Starting phenix.real_space_refine
on Tue Jul 29 02:49:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8clk_16715/07_2025/8clk_16715.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8clk_16715/07_2025/8clk_16715.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8clk_16715/07_2025/8clk_16715.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8clk_16715/07_2025/8clk_16715.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8clk_16715/07_2025/8clk_16715.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8clk_16715/07_2025/8clk_16715.cif"
  }
  resolution = 3.5
  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=   0.005 sd=   0.082
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      72      5.16       5
     C    6885      2.51       5
     N    1856      2.21       5
     O    1986      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10799
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4899
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 611, 4899
          Classifications: {'peptide': 611}
          Link IDs: {'PTRANS': 31, 'TRANS': 579}
          Chain breaks: 3
    Chain: "D"
      Number of atoms: 3667
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 457, 3667
          Classifications: {'peptide': 457}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 444}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 1421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 1421
          Classifications: {'peptide': 174}
          Link IDs: {'PTRANS': 14, 'TRANS': 159}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 812
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 1, 'TRANS': 100}
          Chain breaks: 2
  Time building chain proxies: 6.48, per 1000 atoms: 0.60
  Number of scatterers: 10799
  At special positions: 0
  Unit cell: (105.216, 114.258, 155.358, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      72     16.00
     O    1986      8.00
     N    1856      7.00
     C    6885      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: 2.53
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2558

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 8 sheets defined
      54.7% alpha, 10.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1266 through 1284
    Processing helix  chain 'A' and resid 1294 through 1305
    Processing helix  chain 'A' and resid 1306 through 1311
    Processing helix  chain 'A' and resid 1312 through 1323
      removed outlier: 4.208A  pdb=" N   ARG A1321 " --> pdb=" O   GLY A1317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1326 through 1342
    Processing helix  chain 'A' and resid 1343 through 1346
      removed outlier: 3.738A  pdb=" N   LEU A1346 " --> pdb=" O   ASP A1343 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1343 through 1346'
    Processing helix  chain 'A' and resid 1347 through 1352
    Processing helix  chain 'A' and resid 1359 through 1378
      removed outlier: 3.794A  pdb=" N   GLU A1376 " --> pdb=" O   GLU A1372 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LYS A1377 " --> pdb=" O   LYS A1373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1392 through 1399
    Processing helix  chain 'A' and resid 1420 through 1438
      removed outlier: 5.072A  pdb=" N   ASN A1431 " --> pdb=" O   LEU A1427 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   GLN A1434 " --> pdb=" O   GLN A1430 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ALA A1438 " --> pdb=" O   GLN A1434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1440 through 1447
    Processing helix  chain 'A' and resid 1448 through 1457
      removed outlier: 3.653A  pdb=" N   LEU A1455 " --> pdb=" O   GLN A1451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1460 through 1474
    Processing helix  chain 'A' and resid 1504 through 1512
      removed outlier: 3.527A  pdb=" N   PHE A1511 " --> pdb=" O   TYR A1507 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1518 through 1531
    Processing helix  chain 'A' and resid 1546 through 1548
      No H-bonds generated for 'chain 'A' and resid 1546 through 1548'
    Processing helix  chain 'A' and resid 1565 through 1578
      removed outlier: 3.979A  pdb=" N   VAL A1571 " --> pdb=" O   ASN A1567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1694 through 1698
      removed outlier: 3.706A  pdb=" N   LEU A1698 " --> pdb=" O   LEU A1695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1701 through 1705
    Processing helix  chain 'A' and resid 1706 through 1710
    Processing helix  chain 'A' and resid 1714 through 1718
      removed outlier: 4.175A  pdb=" N   ASN A1718 " --> pdb=" O   PRO A1715 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1721 through 1732
      removed outlier: 4.124A  pdb=" N   PHE A1725 " --> pdb=" O   SER A1721 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1735 through 1752
      removed outlier: 3.865A  pdb=" N   ALA A1748 " --> pdb=" O   GLU A1744 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ILE A1749 " --> pdb=" O   ILE A1745 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   THR A1752 " --> pdb=" O   ALA A1748 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1759 through 1766
    Processing helix  chain 'A' and resid 1767 through 1770
    Processing helix  chain 'A' and resid 1779 through 1790
    Processing helix  chain 'A' and resid 1807 through 1811
      removed outlier: 5.643A  pdb=" N   TRP A1810 " --> pdb=" O   GLY A1807 " (cutoff:3.500A)
      Proline residue:  A1811  - end of helix
      No H-bonds generated for 'chain 'A' and resid 1807 through 1811'
    Processing helix  chain 'A' and resid 1996 through 1999
    Processing helix  chain 'A' and resid 2000 through 2013
    Processing helix  chain 'A' and resid 2017 through 2025
      removed outlier: 3.947A  pdb=" N   ARG A2023 " --> pdb=" O   SER A2019 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   TYR A2025 " --> pdb=" O   LEU A2021 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2030 through 2044
      removed outlier: 3.652A  pdb=" N   VAL A2034 " --> pdb=" O   GLN A2030 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LEU A2035 " --> pdb=" O   PRO A2031 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2088 through 2095
    Processing helix  chain 'A' and resid 2102 through 2108
      removed outlier: 4.236A  pdb=" N   LYS A2105 " --> pdb=" O   ASN A2102 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   TRP A2106 " --> pdb=" O   TRP A2103 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   HIS A2108 " --> pdb=" O   LYS A2105 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 420 through 433
    Processing helix  chain 'D' and resid 439 through 448
    Processing helix  chain 'D' and resid 457 through 469
    Processing helix  chain 'D' and resid 471 through 486
    Processing helix  chain 'D' and resid 489 through 504
      removed outlier: 3.523A  pdb=" N   SER D 497 " --> pdb=" O   ARG D 493 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 521 through 547
      removed outlier: 6.596A  pdb=" N   ASN D 527 " --> pdb=" O   ALA D 523 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ALA D 528 " --> pdb=" O   GLN D 524 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLN D 530 " --> pdb=" O   ALA D 526 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   GLN D 531 " --> pdb=" O   ASN D 527 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 548 through 569
      removed outlier: 6.335A  pdb=" N   VAL D 566 " --> pdb=" O   MET D 562 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ALA D 567 " --> pdb=" O   LEU D 563 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 579 through 582
    Processing helix  chain 'D' and resid 604 through 606
      No H-bonds generated for 'chain 'D' and resid 604 through 606'
    Processing helix  chain 'D' and resid 607 through 620
      removed outlier: 3.657A  pdb=" N   VAL D 619 " --> pdb=" O   VAL D 615 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 621 through 639
    Processing helix  chain 'D' and resid 641 through 655
    Processing helix  chain 'D' and resid 655 through 660
    Processing helix  chain 'D' and resid 661 through 679
    Processing helix  chain 'D' and resid 681 through 696
      removed outlier: 3.564A  pdb=" N   ASN D 687 " --> pdb=" O   ARG D 683 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   TYR D 688 " --> pdb=" O   LYS D 684 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   ILE D 691 " --> pdb=" O   ASN D 687 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 699 through 713
      removed outlier: 3.563A  pdb=" N   TRP D 703 " --> pdb=" O   LYS D 699 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   ILE D 705 " --> pdb=" O   GLN D 701 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   GLN D 708 " --> pdb=" O   ASN D 704 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 717 through 729
      removed outlier: 3.568A  pdb=" N   PHE D 721 " --> pdb=" O   ARG D 717 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 732 through 746
      removed outlier: 3.580A  pdb=" N   GLY D 740 " --> pdb=" O   CYS D 736 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 748 through 763
      removed outlier: 4.099A  pdb=" N   GLY D 754 " --> pdb=" O   LYS D 750 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   GLN D 755 " --> pdb=" O   HIS D 751 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   THR D 762 " --> pdb=" O   GLN D 758 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 766 through 783
      removed outlier: 3.844A  pdb=" N   ILE D 778 " --> pdb=" O   GLY D 774 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   GLN D 783 " --> pdb=" O   HIS D 779 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 788 through 808
      removed outlier: 3.593A  pdb=" N   LEU D 792 " --> pdb=" O   ARG D 788 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   PHE D 799 " --> pdb=" O   GLN D 795 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 810 through 824
      removed outlier: 3.739A  pdb=" N   LEU D 824 " --> pdb=" O   GLY D 820 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 826 through 840
      removed outlier: 4.958A  pdb=" N   HIS D 832 " --> pdb=" O   HIS D 828 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 849 through 854
    Processing helix  chain 'D' and resid 855 through 870
    Processing helix  chain 'D' and resid 872 through 884
    Processing helix  chain 'E' and resid 35 through 43
      Proline residue:  E  41  - end of helix
    Processing helix  chain 'E' and resid 44 through 54
    Processing helix  chain 'F' and resid 34 through 39
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1400 through 1405
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 1400 through 1405
    current: chain 'E' and resid 74 through 95
      removed outlier: 7.305A  pdb=" N   CYS E  75 " --> pdb=" O   GLN E 124 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   GLN E 124 " --> pdb=" O   CYS E  75 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   SER E 118 " --> pdb=" O   THR E  81 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   SER E  83 " --> pdb=" O   ILE E 116 " (cutoff:3.500A)
      removed outlier: 4.802A  pdb=" N   ILE E 116 " --> pdb=" O   SER E  83 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   LEU E  85 " --> pdb=" O   LEU E 114 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 104 through 125
    current: chain 'F' and resid 54 through 57
      removed outlier: 5.487A  pdb=" N   VAL F  61 " --> pdb=" O   THR F 108 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLU F  65 " --> pdb=" O   SER F 104 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   MET F 100 " --> pdb=" O   THR F  69 " (cutoff:3.500A)
      removed outlier: 11.874A  pdb=" N   GLY F  71 " --> pdb=" O   HIS F  98 " (cutoff:3.500A)
      removed outlier: 10.196A  pdb=" N   HIS F  98 " --> pdb=" O   GLY F  71 " (cutoff:3.500A)
      removed outlier: 11.698A  pdb=" N   CYS F  73 " --> pdb=" O   LYS F  96 " (cutoff:3.500A)
      removed outlier: 8.861A  pdb=" N   LYS F  96 " --> pdb=" O   CYS F  73 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   ILE F  75 " --> pdb=" O   LYS F  94 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   LYS F  94 " --> pdb=" O   ILE F  75 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   GLU F  77 " --> pdb=" O   VAL F  92 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   VAL F  92 " --> pdb=" O   GLU F  77 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   ASN F  79 " --> pdb=" O   LYS F  90 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   LYS F  90 " --> pdb=" O   ASN F  79 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1477 through 1479
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1535 through 1536
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 1535 through 1536
    current: chain 'A' and resid 1675 through 1680
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1757 through 1758
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1813 through 1818
    Processing sheet with id=AA6, first strand: chain 'A' and resid 2068 through 2069
      removed outlier: 4.132A  pdb=" N   TRP A2051 " --> pdb=" O   VAL A2069 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 573 through 578
    Processing sheet with id=AA8, first strand: chain 'E' and resid 134 through 136

    501 hydrogen bonds defined for protein.
    1446 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.29

  Time building geometry restraints manager: 3.05 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: 3538
        1.34 -     1.46: 1564
        1.46 -     1.57: 5809
        1.57 -     1.69: 0
        1.69 -     1.81: 109
  Bond restraints: 11020
  Sorted by residual:
  bond pdb=" CG  LEU F  24 "
       pdb=" CD1 LEU F  24 "
    ideal  model  delta    sigma   weight residual
    1.521  1.468  0.053 3.30e-02 9.18e+02 2.56e+00
  bond pdb=" CG1 ILE E 117 "
       pdb=" CD1 ILE E 117 "
    ideal  model  delta    sigma   weight residual
    1.513  1.459  0.054 3.90e-02 6.57e+02 1.91e+00
  bond pdb=" CG1 ILE A2010 "
       pdb=" CD1 ILE A2010 "
    ideal  model  delta    sigma   weight residual
    1.513  1.462  0.051 3.90e-02 6.57e+02 1.69e+00
  bond pdb=" CG1 ILE D 859 "
       pdb=" CD1 ILE D 859 "
    ideal  model  delta    sigma   weight residual
    1.513  1.463  0.050 3.90e-02 6.57e+02 1.64e+00
  bond pdb=" CA  ALA E 133 "
       pdb=" C   ALA E 133 "
    ideal  model  delta    sigma   weight residual
    1.531  1.517  0.014 1.12e-02 7.97e+03 1.64e+00
  ... (remaining 11015 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 13640
        1.26 -     2.53: 1033
        2.53 -     3.79: 184
        3.79 -     5.06: 40
        5.06 -     6.32: 5
  Bond angle restraints: 14902
  Sorted by residual:
  angle pdb=" C   CYS A1673 "
        pdb=" N   GLN A1674 "
        pdb=" CA  GLN A1674 "
      ideal   model   delta    sigma   weight residual
     120.75  125.07   -4.32 1.51e+00 4.39e-01 8.17e+00
  angle pdb=" N   CYS A1673 "
        pdb=" CA  CYS A1673 "
        pdb=" C   CYS A1673 "
      ideal   model   delta    sigma   weight residual
     109.24  113.82   -4.58 1.67e+00 3.59e-01 7.52e+00
  angle pdb=" C   ILE A1519 "
        pdb=" CA  ILE A1519 "
        pdb=" CB  ILE A1519 "
      ideal   model   delta    sigma   weight residual
     111.88  108.42    3.46 1.28e+00 6.10e-01 7.29e+00
  angle pdb=" N   THR A1518 "
        pdb=" CA  THR A1518 "
        pdb=" C   THR A1518 "
      ideal   model   delta    sigma   weight residual
     111.71  114.63   -2.92 1.15e+00 7.56e-01 6.46e+00
  angle pdb=" N   CYS A2089 "
        pdb=" CA  CYS A2089 "
        pdb=" C   CYS A2089 "
      ideal   model   delta    sigma   weight residual
     111.33  114.30   -2.97 1.21e+00 6.83e-01 6.03e+00
  ... (remaining 14897 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 6168
       17.86 -    35.72: 432
       35.72 -    53.58: 62
       53.58 -    71.45: 19
       71.45 -    89.31: 10
  Dihedral angle restraints: 6691
    sinusoidal: 2747
      harmonic: 3944
  Sorted by residual:
  dihedral pdb=" CA  TYR A1400 "
           pdb=" C   TYR A1400 "
           pdb=" N   ARG A1401 "
           pdb=" CA  ARG A1401 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.18   28.82     0      5.00e+00 4.00e-02 3.32e+01
  dihedral pdb=" CA  LYS A2000 "
           pdb=" C   LYS A2000 "
           pdb=" N   GLY A2001 "
           pdb=" CA  GLY A2001 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.06   27.94     0      5.00e+00 4.00e-02 3.12e+01
  dihedral pdb=" CA  LEU F  70 "
           pdb=" C   LEU F  70 "
           pdb=" N   GLY F  71 "
           pdb=" CA  GLY F  71 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.11   27.89     0      5.00e+00 4.00e-02 3.11e+01
  ... (remaining 6688 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 963
       0.033 -    0.067: 458
       0.067 -    0.100: 165
       0.100 -    0.133: 71
       0.133 -    0.166: 13
  Chirality restraints: 1670
  Sorted by residual:
  chirality pdb=" CA  ARG E 185 "
            pdb=" N   ARG E 185 "
            pdb=" C   ARG E 185 "
            pdb=" CB  ARG E 185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 6.93e-01
  chirality pdb=" CA  VAL F  45 "
            pdb=" N   VAL F  45 "
            pdb=" C   VAL F  45 "
            pdb=" CB  VAL F  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.20e-01
  chirality pdb=" CB  ILE A1519 "
            pdb=" CA  ILE A1519 "
            pdb=" CG1 ILE A1519 "
            pdb=" CG2 ILE A1519 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.88e-01
  ... (remaining 1667 not shown)

  Planarity restraints: 1909
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG E  22 "   -0.272 9.50e-02 1.11e+02   1.23e-01 1.14e+01
        pdb=" NE  ARG E  22 "    0.025 2.00e-02 2.50e+03
        pdb=" CZ  ARG E  22 "   -0.023 2.00e-02 2.50e+03
        pdb=" NH1 ARG E  22 "    0.011 2.00e-02 2.50e+03
        pdb=" NH2 ARG E  22 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG E  65 "   -0.241 9.50e-02 1.11e+02   1.09e-01 9.18e+00
        pdb=" NE  ARG E  65 "    0.023 2.00e-02 2.50e+03
        pdb=" CZ  ARG E  65 "   -0.022 2.00e-02 2.50e+03
        pdb=" NH1 ARG E  65 "    0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG E  65 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1776 "   -0.211 9.50e-02 1.11e+02   9.54e-02 7.35e+00
        pdb=" NE  ARG A1776 "    0.021 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1776 "   -0.021 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1776 "    0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1776 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1906 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1379
        2.75 -     3.29: 11684
        3.29 -     3.83: 17733
        3.83 -     4.36: 21907
        4.36 -     4.90: 36328
  Nonbonded interactions: 89031
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG E  65 "
            pdb=" OD2 ASP E  68 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" NZ  LYS A1535 "
            pdb=" O   ARG A1680 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" O   PHE A1544 "
            pdb=" NH1 ARG A1585 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" O   ILE F  48 "
            pdb=" OH  TYR F  66 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" O   GLU A1388 "
            pdb=" OH  TYR A1400 "
     model   vdw
     2.299 3.040
  ... (remaining 89026 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     26.680
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.080
  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:             0.010
  Load rotamer database and sin/cos tables:3.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
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      :  0.005   0.054  11020  Z= 0.217
  Angle     :  0.754   6.321  14902  Z= 0.429
  Chirality :  0.047   0.166   1670
  Planarity :  0.009   0.123   1909
  Dihedral  : 13.293  89.307   4133
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.21), residues: 1320
  helix: -1.12 (0.17), residues: 639
  sheet: -0.30 (0.45), residues: 110
  loop : -0.63 (0.26), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP A1987 
 HIS   0.007   0.001   HIS A2024 
 PHE   0.035   0.003   PHE D 744 
 TYR   0.027   0.005   TYR D 756 
 ARG   0.026   0.003   ARG E  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19761 (  501)
  hydrogen bonds       : angle       7.75882 ( 1446)
  covalent geometry    : bond        0.00518 (11020)
  covalent geometry    : angle       0.75399 (14902)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 258
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1269 GLU cc_start: 0.8615 (mp0) cc_final: 0.8216 (mp0)
REVERT: A 1270 ASP cc_start: 0.8213 (m-30) cc_final: 0.7686 (m-30)
REVERT: A 1305 PHE cc_start: 0.8302 (m-80) cc_final: 0.8022 (m-80)
REVERT: A 1330 TYR cc_start: 0.8230 (t80) cc_final: 0.7943 (t80)
REVERT: A 1341 TYR cc_start: 0.8088 (t80) cc_final: 0.7860 (t80)
REVERT: A 1530 MET cc_start: 0.6565 (tpp) cc_final: 0.6207 (mmm)
REVERT: A 1545 LYS cc_start: 0.7992 (tttt) cc_final: 0.7750 (mmtm)
REVERT: A 1729 LEU cc_start: 0.9110 (mp) cc_final: 0.8807 (mt)
REVERT: A 1734 TYR cc_start: 0.6727 (m-80) cc_final: 0.6369 (m-80)
REVERT: A 1760 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6584 (tp30)
REVERT: A 1769 LEU cc_start: 0.7802 (mt) cc_final: 0.7588 (tp)
REVERT: D  564 LEU cc_start: 0.9195 (mt) cc_final: 0.8944 (mm)
REVERT: D  568 MET cc_start: 0.9545 (mtp) cc_final: 0.9151 (mpp)
REVERT: D  667 GLU cc_start: 0.8803 (tp30) cc_final: 0.8124 (tp30)
REVERT: D  736 CYS cc_start: 0.8437 (t) cc_final: 0.8080 (m)
REVERT: D  850 LEU cc_start: 0.6575 (tp) cc_final: 0.6302 (mt)
REVERT: F   34 ASP cc_start: 0.7749 (t0) cc_final: 0.7298 (t0)
REVERT: F  106 THR cc_start: 0.9244 (m) cc_final: 0.8957 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 258
  average time/residue: 0.3138
  time to fit residues: 106.1550
Evaluate side-chains
  161 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 112 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0010
   chunk 67 optimal weight:   50.0000
   chunk 53 optimal weight:    0.9980
   chunk 104 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 63 optimal weight:    6.9990
   chunk 77 optimal weight:    0.9990
   chunk 120 optimal weight:    0.5980
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
A1431 ASN
** A1478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1505 GLN
D 739 ASN
D 823 GLN
E 162 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.169711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.120160 restraints weight = 20929.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.121982 restraints weight = 13573.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.122257 restraints weight = 10395.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11020  Z= 0.161
  Angle     :  0.689   9.684  14902  Z= 0.360
  Chirality :  0.044   0.398   1670
  Planarity :  0.005   0.055   1909
  Dihedral  :  5.891  25.850   1473
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  :  7.70 %
    Favored  : 90.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.23), residues: 1320
  helix:  0.17 (0.19), residues: 654
  sheet: -0.60 (0.43), residues: 122
  loop : -0.16 (0.28), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP D 625 
 HIS   0.010   0.001   HIS E 135 
 PHE   0.024   0.003   PHE A1453 
 TYR   0.020   0.002   TYR D 655 
 ARG   0.011   0.001   ARG A1529 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05604 (  501)
  hydrogen bonds       : angle       5.31377 ( 1446)
  covalent geometry    : bond        0.00352 (11020)
  covalent geometry    : angle       0.68950 (14902)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 183
  time to evaluate  : 1.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1269 GLU cc_start: 0.8689 (mp0) cc_final: 0.8377 (mp0)
REVERT: A 1305 PHE cc_start: 0.8394 (m-80) cc_final: 0.7806 (m-80)
REVERT: A 1341 TYR cc_start: 0.8066 (t80) cc_final: 0.7828 (t80)
REVERT: A 1453 PHE cc_start: 0.7666 (t80) cc_final: 0.7147 (t80)
REVERT: A 1528 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7243 (m-30)
REVERT: A 1545 LYS cc_start: 0.7831 (tttt) cc_final: 0.7529 (mptt)
REVERT: A 1597 MET cc_start: 0.6296 (pmm) cc_final: 0.6000 (pmm)
REVERT: A 1729 LEU cc_start: 0.9118 (mp) cc_final: 0.8807 (mt)
REVERT: A 1734 TYR cc_start: 0.6930 (m-80) cc_final: 0.6664 (m-80)
REVERT: A 1806 MET cc_start: 0.8155 (mmm) cc_final: 0.7207 (mmm)
REVERT: A 2080 MET cc_start: 0.6506 (ttt) cc_final: 0.6224 (ttt)
REVERT: D  472 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7801 (mmm)
REVERT: D  555 THR cc_start: 0.9386 (p) cc_final: 0.8969 (t)
REVERT: D  556 LEU cc_start: 0.9516 (mt) cc_final: 0.9134 (mt)
REVERT: D  568 MET cc_start: 0.9221 (mtp) cc_final: 0.8905 (mtt)
REVERT: D  570 ARG cc_start: 0.8495 (mmm160) cc_final: 0.8269 (mmm160)
REVERT: D  795 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7803 (mp10)
REVERT: E  135 HIS cc_start: 0.6625 (t-170) cc_final: 0.6400 (t-170)
REVERT: E  145 MET cc_start: 0.8183 (mpp) cc_final: 0.7681 (mpp)
REVERT: F   19 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6617 (pt0)
REVERT: F  106 THR cc_start: 0.8831 (m) cc_final: 0.8462 (p)
  outliers start: 23
  outliers final: 13
  residues processed: 195
  average time/residue: 0.2511
  time to fit residues: 68.4376
Evaluate side-chains
  162 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 145
  time to evaluate  : 1.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1273 LEU
Chi-restraints excluded: chain A residue 1314 HIS
Chi-restraints excluded: chain A residue 1333 TYR
Chi-restraints excluded: chain A residue 1455 LEU
Chi-restraints excluded: chain A residue 1499 MET
Chi-restraints excluded: chain A residue 1528 ASP
Chi-restraints excluded: chain A residue 1684 VAL
Chi-restraints excluded: chain A residue 1710 THR
Chi-restraints excluded: chain A residue 1727 LEU
Chi-restraints excluded: chain A residue 1744 GLU
Chi-restraints excluded: chain D residue  472 MET
Chi-restraints excluded: chain D residue  620 LEU
Chi-restraints excluded: chain D residue  795 GLN
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain F residue   19 GLU
Chi-restraints excluded: chain F residue  110 LEU
Chi-restraints excluded: chain F residue  123 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 132 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 131 optimal weight:    0.7980
   chunk 107 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 62 optimal weight:   30.0000
   chunk 91 optimal weight:    1.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A1478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1567 ASN
A1995 ASN
A2024 HIS
** A2030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 739 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.166633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.116633 restraints weight = 21099.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.119320 restraints weight = 13262.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.119076 restraints weight = 9580.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.3343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  11020  Z= 0.212
  Angle     :  0.704  12.572  14902  Z= 0.360
  Chirality :  0.045   0.330   1670
  Planarity :  0.005   0.037   1909
  Dihedral  :  5.535  24.962   1473
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  :  9.87 %
    Favored  : 87.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    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 (0.23), residues: 1320
  helix:  0.20 (0.20), residues: 660
  sheet: -0.70 (0.45), residues: 110
  loop : -0.19 (0.28), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP A1265 
 HIS   0.005   0.001   HIS A1425 
 PHE   0.034   0.003   PHE D 744 
 TYR   0.021   0.002   TYR D 552 
 ARG   0.005   0.001   ARG A1529 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05066 (  501)
  hydrogen bonds       : angle       5.18326 ( 1446)
  covalent geometry    : bond        0.00492 (11020)
  covalent geometry    : angle       0.70413 (14902)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 155
  time to evaluate  : 1.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1269 GLU cc_start: 0.8746 (mp0) cc_final: 0.8513 (mp0)
REVERT: A 1305 PHE cc_start: 0.8381 (m-80) cc_final: 0.7811 (m-80)
REVERT: A 1341 TYR cc_start: 0.8099 (t80) cc_final: 0.7863 (t80)
REVERT: A 1453 PHE cc_start: 0.7671 (t80) cc_final: 0.7140 (t80)
REVERT: A 1528 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7178 (m-30)
REVERT: A 1560 SER cc_start: 0.7475 (t) cc_final: 0.7017 (m)
REVERT: A 1597 MET cc_start: 0.6462 (pmm) cc_final: 0.5907 (mpp)
REVERT: A 1729 LEU cc_start: 0.9136 (mp) cc_final: 0.8816 (mt)
REVERT: A 1806 MET cc_start: 0.7981 (mmm) cc_final: 0.7247 (mmm)
REVERT: A 2080 MET cc_start: 0.6782 (ttt) cc_final: 0.6434 (ttt)
REVERT: D  472 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7798 (mmm)
REVERT: D  565 LYS cc_start: 0.9149 (pttt) cc_final: 0.8943 (ptpp)
REVERT: D  568 MET cc_start: 0.9193 (mtp) cc_final: 0.8905 (mtt)
REVERT: D  570 ARG cc_start: 0.8428 (mmm160) cc_final: 0.8012 (mmm160)
REVERT: D  739 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.8122 (m-40)
REVERT: D  795 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7841 (mp10)
REVERT: D  852 GLN cc_start: 0.5758 (mm-40) cc_final: 0.5546 (mm110)
REVERT: E   23 ARG cc_start: 0.7166 (mmt180) cc_final: 0.6899 (mmp80)
REVERT: F   19 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6826 (mp0)
REVERT: F   34 ASP cc_start: 0.7842 (t0) cc_final: 0.7418 (t0)
REVERT: F  105 MET cc_start: 0.8774 (mmm) cc_final: 0.8184 (mmm)
REVERT: F  106 THR cc_start: 0.8813 (m) cc_final: 0.8178 (p)
  outliers start: 30
  outliers final: 14
  residues processed: 172
  average time/residue: 0.2517
  time to fit residues: 60.5931
Evaluate side-chains
  158 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 1.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1314 HIS
Chi-restraints excluded: chain A residue 1333 TYR
Chi-restraints excluded: chain A residue 1337 LEU
Chi-restraints excluded: chain A residue 1455 LEU
Chi-restraints excluded: chain A residue 1499 MET
Chi-restraints excluded: chain A residue 1528 ASP
Chi-restraints excluded: chain A residue 1684 VAL
Chi-restraints excluded: chain A residue 1727 LEU
Chi-restraints excluded: chain A residue 1990 VAL
Chi-restraints excluded: chain A residue 2003 MET
Chi-restraints excluded: chain D residue  472 MET
Chi-restraints excluded: chain D residue  620 LEU
Chi-restraints excluded: chain D residue  739 ASN
Chi-restraints excluded: chain D residue  795 GLN
Chi-restraints excluded: chain D residue  798 SER
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain F residue   19 GLU
Chi-restraints excluded: chain F residue   82 HIS
Chi-restraints excluded: chain F residue  104 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 114 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 131 optimal weight:    5.9990
   chunk 78 optimal weight:   30.0000
   chunk 115 optimal weight:    0.9980
   chunk 130 optimal weight:    1.9990
   chunk 99 optimal weight:    0.6980
   chunk 62 optimal weight:   20.0000
   chunk 16 optimal weight:    1.9990
   chunk 64 optimal weight:    7.9990
   chunk 98 optimal weight:    0.6980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A1478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2030 GLN
D 739 ASN
** D 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.171579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.127757 restraints weight = 21156.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.125427 restraints weight = 13733.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.125971 restraints weight = 12482.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.3692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11020  Z= 0.165
  Angle     :  0.658   9.916  14902  Z= 0.334
  Chirality :  0.043   0.308   1670
  Planarity :  0.004   0.039   1909
  Dihedral  :  5.243  24.222   1473
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 12.05 %
    Favored  : 85.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    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: -0.03 (0.23), residues: 1320
  helix:  0.27 (0.20), residues: 666
  sheet: -0.41 (0.43), residues: 122
  loop : -0.08 (0.29), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A1265 
 HIS   0.009   0.001   HIS E 135 
 PHE   0.027   0.002   PHE D 744 
 TYR   0.021   0.002   TYR D 655 
 ARG   0.008   0.000   ARG A1509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04562 (  501)
  hydrogen bonds       : angle       5.05510 ( 1446)
  covalent geometry    : bond        0.00380 (11020)
  covalent geometry    : angle       0.65801 (14902)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 150
  time to evaluate  : 1.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1305 PHE cc_start: 0.7928 (m-80) cc_final: 0.7527 (m-80)
REVERT: A 1341 TYR cc_start: 0.8038 (t80) cc_final: 0.7785 (t80)
REVERT: A 1453 PHE cc_start: 0.7478 (t80) cc_final: 0.6905 (t80)
REVERT: A 1528 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7155 (m-30)
REVERT: A 1530 MET cc_start: 0.5829 (mmm) cc_final: 0.5219 (mmm)
REVERT: A 1560 SER cc_start: 0.7135 (t) cc_final: 0.6768 (m)
REVERT: A 1597 MET cc_start: 0.6209 (pmm) cc_final: 0.5974 (mpp)
REVERT: D  570 ARG cc_start: 0.8124 (mmm160) cc_final: 0.7765 (mmm160)
REVERT: D  739 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.7915 (m-40)
REVERT: D  795 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7820 (mp10)
REVERT: D  852 GLN cc_start: 0.5692 (mm-40) cc_final: 0.5468 (mm110)
REVERT: F   19 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7130 (mp0)
REVERT: F   34 ASP cc_start: 0.7578 (t0) cc_final: 0.7146 (t0)
REVERT: F  106 THR cc_start: 0.8884 (m) cc_final: 0.8442 (p)
  outliers start: 30
  outliers final: 16
  residues processed: 169
  average time/residue: 0.2339
  time to fit residues: 56.3428
Evaluate side-chains
  158 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1314 HIS
Chi-restraints excluded: chain A residue 1333 TYR
Chi-restraints excluded: chain A residue 1337 LEU
Chi-restraints excluded: chain A residue 1374 LEU
Chi-restraints excluded: chain A residue 1455 LEU
Chi-restraints excluded: chain A residue 1528 ASP
Chi-restraints excluded: chain A residue 1684 VAL
Chi-restraints excluded: chain A residue 1727 LEU
Chi-restraints excluded: chain A residue 1744 GLU
Chi-restraints excluded: chain A residue 1990 VAL
Chi-restraints excluded: chain D residue  489 HIS
Chi-restraints excluded: chain D residue  620 LEU
Chi-restraints excluded: chain D residue  739 ASN
Chi-restraints excluded: chain D residue  795 GLN
Chi-restraints excluded: chain D residue  798 SER
Chi-restraints excluded: chain D residue  853 LEU
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain E residue  108 THR
Chi-restraints excluded: chain F residue   19 GLU
Chi-restraints excluded: chain F residue  104 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 102 optimal weight:    0.5980
   chunk 84 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9980
   chunk 117 optimal weight:    1.9990
   chunk 77 optimal weight:    8.9990
   chunk 68 optimal weight:    7.9990
   chunk 118 optimal weight:    0.0770
   chunk 129 optimal weight:    0.7980
   chunk 15 optimal weight:    7.9990
   chunk 101 optimal weight:    0.5980
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
** A1478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1550 ASN
D 739 ASN
** D 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 822 HIS
F  79 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.172825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.129597 restraints weight = 21104.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.127196 restraints weight = 13706.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.128374 restraints weight = 12542.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.4025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11020  Z= 0.138
  Angle     :  0.642  11.956  14902  Z= 0.323
  Chirality :  0.042   0.285   1670
  Planarity :  0.004   0.037   1909
  Dihedral  :  5.055  23.479   1473
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 13.47 %
    Favored  : 84.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    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:  0.13 (0.23), residues: 1320
  helix:  0.44 (0.20), residues: 665
  sheet: -0.43 (0.43), residues: 122
  loop : -0.04 (0.29), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP A1265 
 HIS   0.007   0.001   HIS E 135 
 PHE   0.019   0.002   PHE D 744 
 TYR   0.023   0.001   TYR D 756 
 ARG   0.007   0.000   ARG A1509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04268 (  501)
  hydrogen bonds       : angle       4.89229 ( 1446)
  covalent geometry    : bond        0.00307 (11020)
  covalent geometry    : angle       0.64161 (14902)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 150
  time to evaluate  : 1.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1341 TYR cc_start: 0.7970 (t80) cc_final: 0.7711 (t80)
REVERT: A 1453 PHE cc_start: 0.7312 (t80) cc_final: 0.6729 (t80)
REVERT: A 1560 SER cc_start: 0.7030 (t) cc_final: 0.6660 (m)
REVERT: A 1597 MET cc_start: 0.6280 (pmm) cc_final: 0.5950 (mpp)
REVERT: D  570 ARG cc_start: 0.7919 (mmm160) cc_final: 0.7593 (mmm160)
REVERT: D  739 ASN cc_start: 0.8285 (OUTLIER) cc_final: 0.7967 (m-40)
REVERT: D  795 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7746 (mp10)
REVERT: D  852 GLN cc_start: 0.5653 (mm-40) cc_final: 0.5429 (mm110)
REVERT: E  176 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7332 (mt)
REVERT: F   19 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7124 (mp0)
REVERT: F   34 ASP cc_start: 0.7419 (t0) cc_final: 0.7014 (t0)
  outliers start: 30
  outliers final: 16
  residues processed: 168
  average time/residue: 0.2361
  time to fit residues: 56.7586
Evaluate side-chains
  152 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 132
  time to evaluate  : 1.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1293 THR
Chi-restraints excluded: chain A residue 1314 HIS
Chi-restraints excluded: chain A residue 1333 TYR
Chi-restraints excluded: chain A residue 1337 LEU
Chi-restraints excluded: chain A residue 1374 LEU
Chi-restraints excluded: chain A residue 1455 LEU
Chi-restraints excluded: chain A residue 1684 VAL
Chi-restraints excluded: chain A residue 1744 GLU
Chi-restraints excluded: chain A residue 1990 VAL
Chi-restraints excluded: chain D residue  489 HIS
Chi-restraints excluded: chain D residue  564 LEU
Chi-restraints excluded: chain D residue  620 LEU
Chi-restraints excluded: chain D residue  739 ASN
Chi-restraints excluded: chain D residue  795 GLN
Chi-restraints excluded: chain D residue  798 SER
Chi-restraints excluded: chain D residue  853 LEU
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain E residue  176 LEU
Chi-restraints excluded: chain F residue   19 GLU
Chi-restraints excluded: chain F residue  104 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 125 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 28 optimal weight:    0.2980
   chunk 127 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 131 optimal weight:    2.9990
   chunk 80 optimal weight:    7.9990
   chunk 62 optimal weight:    6.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** A1478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2104 ASN
D 739 ASN
** D 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.172911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.126078 restraints weight = 21251.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.127965 restraints weight = 16087.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.127688 restraints weight = 11058.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.4275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  11020  Z= 0.161
  Angle     :  0.665  13.357  14902  Z= 0.331
  Chirality :  0.042   0.257   1670
  Planarity :  0.004   0.035   1909
  Dihedral  :  5.039  25.306   1473
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 14.73 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    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 (0.23), residues: 1320
  helix:  0.52 (0.20), residues: 657
  sheet: -0.51 (0.44), residues: 118
  loop : -0.08 (0.28), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A1265 
 HIS   0.007   0.001   HIS E 135 
 PHE   0.025   0.002   PHE D 744 
 TYR   0.021   0.002   TYR D 655 
 ARG   0.007   0.000   ARG A1509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04225 (  501)
  hydrogen bonds       : angle       4.89006 ( 1446)
  covalent geometry    : bond        0.00375 (11020)
  covalent geometry    : angle       0.66465 (14902)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 141
  time to evaluate  : 1.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1453 PHE cc_start: 0.7343 (t80) cc_final: 0.6742 (t80)
REVERT: A 1530 MET cc_start: 0.5609 (mmm) cc_final: 0.5331 (mtp)
REVERT: A 1560 SER cc_start: 0.7100 (t) cc_final: 0.6732 (m)
REVERT: A 1597 MET cc_start: 0.6311 (pmm) cc_final: 0.6061 (mpp)
REVERT: A 1780 PHE cc_start: 0.7758 (p90) cc_final: 0.7064 (t80)
REVERT: D  472 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7492 (mmm)
REVERT: D  662 ARG cc_start: 0.8519 (mpp-170) cc_final: 0.8085 (mmm-85)
REVERT: D  739 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7956 (m-40)
REVERT: D  795 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7810 (mp10)
REVERT: F   19 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7117 (mp0)
REVERT: F   34 ASP cc_start: 0.7596 (t0) cc_final: 0.7140 (t0)
REVERT: F  107 ARG cc_start: 0.8490 (ttm170) cc_final: 0.8165 (ttt180)
  outliers start: 27
  outliers final: 17
  residues processed: 157
  average time/residue: 0.2431
  time to fit residues: 54.9625
Evaluate side-chains
  155 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 134
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1314 HIS
Chi-restraints excluded: chain A residue 1333 TYR
Chi-restraints excluded: chain A residue 1337 LEU
Chi-restraints excluded: chain A residue 1374 LEU
Chi-restraints excluded: chain A residue 1455 LEU
Chi-restraints excluded: chain A residue 1684 VAL
Chi-restraints excluded: chain A residue 1744 GLU
Chi-restraints excluded: chain A residue 1990 VAL
Chi-restraints excluded: chain D residue  472 MET
Chi-restraints excluded: chain D residue  489 HIS
Chi-restraints excluded: chain D residue  564 LEU
Chi-restraints excluded: chain D residue  620 LEU
Chi-restraints excluded: chain D residue  739 ASN
Chi-restraints excluded: chain D residue  795 GLN
Chi-restraints excluded: chain D residue  798 SER
Chi-restraints excluded: chain D residue  844 VAL
Chi-restraints excluded: chain D residue  853 LEU
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain F residue   19 GLU
Chi-restraints excluded: chain F residue   99 THR
Chi-restraints excluded: chain F residue  104 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 20 optimal weight:    5.9990
   chunk 82 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 122 optimal weight:    0.3980
   chunk 57 optimal weight:    2.9990
   chunk 43 optimal weight:    9.9990
   chunk 66 optimal weight:    6.9990
   chunk 30 optimal weight:    0.0670
   chunk 60 optimal weight:    0.6980
   chunk 56 optimal weight:    0.0070
   overall best weight:    0.3736

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

Flipped N/Q/H residues before XYZ refinement:
** A1478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1550 ASN
A1674 GLN
D 712 HIS
** D 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 779 HIS
** D 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.174661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.131441 restraints weight = 21312.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.129419 restraints weight = 14168.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.130752 restraints weight = 13363.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.4538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11020  Z= 0.125
  Angle     :  0.647  12.465  14902  Z= 0.317
  Chirality :  0.041   0.227   1670
  Planarity :  0.004   0.038   1909
  Dihedral  :  4.861  23.699   1473
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 15.65 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.23), residues: 1320
  helix:  0.61 (0.20), residues: 664
  sheet: -0.54 (0.43), residues: 124
  loop : -0.15 (0.29), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP D 625 
 HIS   0.008   0.001   HIS E 135 
 PHE   0.017   0.002   PHE A2097 
 TYR   0.028   0.001   TYR D 756 
 ARG   0.008   0.000   ARG A1509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03930 (  501)
  hydrogen bonds       : angle       4.79181 ( 1446)
  covalent geometry    : bond        0.00272 (11020)
  covalent geometry    : angle       0.64681 (14902)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 145
  time to evaluate  : 1.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1453 PHE cc_start: 0.7205 (t80) cc_final: 0.6637 (t80)
REVERT: A 1530 MET cc_start: 0.5922 (mmm) cc_final: 0.5318 (mmm)
REVERT: A 1560 SER cc_start: 0.7038 (t) cc_final: 0.6710 (m)
REVERT: A 1597 MET cc_start: 0.6287 (pmm) cc_final: 0.6026 (mpp)
REVERT: A 1780 PHE cc_start: 0.7589 (p90) cc_final: 0.7022 (t80)
REVERT: D  739 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.7841 (m-40)
REVERT: D  795 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7783 (mp10)
REVERT: E  176 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7366 (mt)
REVERT: F   19 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7090 (mp0)
REVERT: F   34 ASP cc_start: 0.7428 (t0) cc_final: 0.7038 (t0)
REVERT: F   44 LYS cc_start: 0.6417 (OUTLIER) cc_final: 0.6042 (ttpt)
  outliers start: 24
  outliers final: 13
  residues processed: 159
  average time/residue: 0.2376
  time to fit residues: 53.9835
Evaluate side-chains
  153 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 1.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1314 HIS
Chi-restraints excluded: chain A residue 1333 TYR
Chi-restraints excluded: chain A residue 1337 LEU
Chi-restraints excluded: chain A residue 1374 LEU
Chi-restraints excluded: chain A residue 1455 LEU
Chi-restraints excluded: chain A residue 1684 VAL
Chi-restraints excluded: chain A residue 1710 THR
Chi-restraints excluded: chain D residue  489 HIS
Chi-restraints excluded: chain D residue  620 LEU
Chi-restraints excluded: chain D residue  739 ASN
Chi-restraints excluded: chain D residue  795 GLN
Chi-restraints excluded: chain D residue  798 SER
Chi-restraints excluded: chain D residue  844 VAL
Chi-restraints excluded: chain D residue  853 LEU
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain E residue  176 LEU
Chi-restraints excluded: chain F residue   19 GLU
Chi-restraints excluded: chain F residue   44 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 123 optimal weight:    4.9990
   chunk 122 optimal weight:    0.2980
   chunk 59 optimal weight:    0.6980
   chunk 61 optimal weight:    6.9990
   chunk 127 optimal weight:    2.9990
   chunk 47 optimal weight:    0.5980
   chunk 81 optimal weight:    1.9990
   chunk 13 optimal weight:    7.9990
   chunk 99 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 76 optimal weight:    8.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A1478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1674 GLN
D 739 ASN
** D 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.173914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.130166 restraints weight = 20984.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.127902 restraints weight = 13475.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.129097 restraints weight = 11690.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.4675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11020  Z= 0.138
  Angle     :  0.660  12.524  14902  Z= 0.324
  Chirality :  0.041   0.249   1670
  Planarity :  0.004   0.035   1909
  Dihedral  :  4.767  24.903   1473
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 15.06 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    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:  0.25 (0.23), residues: 1320
  helix:  0.71 (0.20), residues: 664
  sheet: -0.52 (0.44), residues: 121
  loop : -0.19 (0.28), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP D 625 
 HIS   0.008   0.001   HIS E 135 
 PHE   0.022   0.002   PHE D 744 
 TYR   0.040   0.001   TYR D 756 
 ARG   0.007   0.000   ARG A1509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03906 (  501)
  hydrogen bonds       : angle       4.81429 ( 1446)
  covalent geometry    : bond        0.00313 (11020)
  covalent geometry    : angle       0.65957 (14902)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 141
  time to evaluate  : 1.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1453 PHE cc_start: 0.7271 (t80) cc_final: 0.6689 (t80)
REVERT: A 1597 MET cc_start: 0.6348 (pmm) cc_final: 0.6089 (mpp)
REVERT: D  739 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7940 (m-40)
REVERT: D  775 LEU cc_start: 0.8194 (tp) cc_final: 0.7689 (tp)
REVERT: D  795 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7738 (mp10)
REVERT: E  176 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7406 (mt)
REVERT: F   19 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7064 (mp0)
REVERT: F   34 ASP cc_start: 0.7526 (t0) cc_final: 0.7072 (t0)
REVERT: F   44 LYS cc_start: 0.6315 (OUTLIER) cc_final: 0.6020 (pttt)
  outliers start: 27
  outliers final: 16
  residues processed: 157
  average time/residue: 0.2373
  time to fit residues: 53.5700
Evaluate side-chains
  153 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1333 TYR
Chi-restraints excluded: chain A residue 1337 LEU
Chi-restraints excluded: chain A residue 1374 LEU
Chi-restraints excluded: chain A residue 1455 LEU
Chi-restraints excluded: chain A residue 1478 ASN
Chi-restraints excluded: chain A residue 1546 ASP
Chi-restraints excluded: chain A residue 1684 VAL
Chi-restraints excluded: chain A residue 1710 THR
Chi-restraints excluded: chain D residue  489 HIS
Chi-restraints excluded: chain D residue  588 LEU
Chi-restraints excluded: chain D residue  620 LEU
Chi-restraints excluded: chain D residue  739 ASN
Chi-restraints excluded: chain D residue  795 GLN
Chi-restraints excluded: chain D residue  798 SER
Chi-restraints excluded: chain D residue  844 VAL
Chi-restraints excluded: chain D residue  853 LEU
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain E residue  176 LEU
Chi-restraints excluded: chain F residue   19 GLU
Chi-restraints excluded: chain F residue   44 LYS
Chi-restraints excluded: chain F residue   99 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 77 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 84 optimal weight:    5.9990
   chunk 116 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 90 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0970
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A1478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1550 ASN
D 739 ASN
** D 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.174257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.130136 restraints weight = 21266.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.130604 restraints weight = 15365.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.130736 restraints weight = 11888.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.4823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11020  Z= 0.132
  Angle     :  0.674  13.012  14902  Z= 0.328
  Chirality :  0.042   0.259   1670
  Planarity :  0.004   0.034   1909
  Dihedral  :  4.711  24.476   1473
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 15.48 %
    Favored  : 82.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    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:  0.30 (0.23), residues: 1320
  helix:  0.79 (0.20), residues: 661
  sheet: -0.69 (0.43), residues: 124
  loop : -0.17 (0.28), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP D 625 
 HIS   0.007   0.001   HIS E 135 
 PHE   0.023   0.002   PHE A1496 
 TYR   0.050   0.002   TYR D 756 
 ARG   0.003   0.000   ARG A2056 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03840 (  501)
  hydrogen bonds       : angle       4.85318 ( 1446)
  covalent geometry    : bond        0.00295 (11020)
  covalent geometry    : angle       0.67446 (14902)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 137
  time to evaluate  : 1.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1597 MET cc_start: 0.6323 (pmm) cc_final: 0.5706 (mpp)
REVERT: D  568 MET cc_start: 0.8410 (ptp) cc_final: 0.8023 (mpp)
REVERT: D  795 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7720 (mp10)
REVERT: D  844 VAL cc_start: 0.8190 (OUTLIER) cc_final: 0.7941 (p)
REVERT: E  176 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7404 (mt)
REVERT: F   34 ASP cc_start: 0.7383 (t0) cc_final: 0.7000 (t0)
REVERT: F   44 LYS cc_start: 0.6330 (OUTLIER) cc_final: 0.6078 (pttt)
  outliers start: 28
  outliers final: 13
  residues processed: 151
  average time/residue: 0.2301
  time to fit residues: 50.3746
Evaluate side-chains
  148 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 1.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1267 MET
Chi-restraints excluded: chain A residue 1333 TYR
Chi-restraints excluded: chain A residue 1337 LEU
Chi-restraints excluded: chain A residue 1546 ASP
Chi-restraints excluded: chain A residue 1684 VAL
Chi-restraints excluded: chain A residue 1710 THR
Chi-restraints excluded: chain D residue  489 HIS
Chi-restraints excluded: chain D residue  588 LEU
Chi-restraints excluded: chain D residue  620 LEU
Chi-restraints excluded: chain D residue  795 GLN
Chi-restraints excluded: chain D residue  798 SER
Chi-restraints excluded: chain D residue  844 VAL
Chi-restraints excluded: chain D residue  853 LEU
Chi-restraints excluded: chain E residue  176 LEU
Chi-restraints excluded: chain F residue   31 ILE
Chi-restraints excluded: chain F residue   44 LYS
Chi-restraints excluded: chain F residue   99 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 81 optimal weight:    0.7980
   chunk 107 optimal weight:    0.4980
   chunk 27 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 102 optimal weight:    0.9980
   chunk 85 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 93 optimal weight:    0.0870
   chunk 32 optimal weight:    4.9990
   chunk 130 optimal weight:    1.9990
   chunk 121 optimal weight:    0.7980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
** D 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 852 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 = 0.4444 r_free = 0.4444 target = 0.174516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.127936 restraints weight = 21256.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.128442 restraints weight = 14336.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.129187 restraints weight = 12762.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.4958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11020  Z= 0.135
  Angle     :  0.708  14.072  14902  Z= 0.344
  Chirality :  0.043   0.363   1670
  Planarity :  0.004   0.035   1909
  Dihedral  :  4.671  24.491   1473
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 15.98 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    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:  0.38 (0.23), residues: 1320
  helix:  0.88 (0.20), residues: 655
  sheet: -0.69 (0.45), residues: 115
  loop : -0.15 (0.28), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.002   TRP D 625 
 HIS   0.006   0.001   HIS E 135 
 PHE   0.017   0.002   PHE D 744 
 TYR   0.053   0.002   TYR A1501 
 ARG   0.003   0.000   ARG A2056 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03910 (  501)
  hydrogen bonds       : angle       4.88835 ( 1446)
  covalent geometry    : bond        0.00300 (11020)
  covalent geometry    : angle       0.70791 (14902)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 143
  time to evaluate  : 1.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1453 PHE cc_start: 0.7035 (t80) cc_final: 0.6574 (t80)
REVERT: A 1597 MET cc_start: 0.6240 (pmm) cc_final: 0.5815 (mpp)
REVERT: A 1780 PHE cc_start: 0.7645 (p90) cc_final: 0.7126 (t80)
REVERT: D  795 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7739 (mp10)
REVERT: D  844 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7890 (p)
REVERT: E  176 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7467 (mt)
REVERT: F   34 ASP cc_start: 0.7597 (t0) cc_final: 0.7152 (t0)
REVERT: F   44 LYS cc_start: 0.6321 (OUTLIER) cc_final: 0.6031 (pttt)
  outliers start: 20
  outliers final: 13
  residues processed: 153
  average time/residue: 0.2297
  time to fit residues: 51.3103
Evaluate side-chains
  154 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 137
  time to evaluate  : 1.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1267 MET
Chi-restraints excluded: chain A residue 1333 TYR
Chi-restraints excluded: chain A residue 1337 LEU
Chi-restraints excluded: chain A residue 1546 ASP
Chi-restraints excluded: chain A residue 1684 VAL
Chi-restraints excluded: chain A residue 1710 THR
Chi-restraints excluded: chain D residue  489 HIS
Chi-restraints excluded: chain D residue  588 LEU
Chi-restraints excluded: chain D residue  620 LEU
Chi-restraints excluded: chain D residue  795 GLN
Chi-restraints excluded: chain D residue  798 SER
Chi-restraints excluded: chain D residue  844 VAL
Chi-restraints excluded: chain D residue  853 LEU
Chi-restraints excluded: chain E residue  176 LEU
Chi-restraints excluded: chain F residue   31 ILE
Chi-restraints excluded: chain F residue   44 LYS
Chi-restraints excluded: chain F residue   99 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 67 optimal weight:   10.0000
   chunk 117 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 34 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 99 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 60 optimal weight:    0.0030
   chunk 72 optimal weight:    6.9990
   chunk 100 optimal weight:    0.9990
   overall best weight:    0.7190

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

Flipped N/Q/H residues before XYZ refinement:
A1281 ASN
** D 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.174046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.128293 restraints weight = 21049.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.129797 restraints weight = 13959.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.129636 restraints weight = 10276.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
moved from start:          0.5051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11020  Z= 0.142
  Angle     :  0.708  12.688  14902  Z= 0.346
  Chirality :  0.043   0.346   1670
  Planarity :  0.004   0.039   1909
  Dihedral  :  4.683  27.354   1473
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 16.57 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    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 (0.23), residues: 1320
  helix:  0.88 (0.20), residues: 654
  sheet: -0.67 (0.45), residues: 117
  loop : -0.23 (0.28), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.071   0.002   TRP D 625 
 HIS   0.006   0.001   HIS E 135 
 PHE   0.021   0.002   PHE A1496 
 TYR   0.080   0.002   TYR A1501 
 ARG   0.008   0.000   ARG A1454 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03964 (  501)
  hydrogen bonds       : angle       4.94102 ( 1446)
  covalent geometry    : bond        0.00320 (11020)
  covalent geometry    : angle       0.70792 (14902)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4021.68 seconds
wall clock time: 70 minutes 28.47 seconds (4228.47 seconds total)