Starting phenix.real_space_refine
on Sat Aug 23 08:41:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8clk_16715/08_2025/8clk_16715.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8clk_16715/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8clk_16715/08_2025/8clk_16715.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8clk_16715/08_2025/8clk_16715.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8clk_16715/08_2025/8clk_16715.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8clk_16715/08_2025/8clk_16715.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.19, per 1000 atoms: 0.20
  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: 0.68
  Conformation dependent library (CDL) restraints added in 245.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.34
  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: 1.60

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 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:             4.440
  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:          0.260
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.830
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.130
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.026   0.003   ARG E  22 
 TYR   0.027   0.005   TYR D 756 
 PHE   0.035   0.003   PHE D 744 
 TRP   0.027   0.003   TRP A1987 
 HIS   0.007   0.001   HIS A2024 

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

*********************** 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  : 0.430 
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: 0.1291
  time to fit residues: 44.0278
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  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    0.4980
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    0.0980
   chunk 91 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.4365 r_free = 0.4365 target = 0.170295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.122360 restraints weight = 21069.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.123384 restraints weight = 13767.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.124122 restraints weight = 9603.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.124689 restraints weight = 9749.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.124730 restraints weight = 8723.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11020  Z= 0.156
  Angle     :  0.695   9.702  14902  Z= 0.361
  Chirality :  0.045   0.403   1670
  Planarity :  0.005   0.056   1909
  Dihedral  :  5.835  26.062   1473
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  :  7.03 %
    Favored  : 90.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.23), residues: 1320
  helix:  0.19 (0.19), residues: 654
  sheet: -0.61 (0.43), residues: 122
  loop : -0.12 (0.28), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A1529 
 TYR   0.020   0.002   TYR D 655 
 PHE   0.024   0.002   PHE A1453 
 TRP   0.031   0.002   TRP D 625 
 HIS   0.010   0.001   HIS E 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (11020)
  covalent geometry    : angle       0.69507 (14902)
  hydrogen bonds       : bond        0.05236 (  501)
  hydrogen bonds       : angle       5.25173 ( 1446)

*********************** 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
  210 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 185
  time to evaluate  : 0.525 
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: 0.8622 (mp0) cc_final: 0.8360 (mp0)
REVERT: A 1305 PHE cc_start: 0.8254 (m-80) cc_final: 0.7699 (m-80)
REVERT: A 1341 TYR cc_start: 0.8055 (t80) cc_final: 0.7811 (t80)
REVERT: A 1453 PHE cc_start: 0.7642 (t80) cc_final: 0.7097 (t80)
REVERT: A 1528 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7244 (m-30)
REVERT: A 1545 LYS cc_start: 0.7859 (tttt) cc_final: 0.7548 (mptt)
REVERT: A 1597 MET cc_start: 0.6320 (pmm) cc_final: 0.5978 (pmm)
REVERT: A 1729 LEU cc_start: 0.9078 (mp) cc_final: 0.8756 (mt)
REVERT: A 1734 TYR cc_start: 0.6808 (m-80) cc_final: 0.6532 (m-80)
REVERT: A 1806 MET cc_start: 0.8017 (mmm) cc_final: 0.7071 (mmm)
REVERT: A 2080 MET cc_start: 0.6435 (ttt) cc_final: 0.6167 (ttt)
REVERT: D  472 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7809 (mmm)
REVERT: D  555 THR cc_start: 0.9351 (p) cc_final: 0.8932 (t)
REVERT: D  556 LEU cc_start: 0.9493 (mt) cc_final: 0.9129 (mt)
REVERT: D  565 LYS cc_start: 0.9049 (pttt) cc_final: 0.8753 (ptpp)
REVERT: D  568 MET cc_start: 0.9140 (mtp) cc_final: 0.8827 (mtt)
REVERT: D  570 ARG cc_start: 0.8411 (mmm160) cc_final: 0.8185 (mmm160)
REVERT: D  795 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7679 (mp10)
REVERT: E  135 HIS cc_start: 0.6638 (t-170) cc_final: 0.6387 (t-170)
REVERT: E  145 MET cc_start: 0.8206 (mpp) cc_final: 0.7708 (mpp)
REVERT: F   19 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6535 (pt0)
REVERT: F  105 MET cc_start: 0.8732 (mmm) cc_final: 0.7615 (mmm)
REVERT: F  106 THR cc_start: 0.8833 (m) cc_final: 0.8329 (p)
  outliers start: 25
  outliers final: 15
  residues processed: 198
  average time/residue: 0.0956
  time to fit residues: 26.7038
Evaluate side-chains
  166 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 147
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
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 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 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 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  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 74 optimal weight:    0.8980
   chunk 67 optimal weight:   30.0000
   chunk 1 optimal weight:    0.9990
   chunk 54 optimal weight:    0.6980
   chunk 57 optimal weight:    4.9990
   chunk 59 optimal weight:    0.6980
   chunk 119 optimal weight:    5.9990
   chunk 22 optimal weight:    0.7980
   chunk 101 optimal weight:    1.9990
   chunk 82 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.169115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.119680 restraints weight = 21186.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.122843 restraints weight = 12891.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.122604 restraints weight = 8906.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.122962 restraints weight = 9973.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.123085 restraints weight = 9168.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7346
moved from start:          0.3395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11020  Z= 0.145
  Angle     :  0.655  10.411  14902  Z= 0.331
  Chirality :  0.043   0.325   1670
  Planarity :  0.004   0.038   1909
  Dihedral  :  5.365  24.585   1473
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  :  9.29 %
    Favored  : 88.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.23), residues: 1320
  helix:  0.34 (0.20), residues: 658
  sheet: -0.74 (0.43), residues: 125
  loop : -0.06 (0.28), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1802 
 TYR   0.026   0.002   TYR D 655 
 PHE   0.021   0.002   PHE D 658 
 TRP   0.032   0.002   TRP A1265 
 HIS   0.005   0.001   HIS E 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (11020)
  covalent geometry    : angle       0.65463 (14902)
  hydrogen bonds       : bond        0.04694 (  501)
  hydrogen bonds       : angle       5.00992 ( 1446)

*********************** 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
  186 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 158
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1305 PHE cc_start: 0.8191 (m-80) cc_final: 0.7671 (m-80)
REVERT: A 1341 TYR cc_start: 0.8050 (t80) cc_final: 0.7802 (t80)
REVERT: A 1453 PHE cc_start: 0.7604 (t80) cc_final: 0.7038 (t80)
REVERT: A 1528 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.7237 (m-30)
REVERT: A 1530 MET cc_start: 0.5747 (mmm) cc_final: 0.5250 (mmm)
REVERT: A 1545 LYS cc_start: 0.7891 (tttt) cc_final: 0.7582 (mptt)
REVERT: A 1597 MET cc_start: 0.6227 (pmm) cc_final: 0.5823 (mpp)
REVERT: A 1729 LEU cc_start: 0.9091 (mp) cc_final: 0.8829 (mt)
REVERT: A 2054 LYS cc_start: 0.8561 (ttpt) cc_final: 0.8348 (ttmt)
REVERT: A 2080 MET cc_start: 0.6533 (ttt) cc_final: 0.6232 (ttt)
REVERT: D  472 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7816 (mmm)
REVERT: D  565 LYS cc_start: 0.9074 (pttt) cc_final: 0.8870 (ptpp)
REVERT: D  568 MET cc_start: 0.9115 (mtp) cc_final: 0.8832 (mtt)
REVERT: D  570 ARG cc_start: 0.8351 (mmm160) cc_final: 0.7938 (mmm160)
REVERT: D  795 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7880 (mp10)
REVERT: E   23 ARG cc_start: 0.7098 (mmt180) cc_final: 0.6815 (mmp80)
REVERT: E  145 MET cc_start: 0.8212 (mpp) cc_final: 0.7756 (mpp)
REVERT: F   34 ASP cc_start: 0.7688 (t0) cc_final: 0.7310 (t0)
REVERT: F   35 PHE cc_start: 0.6179 (m-10) cc_final: 0.5957 (m-80)
REVERT: F  105 MET cc_start: 0.8651 (mmm) cc_final: 0.7961 (mmm)
REVERT: F  106 THR cc_start: 0.8788 (m) cc_final: 0.8259 (p)
  outliers start: 28
  outliers final: 15
  residues processed: 173
  average time/residue: 0.0998
  time to fit residues: 24.2228
Evaluate side-chains
  160 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 142
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
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 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 A residue 1990 VAL
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 E residue  108 THR
Chi-restraints excluded: chain F residue   19 GLU
Chi-restraints excluded: chain F residue   69 THR
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 12 optimal weight:    5.9990
   chunk 99 optimal weight:    1.9990
   chunk 124 optimal weight:    0.0470
   chunk 78 optimal weight:   30.0000
   chunk 56 optimal weight:    5.9990
   chunk 32 optimal weight:    9.9990
   chunk 71 optimal weight:    6.9990
   chunk 102 optimal weight:    0.0050
   chunk 22 optimal weight:    4.9990
   chunk 67 optimal weight:   40.0000
   chunk 96 optimal weight:    1.9990
   overall best weight:    1.8098

-------------------------------------------------------------------------------
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**
A1502 GLN
A1550 ASN
A1567 ASN
A1995 ASN
A2024 HIS
** D 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.166534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.114066 restraints weight = 21147.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.117348 restraints weight = 11695.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.119425 restraints weight = 8410.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.120783 restraints weight = 6994.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.121358 restraints weight = 6318.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.3664

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= 0.233
  Angle     :  0.708  10.966  14902  Z= 0.360
  Chirality :  0.045   0.282   1670
  Planarity :  0.005   0.051   1909
  Dihedral  :  5.368  27.470   1473
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 12.13 %
    Favored  : 85.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.23), residues: 1320
  helix:  0.32 (0.20), residues: 659
  sheet: -0.68 (0.42), residues: 129
  loop : -0.07 (0.29), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1319 
 TYR   0.018   0.002   TYR A1507 
 PHE   0.037   0.003   PHE D 744 
 TRP   0.039   0.003   TRP A1265 
 HIS   0.007   0.001   HIS E 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00550 (11020)
  covalent geometry    : angle       0.70817 (14902)
  hydrogen bonds       : bond        0.04823 (  501)
  hydrogen bonds       : angle       5.14243 ( 1446)

*********************** 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
  183 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 153
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1341 TYR cc_start: 0.8048 (t80) cc_final: 0.7789 (t80)
REVERT: A 1453 PHE cc_start: 0.7313 (t80) cc_final: 0.6748 (t80)
REVERT: A 1528 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7123 (m-30)
REVERT: A 1560 SER cc_start: 0.7284 (t) cc_final: 0.6817 (m)
REVERT: A 2080 MET cc_start: 0.6702 (ttt) cc_final: 0.6412 (ttt)
REVERT: D  472 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.7857 (mmm)
REVERT: D  568 MET cc_start: 0.9145 (mtp) cc_final: 0.8886 (mtt)
REVERT: D  570 ARG cc_start: 0.8309 (mmm160) cc_final: 0.7918 (mmm160)
REVERT: D  795 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7686 (mp10)
REVERT: D  852 GLN cc_start: 0.5583 (mm-40) cc_final: 0.5301 (mm110)
REVERT: E   23 ARG cc_start: 0.7048 (mmt180) cc_final: 0.6814 (mmp80)
REVERT: F   19 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7110 (mp0)
REVERT: F   34 ASP cc_start: 0.7401 (t0) cc_final: 0.7127 (t0)
REVERT: F  105 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8433 (mmm)
REVERT: F  106 THR cc_start: 0.8858 (m) cc_final: 0.8379 (p)
  outliers start: 30
  outliers final: 13
  residues processed: 170
  average time/residue: 0.1090
  time to fit residues: 26.0951
Evaluate side-chains
  156 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 138
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
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 2003 MET
Chi-restraints excluded: chain D residue  472 MET
Chi-restraints excluded: chain D residue  489 HIS
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 E residue  108 THR
Chi-restraints excluded: chain F residue   19 GLU
Chi-restraints excluded: chain F residue  104 SER
Chi-restraints excluded: chain F residue  105 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 109 optimal weight:    0.5980
   chunk 123 optimal weight:    3.9990
   chunk 48 optimal weight:    0.5980
   chunk 37 optimal weight:    0.4980
   chunk 72 optimal weight:    5.9990
   chunk 82 optimal weight:    0.7980
   chunk 58 optimal weight:    0.5980
   chunk 111 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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**
D 712 HIS
** D 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 822 HIS

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 = 0.174593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.129482 restraints weight = 21300.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.131361 restraints weight = 14272.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.130040 restraints weight = 10146.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.130472 restraints weight = 11630.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.130838 restraints weight = 9928.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.4072

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= 0.135
  Angle     :  0.643  11.102  14902  Z= 0.324
  Chirality :  0.042   0.261   1670
  Planarity :  0.004   0.035   1909
  Dihedral  :  5.008  23.472   1473
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 13.56 %
    Favored  : 84.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.23), residues: 1320
  helix:  0.46 (0.20), residues: 665
  sheet: -0.48 (0.43), residues: 126
  loop : -0.04 (0.29), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 662 
 TYR   0.013   0.001   TYR D 634 
 PHE   0.017   0.002   PHE D 744 
 TRP   0.042   0.002   TRP A1265 
 HIS   0.007   0.001   HIS E 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (11020)
  covalent geometry    : angle       0.64300 (14902)
  hydrogen bonds       : bond        0.04160 (  501)
  hydrogen bonds       : angle       4.83826 ( 1446)

*********************** 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
  177 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 150
  time to evaluate  : 0.440 
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: 0.7466 (t80) cc_final: 0.6862 (t80)
REVERT: A 1560 SER cc_start: 0.7005 (t) cc_final: 0.6724 (m)
REVERT: D  472 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7621 (mmm)
REVERT: D  570 ARG cc_start: 0.8006 (mmm160) cc_final: 0.7737 (mmm160)
REVERT: D  795 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7848 (mp10)
REVERT: E  176 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7230 (mt)
REVERT: F   19 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7157 (mp0)
REVERT: F   34 ASP cc_start: 0.7509 (t0) cc_final: 0.7126 (t0)
REVERT: F  106 THR cc_start: 0.8869 (m) cc_final: 0.8472 (p)
  outliers start: 27
  outliers final: 12
  residues processed: 161
  average time/residue: 0.1087
  time to fit residues: 24.6909
Evaluate side-chains
  145 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
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 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  795 GLN
Chi-restraints excluded: chain D residue  853 LEU
Chi-restraints excluded: chain E residue  176 LEU
Chi-restraints excluded: chain F residue   19 GLU
Chi-restraints excluded: chain F residue   31 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 60 optimal weight:    6.9990
   chunk 98 optimal weight:    0.7980
   chunk 131 optimal weight:    3.9990
   chunk 80 optimal weight:    5.9990
   chunk 118 optimal weight:    6.9990
   chunk 42 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 76 optimal weight:    4.9990
   chunk 35 optimal weight:    5.9990
   chunk 86 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
A1281 ASN
** A1478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1550 ASN
** A1674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2104 ASN
D 739 ASN
** 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 = 0.4407 r_free = 0.4407 target = 0.171723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.121906 restraints weight = 21128.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.124380 restraints weight = 15260.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.124789 restraints weight = 12050.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.125192 restraints weight = 10473.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.125537 restraints weight = 10839.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.4221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080  11020  Z= 0.218
  Angle     :  0.715  13.349  14902  Z= 0.358
  Chirality :  0.044   0.225   1670
  Planarity :  0.005   0.040   1909
  Dihedral  :  5.169  27.793   1473
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 14.73 %
    Favored  : 82.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.23), residues: 1320
  helix:  0.44 (0.20), residues: 656
  sheet: -0.67 (0.43), residues: 127
  loop : -0.10 (0.29), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1509 
 TYR   0.017   0.002   TYR D 756 
 PHE   0.034   0.002   PHE D 744 
 TRP   0.027   0.002   TRP A1265 
 HIS   0.006   0.001   HIS E 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 (11020)
  covalent geometry    : angle       0.71473 (14902)
  hydrogen bonds       : bond        0.04512 (  501)
  hydrogen bonds       : angle       4.99540 ( 1446)

*********************** 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
  166 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 138
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1267 MET cc_start: 0.8180 (tpp) cc_final: 0.7918 (tpt)
REVERT: A 1453 PHE cc_start: 0.7461 (t80) cc_final: 0.6868 (t80)
REVERT: A 1560 SER cc_start: 0.7195 (t) cc_final: 0.6803 (m)
REVERT: D  472 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7658 (mmm)
REVERT: D  795 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7781 (mp10)
REVERT: D  852 GLN cc_start: 0.5910 (mm-40) cc_final: 0.5678 (mm110)
REVERT: F   19 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7077 (mp0)
REVERT: F   34 ASP cc_start: 0.7677 (t0) cc_final: 0.7259 (t0)
  outliers start: 28
  outliers final: 17
  residues processed: 154
  average time/residue: 0.1010
  time to fit residues: 22.2672
Evaluate side-chains
  153 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
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 2003 MET
Chi-restraints excluded: chain D residue  472 MET
Chi-restraints excluded: chain D residue  489 HIS
Chi-restraints excluded: chain D residue  562 MET
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 F residue   19 GLU
Chi-restraints excluded: chain F residue   82 HIS
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 10 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 67 optimal weight:    7.9990
   chunk 50 optimal weight:    0.5980
   chunk 63 optimal weight:    8.9990
   chunk 122 optimal weight:    0.0370
   chunk 23 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 102 optimal weight:    0.8980
   chunk 14 optimal weight:   10.0000
   chunk 116 optimal weight:    0.6980
   overall best weight:    0.6058

-------------------------------------------------------------------------------
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 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 822 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.174058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.130009 restraints weight = 21134.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.131204 restraints weight = 13659.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.130629 restraints weight = 10868.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.131065 restraints weight = 10705.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.131145 restraints weight = 9485.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.4470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11020  Z= 0.137
  Angle     :  0.673  13.232  14902  Z= 0.332
  Chirality :  0.041   0.240   1670
  Planarity :  0.004   0.047   1909
  Dihedral  :  4.920  24.741   1473
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 15.82 %
    Favored  : 82.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.24), residues: 1320
  helix:  0.56 (0.20), residues: 664
  sheet: -0.68 (0.44), residues: 127
  loop : -0.18 (0.29), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1454 
 TYR   0.013   0.001   TYR D 655 
 PHE   0.024   0.002   PHE A1450 
 TRP   0.053   0.003   TRP D 625 
 HIS   0.009   0.001   HIS E 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (11020)
  covalent geometry    : angle       0.67314 (14902)
  hydrogen bonds       : bond        0.04041 (  501)
  hydrogen bonds       : angle       4.86682 ( 1446)

*********************** 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
  167 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 147
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1453 PHE cc_start: 0.7292 (t80) cc_final: 0.6856 (t80)
REVERT: A 1560 SER cc_start: 0.7114 (t) cc_final: 0.6745 (m)
REVERT: A 1780 PHE cc_start: 0.7597 (p90) cc_final: 0.6989 (t80)
REVERT: D  568 MET cc_start: 0.8602 (ptp) cc_final: 0.8263 (mpp)
REVERT: D  795 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7746 (mp10)
REVERT: F   34 ASP cc_start: 0.7333 (t0) cc_final: 0.7051 (t0)
  outliers start: 20
  outliers final: 12
  residues processed: 156
  average time/residue: 0.0960
  time to fit residues: 21.3943
Evaluate side-chains
  150 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 137
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
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 1557 VAL
Chi-restraints excluded: chain A residue 1684 VAL
Chi-restraints excluded: chain D residue  489 HIS
Chi-restraints excluded: chain D residue  562 MET
Chi-restraints excluded: chain D residue  620 LEU
Chi-restraints excluded: chain D residue  795 GLN
Chi-restraints excluded: chain D residue  844 VAL
Chi-restraints excluded: chain D residue  853 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 105 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0170
   chunk 61 optimal weight:   40.0000
   chunk 109 optimal weight:    1.9990
   chunk 32 optimal weight:    8.9990
   chunk 17 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 84 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9980
   chunk 112 optimal weight:    0.7980
   overall best weight:    0.9420

-------------------------------------------------------------------------------
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 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  95 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 = 0.4427 r_free = 0.4427 target = 0.173306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.125640 restraints weight = 21128.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.127262 restraints weight = 15985.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.127555 restraints weight = 11631.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.127680 restraints weight = 11160.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.127996 restraints weight = 10005.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.4626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  11020  Z= 0.156
  Angle     :  0.681  13.233  14902  Z= 0.334
  Chirality :  0.042   0.256   1670
  Planarity :  0.004   0.036   1909
  Dihedral  :  4.878  25.728   1473
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.49 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (0.23), residues: 1320
  helix:  0.69 (0.21), residues: 656
  sheet: -0.66 (0.44), residues: 122
  loop : -0.20 (0.28), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1509 
 TYR   0.032   0.002   TYR A1447 
 PHE   0.026   0.002   PHE A1450 
 TRP   0.040   0.002   TRP D 625 
 HIS   0.008   0.001   HIS E 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (11020)
  covalent geometry    : angle       0.68135 (14902)
  hydrogen bonds       : bond        0.04057 (  501)
  hydrogen bonds       : angle       4.90599 ( 1446)

*********************** 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
  164 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 141
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1453 PHE cc_start: 0.7309 (t80) cc_final: 0.6837 (t80)
REVERT: A 1780 PHE cc_start: 0.7742 (p90) cc_final: 0.7125 (t80)
REVERT: D  568 MET cc_start: 0.8767 (ptp) cc_final: 0.8285 (mpp)
REVERT: D  795 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7749 (mp10)
REVERT: F   34 ASP cc_start: 0.7579 (t0) cc_final: 0.7173 (t0)
  outliers start: 23
  outliers final: 14
  residues processed: 151
  average time/residue: 0.1008
  time to fit residues: 21.8534
Evaluate side-chains
  150 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
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 1546 ASP
Chi-restraints excluded: chain A residue 1557 VAL
Chi-restraints excluded: chain A residue 1684 VAL
Chi-restraints excluded: chain D residue  489 HIS
Chi-restraints excluded: chain D residue  620 LEU
Chi-restraints excluded: chain D residue  795 GLN
Chi-restraints excluded: chain D residue  844 VAL
Chi-restraints excluded: chain D residue  853 LEU
Chi-restraints excluded: chain D residue  875 MET
Chi-restraints excluded: chain E residue  176 LEU
Chi-restraints excluded: chain F residue   31 ILE
Chi-restraints excluded: chain F residue   99 THR
Chi-restraints excluded: chain F residue  104 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 129 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 79 optimal weight:    7.9990
   chunk 83 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 115 optimal weight:    0.9980
   chunk 69 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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**
** D 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  95 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 = 0.4420 r_free = 0.4420 target = 0.172314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.123532 restraints weight = 21098.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.126245 restraints weight = 15306.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.126870 restraints weight = 10436.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.126794 restraints weight = 10251.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.126968 restraints weight = 10642.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.4728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  11020  Z= 0.160
  Angle     :  0.727  14.629  14902  Z= 0.352
  Chirality :  0.043   0.359   1670
  Planarity :  0.004   0.036   1909
  Dihedral  :  4.868  25.901   1473
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 16.40 %
    Favored  : 82.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.23), residues: 1320
  helix:  0.68 (0.21), residues: 656
  sheet: -0.73 (0.44), residues: 122
  loop : -0.21 (0.28), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  23 
 TYR   0.040   0.002   TYR A1501 
 PHE   0.024   0.002   PHE D 744 
 TRP   0.048   0.002   TRP D 625 
 HIS   0.007   0.001   HIS E 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (11020)
  covalent geometry    : angle       0.72743 (14902)
  hydrogen bonds       : bond        0.04102 (  501)
  hydrogen bonds       : angle       5.01569 ( 1446)

*********************** 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
  158 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1453 PHE cc_start: 0.7336 (t80) cc_final: 0.6871 (t80)
REVERT: A 1780 PHE cc_start: 0.7741 (p90) cc_final: 0.7109 (t80)
REVERT: D  495 SER cc_start: 0.9085 (m) cc_final: 0.8825 (p)
REVERT: D  568 MET cc_start: 0.8768 (ptp) cc_final: 0.8285 (mpp)
REVERT: D  795 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7738 (mp10)
REVERT: F   34 ASP cc_start: 0.7605 (t0) cc_final: 0.7179 (t0)
  outliers start: 18
  outliers final: 14
  residues processed: 148
  average time/residue: 0.0973
  time to fit residues: 21.0552
Evaluate side-chains
  149 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 134
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
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 1546 ASP
Chi-restraints excluded: chain A residue 1557 VAL
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  795 GLN
Chi-restraints excluded: chain D residue  844 VAL
Chi-restraints excluded: chain D residue  853 LEU
Chi-restraints excluded: chain D residue  875 MET
Chi-restraints excluded: chain F residue   31 ILE
Chi-restraints excluded: chain F residue   99 THR
Chi-restraints excluded: chain F residue  104 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 56 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 39 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 130 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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**
** D 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  95 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 = 0.4425 r_free = 0.4425 target = 0.172845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.126192 restraints weight = 20989.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.128450 restraints weight = 14696.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.127855 restraints weight = 10145.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.128221 restraints weight = 10586.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.128596 restraints weight = 9570.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7383
moved from start:          0.4887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11020  Z= 0.145
  Angle     :  0.736  12.969  14902  Z= 0.354
  Chirality :  0.043   0.360   1670
  Planarity :  0.004   0.041   1909
  Dihedral  :  4.807  24.491   1473
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 16.99 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.19 (0.24), residues: 1320
  helix:  0.72 (0.21), residues: 654
  sheet: -0.83 (0.43), residues: 126
  loop : -0.20 (0.28), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2056 
 TYR   0.051   0.002   TYR A1501 
 PHE   0.020   0.002   PHE A1450 
 TRP   0.062   0.002   TRP D 625 
 HIS   0.007   0.001   HIS E 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (11020)
  covalent geometry    : angle       0.73556 (14902)
  hydrogen bonds       : bond        0.04127 (  501)
  hydrogen bonds       : angle       5.01291 ( 1446)

********************** 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
  158 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 142
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1267 MET cc_start: 0.7049 (tpt) cc_final: 0.6785 (mpp)
REVERT: A 1453 PHE cc_start: 0.7331 (t80) cc_final: 0.6894 (t80)
REVERT: A 1530 MET cc_start: 0.5840 (mmm) cc_final: 0.5575 (mmm)
REVERT: A 1780 PHE cc_start: 0.7682 (p90) cc_final: 0.7156 (t80)
REVERT: D  495 SER cc_start: 0.9061 (m) cc_final: 0.8797 (p)
REVERT: D  568 MET cc_start: 0.8724 (ptp) cc_final: 0.8274 (mpp)
REVERT: D  795 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7742 (mp10)
REVERT: F   34 ASP cc_start: 0.7697 (t0) cc_final: 0.7278 (t0)
  outliers start: 16
  outliers final: 15
  residues processed: 149
  average time/residue: 0.0987
  time to fit residues: 21.2828
Evaluate side-chains
  154 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 138
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1305 PHE
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 1546 ASP
Chi-restraints excluded: chain A residue 1557 VAL
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  795 GLN
Chi-restraints excluded: chain D residue  844 VAL
Chi-restraints excluded: chain D residue  853 LEU
Chi-restraints excluded: chain D residue  875 MET
Chi-restraints excluded: chain F residue   31 ILE
Chi-restraints excluded: chain F residue   99 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 51.1398 > 50:
  distance: 18 - 22:  14.185
  distance: 22 - 23:   9.763
  distance: 23 - 24:  16.351
  distance: 23 - 26:  29.017
  distance: 24 - 25:  10.362
  distance: 24 - 31:   8.130
  distance: 26 - 27:  23.056
  distance: 27 - 28:   5.022
  distance: 28 - 29:  23.265
  distance: 28 - 30:  24.436
  distance: 31 - 32:  11.777
  distance: 31 - 37:  17.409
  distance: 32 - 33:   8.551
  distance: 32 - 35:  22.478
  distance: 33 - 34:  42.403
  distance: 33 - 38:  17.007
  distance: 35 - 36:  12.787
  distance: 36 - 37:  21.627
  distance: 38 - 39:  12.388
  distance: 39 - 40:  15.161
  distance: 39 - 42:   6.334
  distance: 40 - 41:  20.735
  distance: 40 - 46:  17.683
  distance: 42 - 43:  22.590
  distance: 43 - 44:  10.924
  distance: 44 - 45:  19.515
  distance: 46 - 47:  21.743
  distance: 47 - 48:  19.784
  distance: 47 - 50:  18.263
  distance: 48 - 49:  26.149
  distance: 48 - 58:  10.163
  distance: 50 - 51:   5.073
  distance: 51 - 52:  10.133
  distance: 51 - 53:   4.963
  distance: 52 - 54:   8.025
  distance: 53 - 55:   5.723
  distance: 54 - 56:   4.623
  distance: 55 - 56:  11.033
  distance: 56 - 57:  12.879
  distance: 58 - 59:  13.467
  distance: 59 - 60:  15.852
  distance: 59 - 62:  18.774
  distance: 60 - 61:  14.238
  distance: 60 - 66:  32.811
  distance: 62 - 63:   8.300
  distance: 63 - 64:  25.712
  distance: 63 - 65:  34.928
  distance: 66 - 67:  16.480
  distance: 66 - 72:  19.872
  distance: 67 - 68:  17.867
  distance: 67 - 70:  23.606
  distance: 68 - 69:  33.285
  distance: 68 - 73:   7.422
  distance: 70 - 71:  19.232
  distance: 71 - 72:  22.875
  distance: 73 - 74:  10.521
  distance: 74 - 75:  10.674
  distance: 74 - 77:  16.393
  distance: 75 - 76:   5.726
  distance: 75 - 81:   5.867
  distance: 77 - 78:   6.959
  distance: 78 - 79:   6.168
  distance: 78 - 80:  22.464
  distance: 81 - 82:   5.309
  distance: 82 - 83:  15.071
  distance: 82 - 85:  15.223
  distance: 83 - 84:  15.868
  distance: 83 - 88:  30.110
  distance: 84 - 109:  27.064
  distance: 85 - 86:  16.428
  distance: 85 - 87:  10.416
  distance: 88 - 89:  14.797
  distance: 89 - 90:  20.672
  distance: 89 - 92:  27.702
  distance: 90 - 91:  19.734
  distance: 90 - 96:  10.495
  distance: 91 - 117:  25.953
  distance: 92 - 93:   5.920
  distance: 93 - 94:  20.340
  distance: 93 - 95:  30.485
  distance: 96 - 97:  19.165
  distance: 97 - 98:   4.726
  distance: 97 - 100:  41.289
  distance: 98 - 99:  13.645
  distance: 98 - 101:  22.643