Starting phenix.real_space_refine
on Thu Feb 13 19:51:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wdk_32438/02_2025/7wdk_32438_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wdk_32438/02_2025/7wdk_32438.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wdk_32438/02_2025/7wdk_32438.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wdk_32438/02_2025/7wdk_32438.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wdk_32438/02_2025/7wdk_32438_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wdk_32438/02_2025/7wdk_32438_neut.cif"
  }
  resolution = 3.05
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
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      33      5.16       5
     C    5992      2.51       5
     N    1678      2.21       5
     O    1758      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9461
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6635
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 867, 6635
          Classifications: {'peptide': 867}
          Incomplete info: {'truncation_to_alanine': 46}
          Link IDs: {'PTRANS': 48, 'TRANS': 818}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 190
          Unresolved non-hydrogen angles: 228
          Unresolved non-hydrogen dihedrals: 154
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 15, 'ARG:plan': 8, 'ASP:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 127
    Chain: "B"
      Number of atoms: 2826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 348, 2826
          Classifications: {'peptide': 348}
          Link IDs: {'PTRANS': 19, 'TRANS': 328}
  Time building chain proxies: 5.59, per 1000 atoms: 0.59
  Number of scatterers: 9461
  At special positions: 0
  Unit cell: (112.224, 93.52, 84.836, 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      33     16.00
     O    1758      8.00
     N    1678      7.00
     C    5992      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  29 " - pdb=" SG  CYS B 222 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.34
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2248

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 12 sheets defined
      34.9% alpha, 16.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 56 through 71
      removed outlier: 3.705A  pdb=" N   TYR A  60 " --> pdb=" O   THR A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 105
    Processing helix  chain 'A' and resid 128 through 137
      removed outlier: 3.775A  pdb=" N   ASN A 137 " --> pdb=" O   VAL A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 164
      removed outlier: 3.847A  pdb=" N   ALA A 163 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 207
    Processing helix  chain 'A' and resid 225 through 238
      removed outlier: 3.594A  pdb=" N   LEU A 229 " --> pdb=" O   SER A 225 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   MET A 230 " --> pdb=" O   SER A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 429
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'A' and resid 475 through 496
      removed outlier: 3.518A  pdb=" N   ASP A 479 " --> pdb=" O   PRO A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 521
    Processing helix  chain 'A' and resid 575 through 590
    Processing helix  chain 'A' and resid 607 through 619
    Processing helix  chain 'A' and resid 647 through 655
    Processing helix  chain 'A' and resid 660 through 668
      removed outlier: 3.691A  pdb=" N   ARG A 666 " --> pdb=" O   ASP A 662 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ILE A 667 " --> pdb=" O   PHE A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 669 through 676
    Processing helix  chain 'A' and resid 682 through 692
    Processing helix  chain 'A' and resid 694 through 712
      removed outlier: 3.872A  pdb=" N   LYS A 702 " --> pdb=" O   ARG A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 730 through 746
    Processing helix  chain 'A' and resid 765 through 780
    Processing helix  chain 'A' and resid 785 through 799
    Processing helix  chain 'A' and resid 804 through 812
      removed outlier: 4.078A  pdb=" N   ARG A 809 " --> pdb=" O   PRO A 805 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   GLU A 810 " --> pdb=" O   ALA A 806 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 821 through 826
    Processing helix  chain 'A' and resid 874 through 879
    Processing helix  chain 'A' and resid 910 through 924
    Processing helix  chain 'A' and resid 937 through 941
    Processing helix  chain 'A' and resid 942 through 946
      removed outlier: 4.134A  pdb=" N   SER A 945 " --> pdb=" O   ALA A 942 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 949 through 971
      removed outlier: 4.003A  pdb=" N   TRP A 953 " --> pdb=" O   ALA A 949 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 988 through 992
      removed outlier: 3.557A  pdb=" N   LYS A 991 " --> pdb=" O   GLU A 988 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 54
      removed outlier: 5.373A  pdb=" N   TRP B  52 " --> pdb=" O   SER B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 126
      removed outlier: 3.694A  pdb=" N   SER B  97 " --> pdb=" O   PHE B  93 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ALA B 104 " --> pdb=" O   ILE B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 148
    Processing helix  chain 'B' and resid 149 through 153
    Processing helix  chain 'B' and resid 195 through 206
    Processing helix  chain 'B' and resid 355 through 368
      removed outlier: 3.871A  pdb=" N   VAL B 359 " --> pdb=" O   PRO B 355 " (cutoff:3.500A)
      Proline residue:  B 361  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 54
      removed outlier: 6.320A  pdb=" N   ILE A  75 " --> pdb=" O   TYR A 111 " (cutoff:3.500A)
      removed outlier: 7.794A  pdb=" N   MET A 113 " --> pdb=" O   ILE A  75 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   ILE A  77 " --> pdb=" O   MET A 113 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   VAL A 110 " --> pdb=" O   PHE A 147 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 167
      removed outlier: 3.935A  pdb=" N   LEU A 886 " --> pdb=" O   HIS A 167 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   VAL A 890 " --> pdb=" O   ALA A 866 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ALA A 866 " --> pdb=" O   VAL A 890 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   TYR A 624 " --> pdb=" O   ILE A 860 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   ILE A 623 " --> pdb=" O   TYR A 752 " (cutoff:3.500A)
      removed outlier: 8.554A  pdb=" N   VAL A 754 " --> pdb=" O   ILE A 623 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   ILE A 625 " --> pdb=" O   VAL A 754 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   VAL A 751 " --> pdb=" O   THR A 833 " (cutoff:3.500A)
      removed outlier: 8.405A  pdb=" N   LEU A 835 " --> pdb=" O   VAL A 751 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   LEU A 753 " --> pdb=" O   LEU A 835 " (cutoff:3.500A)
      removed outlier: 8.386A  pdb=" N   LEU A 837 " --> pdb=" O   LEU A 753 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ARG A 846 " --> pdb=" O   LEU A 843 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 605 through 606
      removed outlier: 4.118A  pdb=" N   SER A 573 " --> pdb=" O   GLU A 885 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   GLU A 885 " --> pdb=" O   SER A 573 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   VAL A 890 " --> pdb=" O   ALA A 866 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ALA A 866 " --> pdb=" O   VAL A 890 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   TYR A 624 " --> pdb=" O   ILE A 860 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   ILE A 623 " --> pdb=" O   TYR A 752 " (cutoff:3.500A)
      removed outlier: 8.554A  pdb=" N   VAL A 754 " --> pdb=" O   ILE A 623 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   ILE A 625 " --> pdb=" O   VAL A 754 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   VAL A 751 " --> pdb=" O   THR A 833 " (cutoff:3.500A)
      removed outlier: 8.405A  pdb=" N   LEU A 835 " --> pdb=" O   VAL A 751 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   LEU A 753 " --> pdb=" O   LEU A 835 " (cutoff:3.500A)
      removed outlier: 8.386A  pdb=" N   LEU A 837 " --> pdb=" O   LEU A 753 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 465 through 466
    Processing sheet with id=AA5, first strand: chain 'A' and resid 896 through 898
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1005 through 1007
      removed outlier: 3.550A  pdb=" N   GLN A1018 " --> pdb=" O   ALA A1006 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 27 through 30
    Processing sheet with id=AA8, first strand: chain 'B' and resid 41 through 43
      removed outlier: 3.701A  pdb=" N   ARG B 243 " --> pdb=" O   GLU B  42 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   TYR B  83 " --> pdb=" O   TYR B 186 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   TYR B 186 " --> pdb=" O   TYR B  83 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 41 through 43
      removed outlier: 3.701A  pdb=" N   ARG B 243 " --> pdb=" O   GLU B  42 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   PHE B 244 " --> pdb=" O   VAL B 250 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   VAL B 250 " --> pdb=" O   PHE B 244 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   THR B 341 " --> pdb=" O   TRP B 321 " (cutoff:3.500A)
      removed outlier: 5.774A  pdb=" N   TRP B 321 " --> pdb=" O   THR B 341 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ALA B 320 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU B 290 " --> pdb=" O   GLY B 305 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 155 through 157
      removed outlier: 4.340A  pdb=" N   ILE B 166 " --> pdb=" O   HIS B 157 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU B 167 " --> pdb=" O   PHE B 174 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 207 through 208
    Processing sheet with id=AB3, first strand: chain 'B' and resid 294 through 296

    389 hydrogen bonds defined for protein.
    1056 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.15

  Time building geometry restraints manager: 2.77 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1590
        1.31 -     1.44: 2632
        1.44 -     1.56: 5410
        1.56 -     1.69: 0
        1.69 -     1.81: 58
  Bond restraints: 9690
  Sorted by residual:
  bond pdb=" C   SER A1033 "
       pdb=" O   SER A1033 "
    ideal  model  delta    sigma   weight residual
    1.234  1.183  0.052 1.19e-02 7.06e+03 1.88e+01
  bond pdb=" N   SER A1033 "
       pdb=" CA  SER A1033 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.23e-02 6.61e+03 8.58e+00
  bond pdb=" N   THR A 986 "
       pdb=" CA  THR A 986 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.030 1.04e-02 9.25e+03 8.51e+00
  bond pdb=" N   MET B  33 "
       pdb=" CA  MET B  33 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.19e-02 7.06e+03 8.48e+00
  bond pdb=" N   LEU A 985 "
       pdb=" CA  LEU A 985 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.034 1.25e-02 6.40e+03 7.49e+00
  ... (remaining 9685 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 12491
        1.52 -     3.04: 553
        3.04 -     4.56: 91
        4.56 -     6.08: 21
        6.08 -     7.60: 8
  Bond angle restraints: 13164
  Sorted by residual:
  angle pdb=" C   SER A1033 "
        pdb=" N   ASN A1034 "
        pdb=" CA  ASN A1034 "
      ideal   model   delta    sigma   weight residual
     120.28  126.65   -6.37 1.34e+00 5.57e-01 2.26e+01
  angle pdb=" CA  SER A1033 "
        pdb=" C   SER A1033 "
        pdb=" O   SER A1033 "
      ideal   model   delta    sigma   weight residual
     121.19  116.11    5.08 1.10e+00 8.26e-01 2.13e+01
  angle pdb=" N   PRO A 989 "
        pdb=" CA  PRO A 989 "
        pdb=" C   PRO A 989 "
      ideal   model   delta    sigma   weight residual
     110.70  115.68   -4.98 1.22e+00 6.72e-01 1.67e+01
  angle pdb=" C   TYR A 125 "
        pdb=" N   ASP A 126 "
        pdb=" CA  ASP A 126 "
      ideal   model   delta    sigma   weight residual
     122.41  130.01   -7.60 2.09e+00 2.29e-01 1.32e+01
  angle pdb=" C   PRO A 989 "
        pdb=" N   PRO A 990 "
        pdb=" CA  PRO A 990 "
      ideal   model   delta    sigma   weight residual
     119.28  123.06   -3.78 1.10e+00 8.26e-01 1.18e+01
  ... (remaining 13159 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 5161
       17.81 -    35.63: 518
       35.63 -    53.44: 83
       53.44 -    71.26: 18
       71.26 -    89.07: 7
  Dihedral angle restraints: 5787
    sinusoidal: 2290
      harmonic: 3497
  Sorted by residual:
  dihedral pdb=" CA  LEU A 720 "
           pdb=" C   LEU A 720 "
           pdb=" N   GLY A 721 "
           pdb=" CA  GLY A 721 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.66  -19.34     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CA  MET A 218 "
           pdb=" C   MET A 218 "
           pdb=" N   ALA A 219 "
           pdb=" CA  ALA A 219 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.98  -19.02     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  GLU A 626 "
           pdb=" C   GLU A 626 "
           pdb=" N   ASN A 627 "
           pdb=" CA  ASN A 627 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.00  -18.00     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 5784 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1016
       0.044 -    0.089: 294
       0.089 -    0.133: 92
       0.133 -    0.177: 11
       0.177 -    0.222: 3
  Chirality restraints: 1416
  Sorted by residual:
  chirality pdb=" CA  LYS A 991 "
            pdb=" N   LYS A 991 "
            pdb=" C   LYS A 991 "
            pdb=" CB  LYS A 991 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  GLN A 984 "
            pdb=" N   GLN A 984 "
            pdb=" C   GLN A 984 "
            pdb=" CB  GLN A 984 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  CYS B 222 "
            pdb=" N   CYS B 222 "
            pdb=" C   CYS B 222 "
            pdb=" CB  CYS B 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.89e-01
  ... (remaining 1413 not shown)

  Planarity restraints: 1736
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 953 "   -0.035 2.00e-02 2.50e+03   2.68e-02 1.80e+01
        pdb=" CG  TRP A 953 "    0.072 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 953 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 953 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 953 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 953 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 953 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 953 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 953 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 953 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 924 "    0.009 2.00e-02 2.50e+03   1.75e-02 5.39e+00
        pdb=" CG  PHE A 924 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 924 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 924 "    0.012 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 924 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 924 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 924 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 261 "   -0.036 5.00e-02 4.00e+02   5.46e-02 4.76e+00
        pdb=" N   PRO B 262 "    0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO B 262 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 262 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 1733 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 875
        2.74 -     3.28: 9385
        3.28 -     3.82: 15747
        3.82 -     4.36: 18602
        4.36 -     4.90: 31671
  Nonbonded interactions: 76280
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 185 "
            pdb=" O   TYR B 225 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" NE2 GLN A 984 "
            pdb=" OE2 GLU A1021 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" OG1 THR B  63 "
            pdb=" OD2 ASP B 347 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   THR A 717 "
            pdb=" ND2 ASN A1069 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" NH1 ARG A 654 "
            pdb=" O   ASP A1065 "
     model   vdw
     2.260 3.120
  ... (remaining 76275 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.440
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.120
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6351
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      :  0.004   0.052   9690  Z= 0.273
  Angle     :  0.737   7.598  13164  Z= 0.411
  Chirality :  0.047   0.222   1416
  Planarity :  0.005   0.055   1736
  Dihedral  : 14.655  89.069   3536
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  0.41 %
    Favored  : 99.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.23), residues: 1209
  helix:  1.22 (0.26), residues: 365
  sheet: -1.19 (0.37), residues: 187
  loop : -1.70 (0.23), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.072   0.002   TRP A 953 
 HIS   0.008   0.002   HIS A 469 
 PHE   0.038   0.002   PHE A 924 
 TYR   0.014   0.002   TYR A  84 
 ARG   0.009   0.001   ARG A1008 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 0.993 
Fit side-chains
REVERT: A  227 MET cc_start: 0.4136 (tpp) cc_final: 0.3858 (ptm)
REVERT: A  982 GLN cc_start: 0.6134 (tp40) cc_final: 0.5643 (pt0)
  outliers start: 5
  outliers final: 4
  residues processed: 95
  average time/residue: 0.2873
  time to fit residues: 36.4724
Evaluate side-chains
  83 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1033 SER
Chi-restraints excluded: chain B residue   41 MET
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  145 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    7.9990
   chunk 90 optimal weight:    3.9990
   chunk 50 optimal weight:    9.9990
   chunk 31 optimal weight:    0.7980
   chunk 61 optimal weight:    4.9990
   chunk 48 optimal weight:   10.0000
   chunk 94 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 70 optimal weight:    6.9990
   chunk 108 optimal weight:    0.8980
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
A  83 ASN
A 435 GLN
** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4788 r_free = 0.4788 target = 0.271600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4612 r_free = 0.4612 target = 0.249571 restraints weight = 9638.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.4612 rms_B_bonded: 1.01
r_work: 0.4375 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.4375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6548
moved from start:          0.0811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9690  Z= 0.244
  Angle     :  0.650   7.575  13164  Z= 0.331
  Chirality :  0.045   0.144   1416
  Planarity :  0.005   0.048   1736
  Dihedral  :  5.255  49.289   1336
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  7.40 %
    Favored  : 91.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.24), residues: 1209
  helix:  1.12 (0.26), residues: 371
  sheet: -1.29 (0.36), residues: 190
  loop : -1.63 (0.23), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP A 953 
 HIS   0.007   0.002   HIS A 469 
 PHE   0.026   0.002   PHE A 924 
 TYR   0.012   0.002   TYR B 352 
 ARG   0.005   0.000   ARG A1008 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 1.543 
Fit side-chains
REVERT: A  227 MET cc_start: 0.4640 (tpp) cc_final: 0.4156 (ptm)
REVERT: A  230 MET cc_start: 0.4327 (ptt) cc_final: 0.4083 (ttp)
REVERT: A  982 GLN cc_start: 0.6407 (tp40) cc_final: 0.5753 (pt0)
REVERT: A  993 PHE cc_start: 0.5933 (OUTLIER) cc_final: 0.5275 (m-10)
  outliers start: 9
  outliers final: 7
  residues processed: 91
  average time/residue: 0.2719
  time to fit residues: 33.9135
Evaluate side-chains
  88 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  470 CYS
Chi-restraints excluded: chain A residue  767 ASN
Chi-restraints excluded: chain A residue  993 PHE
Chi-restraints excluded: chain A residue 1045 ASN
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  296 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 22 optimal weight:   20.0000
   chunk 9 optimal weight:    1.9990
   chunk 38 optimal weight:    6.9990
   chunk 50 optimal weight:    7.9990
   chunk 17 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   chunk 60 optimal weight:   10.0000
   chunk 24 optimal weight:    0.5980
   chunk 106 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 84 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  94 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4816 r_free = 0.4816 target = 0.275218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.252310 restraints weight = 9819.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.4635 rms_B_bonded: 1.10
r_work: 0.4365 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.4365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6526
moved from start:          0.1196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9690  Z= 0.154
  Angle     :  0.554   7.194  13164  Z= 0.280
  Chirality :  0.042   0.142   1416
  Planarity :  0.004   0.044   1736
  Dihedral  :  4.467  41.608   1329
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  9.76 %
    Favored  : 88.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.24), residues: 1209
  helix:  1.39 (0.27), residues: 371
  sheet: -1.32 (0.35), residues: 203
  loop : -1.55 (0.24), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 953 
 HIS   0.006   0.001   HIS A 469 
 PHE   0.021   0.001   PHE A 924 
 TYR   0.011   0.001   TYR B  83 
 ARG   0.004   0.000   ARG A1008 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.961 
Fit side-chains
REVERT: A   95 TRP cc_start: 0.6692 (t60) cc_final: 0.6473 (t60)
REVERT: A  227 MET cc_start: 0.4513 (tpp) cc_final: 0.3928 (ptm)
REVERT: A  427 MET cc_start: 0.3980 (tpp) cc_final: 0.3549 (tpp)
REVERT: A  982 GLN cc_start: 0.6395 (tp40) cc_final: 0.5703 (pt0)
REVERT: A  993 PHE cc_start: 0.5909 (OUTLIER) cc_final: 0.5310 (m-80)
REVERT: A 1023 MET cc_start: 0.8356 (mmm) cc_final: 0.7510 (mmt)
REVERT: B  340 GLN cc_start: 0.8250 (tt0) cc_final: 0.7974 (tt0)
  outliers start: 16
  outliers final: 10
  residues processed: 105
  average time/residue: 0.2627
  time to fit residues: 38.1856
Evaluate side-chains
  95 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  470 CYS
Chi-restraints excluded: chain A residue  767 ASN
Chi-restraints excluded: chain A residue  889 MET
Chi-restraints excluded: chain A residue  993 PHE
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  252 PHE
Chi-restraints excluded: chain B residue  296 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 87 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 46 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   chunk 50 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 115 optimal weight:    0.4980
   chunk 63 optimal weight:    8.9990
   chunk 85 optimal weight:    0.0970
   chunk 35 optimal weight:    8.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4824 r_free = 0.4824 target = 0.276382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4635 r_free = 0.4635 target = 0.252654 restraints weight = 9746.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.4636 rms_B_bonded: 1.11
r_work: 0.4380 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.4380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6490
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9690  Z= 0.147
  Angle     :  0.538   7.023  13164  Z= 0.271
  Chirality :  0.041   0.135   1416
  Planarity :  0.004   0.046   1736
  Dihedral  :  4.045  18.258   1326
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 13.46 %
    Favored  : 85.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.24), residues: 1209
  helix:  1.62 (0.27), residues: 371
  sheet: -1.25 (0.35), residues: 201
  loop : -1.45 (0.24), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 953 
 HIS   0.006   0.001   HIS A 469 
 PHE   0.028   0.001   PHE A 924 
 TYR   0.010   0.001   TYR B  83 
 ARG   0.006   0.000   ARG A1008 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 1.103 
Fit side-chains
REVERT: A  227 MET cc_start: 0.4537 (tpp) cc_final: 0.4283 (ptm)
REVERT: A  230 MET cc_start: 0.4321 (ptt) cc_final: 0.3631 (ttp)
REVERT: A  427 MET cc_start: 0.3940 (tpp) cc_final: 0.3510 (tpp)
REVERT: A  569 GLN cc_start: 0.6456 (tt0) cc_final: 0.6197 (tp40)
REVERT: A  650 MET cc_start: 0.8538 (tpp) cc_final: 0.8284 (tpp)
REVERT: B  340 GLN cc_start: 0.8269 (tt0) cc_final: 0.8019 (tt0)
  outliers start: 12
  outliers final: 11
  residues processed: 96
  average time/residue: 0.2739
  time to fit residues: 36.3832
Evaluate side-chains
  91 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  470 CYS
Chi-restraints excluded: chain A residue  767 ASN
Chi-restraints excluded: chain A residue  889 MET
Chi-restraints excluded: chain A residue  976 GLN
Chi-restraints excluded: chain A residue 1045 ASN
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  252 PHE
Chi-restraints excluded: chain B residue  296 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 83 optimal weight:    9.9990
   chunk 66 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   chunk 75 optimal weight:    5.9990
   chunk 29 optimal weight:    9.9990
   chunk 38 optimal weight:    9.9990
   chunk 78 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0030
   chunk 114 optimal weight:    2.9990
   chunk 48 optimal weight:    9.9990
   overall best weight:    1.5994

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

Flipped N/Q/H residues before XYZ refinement:
** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4799 r_free = 0.4799 target = 0.272916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4604 r_free = 0.4604 target = 0.248897 restraints weight = 9820.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.4604 rms_B_bonded: 1.09
r_work: 0.4359 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.4359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6566
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9690  Z= 0.206
  Angle     :  0.579   8.454  13164  Z= 0.292
  Chirality :  0.043   0.141   1416
  Planarity :  0.004   0.043   1736
  Dihedral  :  4.232  17.899   1326
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 14.90 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.24), residues: 1209
  helix:  1.52 (0.27), residues: 372
  sheet: -1.19 (0.37), residues: 193
  loop : -1.46 (0.24), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 953 
 HIS   0.006   0.001   HIS A 469 
 PHE   0.040   0.002   PHE A 924 
 TYR   0.010   0.001   TYR A 853 
 ARG   0.005   0.000   ARG A1008 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.929 
Fit side-chains
REVERT: A  153 GLN cc_start: 0.5689 (pp30) cc_final: 0.5209 (pm20)
REVERT: A  227 MET cc_start: 0.4682 (tpp) cc_final: 0.4316 (ptm)
REVERT: A  427 MET cc_start: 0.4048 (tpp) cc_final: 0.3598 (tpp)
REVERT: A  463 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7053 (tmm)
REVERT: A  468 VAL cc_start: 0.7180 (m) cc_final: 0.6786 (t)
REVERT: A  569 GLN cc_start: 0.6438 (tt0) cc_final: 0.6202 (tp40)
REVERT: A  993 PHE cc_start: 0.5884 (OUTLIER) cc_final: 0.5266 (m-10)
REVERT: B  340 GLN cc_start: 0.8291 (tt0) cc_final: 0.8081 (tt0)
  outliers start: 18
  outliers final: 13
  residues processed: 100
  average time/residue: 0.2489
  time to fit residues: 34.2475
Evaluate side-chains
  97 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  463 MET
Chi-restraints excluded: chain A residue  470 CYS
Chi-restraints excluded: chain A residue  753 LEU
Chi-restraints excluded: chain A residue  767 ASN
Chi-restraints excluded: chain A residue  889 MET
Chi-restraints excluded: chain A residue  976 GLN
Chi-restraints excluded: chain A residue  993 PHE
Chi-restraints excluded: chain A residue 1045 ASN
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  222 CYS
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  252 PHE
Chi-restraints excluded: chain B residue  296 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 117 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   chunk 118 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 77 optimal weight:    5.9990
   chunk 15 optimal weight:    6.9990
   chunk 54 optimal weight:    9.9990
   chunk 18 optimal weight:    0.1980
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 428 GLN
** A 747 HIS ** 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 = 0.4787 r_free = 0.4787 target = 0.271555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4596 r_free = 0.4596 target = 0.248275 restraints weight = 9737.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.4594 rms_B_bonded: 1.08
r_work: 0.4341 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.4341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6598
moved from start:          0.1491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9690  Z= 0.236
  Angle     :  0.620   8.904  13164  Z= 0.314
  Chirality :  0.044   0.142   1416
  Planarity :  0.004   0.044   1736
  Dihedral  :  4.428  18.935   1326
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 15.21 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.24), residues: 1209
  helix:  1.36 (0.27), residues: 372
  sheet: -1.16 (0.38), residues: 184
  loop : -1.48 (0.24), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 953 
 HIS   0.006   0.002   HIS B  94 
 PHE   0.043   0.002   PHE A 924 
 TYR   0.010   0.001   TYR A 752 
 ARG   0.008   0.000   ARG A1008 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 82
  time to evaluate  : 0.974 
Fit side-chains
REVERT: A  153 GLN cc_start: 0.5761 (pp30) cc_final: 0.5217 (pm20)
REVERT: A  227 MET cc_start: 0.4369 (tpp) cc_final: 0.4148 (ptm)
REVERT: A  427 MET cc_start: 0.4102 (tpp) cc_final: 0.3632 (tpp)
REVERT: A  463 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7140 (tmm)
REVERT: A  569 GLN cc_start: 0.6422 (tt0) cc_final: 0.6188 (tp40)
REVERT: A  993 PHE cc_start: 0.5973 (OUTLIER) cc_final: 0.5383 (m-10)
REVERT: B  204 ILE cc_start: 0.7028 (pt) cc_final: 0.6827 (tp)
  outliers start: 27
  outliers final: 18
  residues processed: 102
  average time/residue: 0.2618
  time to fit residues: 36.4489
Evaluate side-chains
  101 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 81
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  463 MET
Chi-restraints excluded: chain A residue  470 CYS
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  612 MET
Chi-restraints excluded: chain A residue  753 LEU
Chi-restraints excluded: chain A residue  767 ASN
Chi-restraints excluded: chain A residue  889 MET
Chi-restraints excluded: chain A residue  924 PHE
Chi-restraints excluded: chain A residue  976 GLN
Chi-restraints excluded: chain A residue  993 PHE
Chi-restraints excluded: chain A residue 1045 ASN
Chi-restraints excluded: chain B residue   53 GLN
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  222 CYS
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  252 PHE
Chi-restraints excluded: chain B residue  296 ILE
Chi-restraints excluded: chain B residue  360 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 109 optimal weight:    1.9990
   chunk 103 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 55 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9980
   chunk 94 optimal weight:    9.9990
   chunk 14 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 747 HIS ** 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 = 0.4806 r_free = 0.4806 target = 0.274185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4610 r_free = 0.4610 target = 0.250010 restraints weight = 9810.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.4609 rms_B_bonded: 1.12
r_work: 0.4341 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.4341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6565
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9690  Z= 0.161
  Angle     :  0.555   7.926  13164  Z= 0.281
  Chirality :  0.042   0.141   1416
  Planarity :  0.004   0.046   1736
  Dihedral  :  4.158  17.800   1326
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 16.24 %
    Favored  : 81.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.24), residues: 1209
  helix:  1.56 (0.27), residues: 372
  sheet: -1.23 (0.37), residues: 195
  loop : -1.44 (0.24), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 953 
 HIS   0.005   0.001   HIS B  94 
 PHE   0.038   0.001   PHE A 924 
 TYR   0.009   0.001   TYR A 853 
 ARG   0.009   0.000   ARG A1008 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.985 
Fit side-chains
REVERT: A  153 GLN cc_start: 0.5699 (pp30) cc_final: 0.5154 (pm20)
REVERT: A  427 MET cc_start: 0.4072 (tpp) cc_final: 0.3588 (tpp)
REVERT: A  463 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7162 (tmm)
REVERT: A  468 VAL cc_start: 0.7167 (m) cc_final: 0.6871 (t)
REVERT: A  569 GLN cc_start: 0.6422 (tt0) cc_final: 0.6185 (tp40)
REVERT: A  993 PHE cc_start: 0.5897 (OUTLIER) cc_final: 0.5290 (m-10)
REVERT: B  203 LEU cc_start: 0.7006 (tp) cc_final: 0.6379 (tt)
  outliers start: 21
  outliers final: 17
  residues processed: 105
  average time/residue: 0.2690
  time to fit residues: 38.6965
Evaluate side-chains
  105 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 1.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  463 MET
Chi-restraints excluded: chain A residue  470 CYS
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain A residue  753 LEU
Chi-restraints excluded: chain A residue  767 ASN
Chi-restraints excluded: chain A residue  889 MET
Chi-restraints excluded: chain A residue  924 PHE
Chi-restraints excluded: chain A residue  976 GLN
Chi-restraints excluded: chain A residue  993 PHE
Chi-restraints excluded: chain A residue 1045 ASN
Chi-restraints excluded: chain B residue  174 PHE
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  222 CYS
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  252 PHE
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  296 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 45 optimal weight:    7.9990
   chunk 82 optimal weight:    0.9990
   chunk 100 optimal weight:    0.0030
   chunk 90 optimal weight:    8.9990
   chunk 119 optimal weight:    0.0980
   chunk 94 optimal weight:    8.9990
   chunk 81 optimal weight:    0.0010
   chunk 92 optimal weight:    1.9990
   chunk 23 optimal weight:   20.0000
   chunk 89 optimal weight:    1.9990
   chunk 8 optimal weight:    9.9990
   overall best weight:    0.6200

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

Flipped N/Q/H residues before XYZ refinement:
** A 747 HIS ** 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 = 0.4817 r_free = 0.4817 target = 0.275594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4627 r_free = 0.4627 target = 0.251974 restraints weight = 9869.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.4627 rms_B_bonded: 1.11
r_work: 0.4374 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.4374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6512
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9690  Z= 0.152
  Angle     :  0.549   7.750  13164  Z= 0.276
  Chirality :  0.042   0.152   1416
  Planarity :  0.004   0.045   1736
  Dihedral  :  4.048  18.855   1326
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 16.86 %
    Favored  : 80.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.24), residues: 1209
  helix:  1.62 (0.27), residues: 371
  sheet: -1.26 (0.36), residues: 200
  loop : -1.41 (0.24), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 953 
 HIS   0.005   0.001   HIS A 223 
 PHE   0.035   0.001   PHE A 924 
 TYR   0.010   0.001   TYR B  83 
 ARG   0.009   0.000   ARG A1008 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 1.048 
Fit side-chains
REVERT: A  153 GLN cc_start: 0.5703 (pp30) cc_final: 0.5195 (pm20)
REVERT: A  427 MET cc_start: 0.3979 (tpp) cc_final: 0.3530 (tpp)
REVERT: A  463 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.6973 (tmm)
REVERT: A  569 GLN cc_start: 0.6297 (tt0) cc_final: 0.6078 (tp40)
REVERT: A  993 PHE cc_start: 0.5860 (OUTLIER) cc_final: 0.5204 (m-10)
  outliers start: 22
  outliers final: 19
  residues processed: 103
  average time/residue: 0.2713
  time to fit residues: 38.5994
Evaluate side-chains
  110 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 89
  time to evaluate  : 1.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  463 MET
Chi-restraints excluded: chain A residue  470 CYS
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain A residue  612 MET
Chi-restraints excluded: chain A residue  753 LEU
Chi-restraints excluded: chain A residue  767 ASN
Chi-restraints excluded: chain A residue  889 MET
Chi-restraints excluded: chain A residue  924 PHE
Chi-restraints excluded: chain A residue  976 GLN
Chi-restraints excluded: chain A residue  993 PHE
Chi-restraints excluded: chain A residue 1045 ASN
Chi-restraints excluded: chain B residue   53 GLN
Chi-restraints excluded: chain B residue  174 PHE
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  222 CYS
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  252 PHE
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  296 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 40 optimal weight:   10.0000
   chunk 32 optimal weight:    9.9990
   chunk 80 optimal weight:   10.0000
   chunk 79 optimal weight:    0.8980
   chunk 22 optimal weight:   20.0000
   chunk 74 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   chunk 50 optimal weight:    9.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    1.2784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4802 r_free = 0.4802 target = 0.273432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4601 r_free = 0.4601 target = 0.248736 restraints weight = 9821.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.4600 rms_B_bonded: 1.15
r_work: 0.4340 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.4340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6566
moved from start:          0.1779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9690  Z= 0.186
  Angle     :  0.571   8.342  13164  Z= 0.288
  Chirality :  0.043   0.144   1416
  Planarity :  0.004   0.045   1736
  Dihedral  :  4.154  19.682   1326
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.06 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.24), residues: 1209
  helix:  1.56 (0.27), residues: 371
  sheet: -1.22 (0.37), residues: 194
  loop : -1.40 (0.24), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 953 
 HIS   0.006   0.001   HIS A 223 
 PHE   0.038   0.001   PHE A 924 
 TYR   0.010   0.001   TYR A 853 
 ARG   0.010   0.000   ARG A1008 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 1.071 
Fit side-chains
REVERT: A  153 GLN cc_start: 0.5702 (pp30) cc_final: 0.5162 (pm20)
REVERT: A  427 MET cc_start: 0.4060 (tpp) cc_final: 0.3582 (tpp)
REVERT: A  463 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7020 (tmm)
REVERT: A  468 VAL cc_start: 0.7172 (m) cc_final: 0.6860 (t)
REVERT: A  569 GLN cc_start: 0.6417 (tt0) cc_final: 0.6174 (tp40)
REVERT: A  636 LYS cc_start: 0.6386 (ptpp) cc_final: 0.6109 (ptpp)
REVERT: A  993 PHE cc_start: 0.5922 (OUTLIER) cc_final: 0.5267 (m-10)
  outliers start: 21
  outliers final: 16
  residues processed: 103
  average time/residue: 0.2741
  time to fit residues: 38.6926
Evaluate side-chains
  106 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  463 MET
Chi-restraints excluded: chain A residue  470 CYS
Chi-restraints excluded: chain A residue  753 LEU
Chi-restraints excluded: chain A residue  767 ASN
Chi-restraints excluded: chain A residue  889 MET
Chi-restraints excluded: chain A residue  976 GLN
Chi-restraints excluded: chain A residue  993 PHE
Chi-restraints excluded: chain A residue 1045 ASN
Chi-restraints excluded: chain B residue   53 GLN
Chi-restraints excluded: chain B residue  174 PHE
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  222 CYS
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  252 PHE
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  296 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 30 optimal weight:   20.0000
   chunk 39 optimal weight:    0.0370
   chunk 106 optimal weight:    0.1980
   chunk 35 optimal weight:   20.0000
   chunk 3 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 97 optimal weight:    9.9990
   chunk 90 optimal weight:    6.9990
   chunk 49 optimal weight:    9.9990
   chunk 8 optimal weight:    9.9990
   overall best weight:    1.6262

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4794 r_free = 0.4794 target = 0.272806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.248374 restraints weight = 9949.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.4595 rms_B_bonded: 1.10
r_work: 0.4340 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.4340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6589
moved from start:          0.1788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9690  Z= 0.210
  Angle     :  0.596   8.643  13164  Z= 0.301
  Chirality :  0.043   0.146   1416
  Planarity :  0.004   0.047   1736
  Dihedral  :  4.300  20.474   1326
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 17.16 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.24), residues: 1209
  helix:  1.44 (0.27), residues: 372
  sheet: -1.26 (0.37), residues: 192
  loop : -1.41 (0.24), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 953 
 HIS   0.005   0.001   HIS A 223 
 PHE   0.040   0.002   PHE A 924 
 TYR   0.010   0.001   TYR A 853 
 ARG   0.010   0.000   ARG A1008 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.976 
Fit side-chains
REVERT: A  153 GLN cc_start: 0.5726 (pp30) cc_final: 0.5164 (pm20)
REVERT: A  427 MET cc_start: 0.4067 (tpp) cc_final: 0.3589 (tpp)
REVERT: A  463 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7072 (tmm)
REVERT: A  468 VAL cc_start: 0.7181 (m) cc_final: 0.6834 (t)
REVERT: A  569 GLN cc_start: 0.6395 (tt0) cc_final: 0.6150 (tp40)
REVERT: A  993 PHE cc_start: 0.5961 (OUTLIER) cc_final: 0.5306 (m-10)
REVERT: B  203 LEU cc_start: 0.7008 (tp) cc_final: 0.6380 (tt)
  outliers start: 22
  outliers final: 18
  residues processed: 103
  average time/residue: 0.2577
  time to fit residues: 36.5095
Evaluate side-chains
  103 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 83
  time to evaluate  : 1.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  463 MET
Chi-restraints excluded: chain A residue  470 CYS
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain A residue  753 LEU
Chi-restraints excluded: chain A residue  767 ASN
Chi-restraints excluded: chain A residue  889 MET
Chi-restraints excluded: chain A residue  924 PHE
Chi-restraints excluded: chain A residue  976 GLN
Chi-restraints excluded: chain A residue  993 PHE
Chi-restraints excluded: chain A residue 1045 ASN
Chi-restraints excluded: chain B residue   53 GLN
Chi-restraints excluded: chain B residue  174 PHE
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  222 CYS
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  252 PHE
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  296 ILE
Chi-restraints excluded: chain B residue  324 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 12 optimal weight:   10.0000
   chunk 89 optimal weight:    0.0870
   chunk 110 optimal weight:    5.9990
   chunk 92 optimal weight:    3.9990
   chunk 111 optimal weight:    7.9990
   chunk 2 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   chunk 13 optimal weight:    7.9990
   overall best weight:    2.0164

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

Flipped N/Q/H residues before XYZ refinement:
** A 223 HIS ** 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 = 0.4780 r_free = 0.4780 target = 0.271022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.246626 restraints weight = 9762.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.4580 rms_B_bonded: 1.07
r_work: 0.4322 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.4322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6627
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9690  Z= 0.243
  Angle     :  0.632   9.021  13164  Z= 0.318
  Chirality :  0.044   0.144   1416
  Planarity :  0.005   0.049   1736
  Dihedral  :  4.532  23.441   1326
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.27 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.24), residues: 1209
  helix:  1.25 (0.27), residues: 372
  sheet: -1.22 (0.38), residues: 181
  loop : -1.47 (0.24), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 953 
 HIS   0.006   0.002   HIS A 166 
 PHE   0.043   0.002   PHE A 924 
 TYR   0.012   0.001   TYR A  84 
 ARG   0.011   0.000   ARG A1008 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4080.79 seconds
wall clock time: 73 minutes 8.25 seconds (4388.25 seconds total)