL
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  719 SER
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 54 optimal weight:    8.9990
   chunk 34 optimal weight:    8.9990
   chunk 17 optimal weight:    6.9990
   chunk 78 optimal weight:    0.0020
   chunk 28 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   chunk 4 optimal weight:   10.0000
   overall best weight:    1.7594

-------------------------------------------------------------------------------
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**
A 838 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.054188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.040606 restraints weight = 35416.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.2954 rms_B_bonded: 4.42
r_work: 0.2824 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.2932

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= 0.115
  Angle     :  0.533   7.473   9084  Z= 0.269
  Chirality :  0.041   0.171   1017
  Planarity :  0.004   0.043   1131
  Dihedral  : 10.396  63.887   1030
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 14.76 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.11 (0.31), residues: 780
  helix:  2.19 (0.35), residues: 241
  sheet: -0.70 (0.39), residues: 175
  loop : -1.33 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 382 
 TYR   0.010   0.001   TYR A 893 
 PHE   0.009   0.001   PHE A 211 
 TRP   0.006   0.001   TRP A 897 
 HIS   0.003   0.001   HIS A 838 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 6675)
  covalent geometry    : angle       0.53273 ( 9084)
  hydrogen bonds       : bond        0.02747 (  245)
  hydrogen bonds       : angle       4.30200 (  708)

*********************** 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
  40 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9301 (t0) cc_final: 0.8958 (p0)
REVERT: A  259 LYS cc_start: 0.8615 (mtmm) cc_final: 0.8398 (pttp)
REVERT: A  848 ASP cc_start: 0.8859 (t0) cc_final: 0.8611 (t0)
  outliers start: 5
  outliers final: 3
  residues processed: 40
  average time/residue: 0.0850
  time to fit residues: 4.5078
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  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  678 VAL
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 69 optimal weight:    1.9990
   chunk 7 optimal weight:    9.9990
   chunk 34 optimal weight:    3.9990
   chunk 18 optimal weight:    9.9990
   chunk 33 optimal weight:    6.9990
   chunk 40 optimal weight:   10.0000
   chunk 36 optimal weight:    9.9990
   chunk 44 optimal weight:    6.9990
   chunk 60 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   overall best weight:    2.3588

-------------------------------------------------------------------------------
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 = 0.3424 r_free = 0.3424 target = 0.054025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.040627 restraints weight = 35618.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.2950 rms_B_bonded: 4.35
r_work: 0.2819 rms_B_bonded: 4.86 restraints_weight: 0.5000
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.2987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6675  Z= 0.134
  Angle     :  0.546   6.896   9084  Z= 0.278
  Chirality :  0.041   0.172   1017
  Planarity :  0.004   0.042   1131
  Dihedral  : 10.347  63.921   1029
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 15.48 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.31), residues: 780
  helix:  2.24 (0.35), residues: 241
  sheet: -0.68 (0.39), residues: 176
  loop : -1.30 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 789 
 TYR   0.011   0.001   TYR A 596 
 PHE   0.008   0.001   PHE A 148 
 TRP   0.006   0.001   TRP A 539 
 HIS   0.002   0.001   HIS A 838 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6675)
  covalent geometry    : angle       0.54618 ( 9084)
  hydrogen bonds       : bond        0.02813 (  245)
  hydrogen bonds       : angle       4.29495 (  708)

*********************** 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: 5
    poor density    : 33
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9286 (t0) cc_final: 0.8958 (p0)
REVERT: A  259 LYS cc_start: 0.8668 (mtmm) cc_final: 0.8438 (pttp)
REVERT: A  630 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8545 (pp)
REVERT: A  848 ASP cc_start: 0.8866 (t0) cc_final: 0.8610 (t0)
  outliers start: 5
  outliers final: 4
  residues processed: 38
  average time/residue: 0.0762
  time to fit residues: 3.9664
Evaluate side-chains
  37 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  318 THR
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 6 optimal weight:    7.9990
   chunk 56 optimal weight:    9.9990
   chunk 4 optimal weight:    9.9990
   chunk 76 optimal weight:    6.9990
   chunk 28 optimal weight:    8.9990
   chunk 8 optimal weight:    5.9990
   chunk 35 optimal weight:    9.9990
   chunk 73 optimal weight:    2.9990
   chunk 75 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 79 optimal weight:    9.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 677 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.053094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.039697 restraints weight = 35564.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.2899 rms_B_bonded: 4.33
r_work: 0.2768 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8645
moved from start:          0.3164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   6675  Z= 0.253
  Angle     :  0.656   9.539   9084  Z= 0.332
  Chirality :  0.043   0.160   1017
  Planarity :  0.005   0.069   1131
  Dihedral  : 10.550  63.980   1029
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 15.20 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.31), residues: 780
  helix:  1.93 (0.34), residues: 241
  sheet: -0.68 (0.40), residues: 166
  loop : -1.45 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 562 
 TYR   0.017   0.002   TYR A 596 
 PHE   0.009   0.002   PHE A 779 
 TRP   0.010   0.002   TRP A 732 
 HIS   0.003   0.001   HIS A 894 

Details of bonding type rmsd
  covalent geometry    : bond        0.00572 ( 6675)
  covalent geometry    : angle       0.65550 ( 9084)
  hydrogen bonds       : bond        0.03423 (  245)
  hydrogen bonds       : angle       4.55031 (  708)

********************** 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
  37 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 29
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.9264 (t0) cc_final: 0.8968 (p0)
REVERT: A  254 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8379 (mm-30)
REVERT: A  630 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8636 (pp)
  outliers start: 8
  outliers final: 6
  residues processed: 36
  average time/residue: 0.0767
  time to fit residues: 3.7227
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  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  318 THR
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  945 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 6 optimal weight:   30.0000
   chunk 29 optimal weight:    7.9990
   chunk 3 optimal weight:    9.9990
   chunk 49 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 23 optimal weight:    6.9990
   chunk 64 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    2.5786

-------------------------------------------------------------------------------
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 = 0.3410 r_free = 0.3410 target = 0.053717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.040383 restraints weight = 35142.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 4.30
r_work: 0.2807 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.3111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6675  Z= 0.147
  Angle     :  0.590   7.957   9084  Z= 0.301
  Chirality :  0.042   0.171   1017
  Planarity :  0.005   0.062   1131
  Dihedral  : 10.445  63.912   1029
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 15.34 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.31), residues: 780
  helix:  2.09 (0.35), residues: 240
  sheet: -0.64 (0.40), residues: 170
  loop : -1.40 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 246 
 TYR   0.012   0.001   TYR A 596 
 PHE   0.008   0.001   PHE A 148 
 TRP   0.011   0.001   TRP A 732 
 HIS   0.003   0.001   HIS A 838 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 6675)
  covalent geometry    : angle       0.58994 ( 9084)
  hydrogen bonds       : bond        0.03001 (  245)
  hydrogen bonds       : angle       4.40981 (  708)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1505.08 seconds
wall clock time: 26 minutes 29.94 seconds (1589.94 seconds total)