Starting phenix.real_space_refine
on Sun Jun  8 06:24:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wdk_32438/06_2025/7wdk_32438_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wdk_32438/06_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_32438/06_2025/7wdk_32438.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wdk_32438/06_2025/7wdk_32438.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wdk_32438/06_2025/7wdk_32438_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wdk_32438/06_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 5.72, per 1000 atoms: 0.60
  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: 2.46
  Conformation dependent library (CDL) restraints added in 1.1 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: 1.12
  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: 3.20

  Time building geometry restraints manager: 2.90 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.870
  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:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.820
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.250
-------------------------------------------------------------------------------
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   9691  Z= 0.226
  Angle     :  0.737   7.598  13166  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18600 (  379)
  hydrogen bonds       : angle       6.79563 ( 1056)
  SS BOND              : bond        0.00368 (    1)
  SS BOND              : angle       0.85853 (    2)
  covalent geometry    : bond        0.00422 ( 9690)
  covalent geometry    : angle       0.73685 (13164)

*********************** 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  : 1.015 
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: 0.2806
  time to fit residues: 35.7330
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  : 0.987 
-------------------------------------------------------------------------------
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 = 0.271604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4615 r_free = 0.4615 target = 0.249852 restraints weight = 9637.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.4615 rms_B_bonded: 1.01
r_work: 0.4373 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.4373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6550
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   9691  Z= 0.164
  Angle     :  0.650   7.577  13166  Z= 0.331
  Chirality :  0.045   0.144   1416
  Planarity :  0.005   0.048   1736
  Dihedral  :  5.255  49.293   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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04880 (  379)
  hydrogen bonds       : angle       5.41779 ( 1056)
  SS BOND              : bond        0.00451 (    1)
  SS BOND              : angle       2.18068 (    2)
  covalent geometry    : bond        0.00371 ( 9690)
  covalent geometry    : angle       0.64960 (13164)

*********************** 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  : 1.023 
Fit side-chains
REVERT: A  227 MET cc_start: 0.4657 (tpp) cc_final: 0.4119 (ptm)
REVERT: A  230 MET cc_start: 0.4341 (ptt) cc_final: 0.4088 (ttp)
REVERT: A  982 GLN cc_start: 0.6393 (tp40) cc_final: 0.5743 (pt0)
REVERT: A  993 PHE cc_start: 0.5930 (OUTLIER) cc_final: 0.5274 (m-10)
  outliers start: 9
  outliers final: 7
  residues processed: 91
  average time/residue: 0.2595
  time to fit residues: 32.2119
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  : 0.966 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 38 optimal weight:    5.9990
   chunk 50 optimal weight:   10.0000
   chunk 17 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 60 optimal weight:    9.9990
   chunk 24 optimal weight:    3.9990
   chunk 106 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 84 optimal weight:    0.6980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.4815 r_free = 0.4815 target = 0.275045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.252963 restraints weight = 9828.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.4637 rms_B_bonded: 1.10
r_work: 0.4398 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.4398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6488
moved from start:          0.1169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9691  Z= 0.111
  Angle     :  0.561   7.408  13166  Z= 0.284
  Chirality :  0.042   0.140   1416
  Planarity :  0.004   0.045   1736
  Dihedral  :  4.505  42.101   1329
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  9.97 %
    Favored  : 88.39 %
  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: -0.88 (0.24), residues: 1209
  helix:  1.36 (0.26), residues: 371
  sheet: -1.33 (0.35), residues: 201
  loop : -1.56 (0.24), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 953 
 HIS   0.006   0.001   HIS A 469 
 PHE   0.022   0.001   PHE A 924 
 TYR   0.010   0.001   TYR B  83 
 ARG   0.005   0.000   ARG A1008 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03979 (  379)
  hydrogen bonds       : angle       5.06320 ( 1056)
  SS BOND              : bond        0.00348 (    1)
  SS BOND              : angle       1.14802 (    2)
  covalent geometry    : bond        0.00241 ( 9690)
  covalent geometry    : angle       0.56112 (13164)

*********************** 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
  108 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 1.067 
Fit side-chains
REVERT: A   95 TRP cc_start: 0.6682 (t60) cc_final: 0.6467 (t60)
REVERT: A  227 MET cc_start: 0.4492 (tpp) cc_final: 0.4021 (ptm)
REVERT: A  427 MET cc_start: 0.4047 (tpp) cc_final: 0.3613 (tpp)
REVERT: A  982 GLN cc_start: 0.6409 (tp40) cc_final: 0.5719 (pt0)
REVERT: A  993 PHE cc_start: 0.5869 (OUTLIER) cc_final: 0.5245 (m-80)
REVERT: A 1023 MET cc_start: 0.8387 (mmm) cc_final: 0.7550 (mmt)
REVERT: B  340 GLN cc_start: 0.8256 (tt0) cc_final: 0.7985 (tt0)
  outliers start: 16
  outliers final: 10
  residues processed: 102
  average time/residue: 0.2569
  time to fit residues: 36.0222
Evaluate side-chains
  94 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 87 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 46 optimal weight:    7.9990
   chunk 47 optimal weight:    0.4980
   chunk 50 optimal weight:    0.8980
   chunk 43 optimal weight:    5.9990
   chunk 115 optimal weight:    0.8980
   chunk 63 optimal weight:    8.9990
   chunk 85 optimal weight:    0.9990
   chunk 35 optimal weight:    6.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.4815 r_free = 0.4815 target = 0.275043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4635 r_free = 0.4635 target = 0.252598 restraints weight = 9739.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.4633 rms_B_bonded: 1.06
r_work: 0.4384 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.4384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6506
moved from start:          0.1336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9691  Z= 0.109
  Angle     :  0.555   7.571  13166  Z= 0.279
  Chirality :  0.042   0.136   1416
  Planarity :  0.004   0.045   1736
  Dihedral  :  4.163  18.501   1326
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  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: -0.76 (0.24), residues: 1209
  helix:  1.48 (0.27), residues: 372
  sheet: -1.30 (0.35), residues: 201
  loop : -1.49 (0.24), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 953 
 HIS   0.006   0.001   HIS A 469 
 PHE   0.032   0.001   PHE A 924 
 TYR   0.009   0.001   TYR B  83 
 ARG   0.006   0.000   ARG A1008 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03745 (  379)
  hydrogen bonds       : angle       4.95359 ( 1056)
  SS BOND              : bond        0.00446 (    1)
  SS BOND              : angle       1.21537 (    2)
  covalent geometry    : bond        0.00240 ( 9690)
  covalent geometry    : angle       0.55502 (13164)

*********************** 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  : 1.038 
Fit side-chains
REVERT: A  227 MET cc_start: 0.4570 (tpp) cc_final: 0.4228 (ptm)
REVERT: A  230 MET cc_start: 0.4302 (ptt) cc_final: 0.3646 (ttp)
REVERT: A  427 MET cc_start: 0.4083 (tpp) cc_final: 0.3643 (tpp)
REVERT: A  468 VAL cc_start: 0.7125 (m) cc_final: 0.6776 (t)
REVERT: A  569 GLN cc_start: 0.6371 (tt0) cc_final: 0.6133 (tp40)
REVERT: B  340 GLN cc_start: 0.8246 (tt0) cc_final: 0.8007 (tt0)
  outliers start: 12
  outliers final: 11
  residues processed: 96
  average time/residue: 0.2686
  time to fit residues: 35.2331
Evaluate side-chains
  93 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 66 optimal weight:    6.9990
   chunk 31 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 29 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9990
   chunk 78 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9990
   chunk 114 optimal weight:    2.9990
   chunk 48 optimal weight:    7.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4795 r_free = 0.4795 target = 0.272617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4599 r_free = 0.4599 target = 0.248465 restraints weight = 9804.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.4599 rms_B_bonded: 1.10
r_work: 0.4340 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.4340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6593
moved from start:          0.1414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9691  Z= 0.135
  Angle     :  0.583   8.460  13166  Z= 0.295
  Chirality :  0.043   0.140   1416
  Planarity :  0.004   0.046   1736
  Dihedral  :  4.288  18.844   1326
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  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: -0.77 (0.24), residues: 1209
  helix:  1.44 (0.27), residues: 372
  sheet: -1.25 (0.37), residues: 194
  loop : -1.48 (0.24), residues: 643

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   0.006   0.000   ARG A1008 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04085 (  379)
  hydrogen bonds       : angle       4.93780 ( 1056)
  SS BOND              : bond        0.00379 (    1)
  SS BOND              : angle       1.30316 (    2)
  covalent geometry    : bond        0.00305 ( 9690)
  covalent geometry    : angle       0.58281 (13164)

*********************** 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
  101 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.951 
Fit side-chains
REVERT: A  227 MET cc_start: 0.4554 (tpp) cc_final: 0.4177 (ptm)
REVERT: A  427 MET cc_start: 0.4087 (tpp) cc_final: 0.3626 (tpp)
REVERT: A  463 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7065 (tmm)
REVERT: A  569 GLN cc_start: 0.6481 (tt0) cc_final: 0.6232 (tp40)
REVERT: A  993 PHE cc_start: 0.5937 (OUTLIER) cc_final: 0.5320 (m-10)
REVERT: B  340 GLN cc_start: 0.8295 (tt0) cc_final: 0.8085 (tt0)
  outliers start: 18
  outliers final: 13
  residues processed: 96
  average time/residue: 0.2466
  time to fit residues: 32.7730
Evaluate side-chains
  93 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 117 optimal weight:    6.9990
   chunk 11 optimal weight:   20.0000
   chunk 118 optimal weight:    5.9990
   chunk 72 optimal weight:   10.0000
   chunk 82 optimal weight:    0.9990
   chunk 78 optimal weight:    3.9990
   chunk 77 optimal weight:    5.9990
   chunk 15 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0370
   overall best weight:    2.8066

-------------------------------------------------------------------------------
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 = 0.4766 r_free = 0.4766 target = 0.268898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.244791 restraints weight = 9741.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.4565 rms_B_bonded: 1.10
r_work: 0.4288 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.4288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6684
moved from start:          0.1516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   9691  Z= 0.198
  Angle     :  0.682   9.815  13166  Z= 0.346
  Chirality :  0.046   0.165   1416
  Planarity :  0.005   0.049   1736
  Dihedral  :  4.770  22.237   1326
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 15.83 %
    Favored  : 81.40 %
  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: -1.01 (0.24), residues: 1209
  helix:  1.12 (0.27), residues: 371
  sheet: -1.31 (0.38), residues: 183
  loop : -1.59 (0.24), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 953 
 HIS   0.008   0.002   HIS A 913 
 PHE   0.046   0.002   PHE A 924 
 TYR   0.012   0.002   TYR A 752 
 ARG   0.007   0.000   ARG A1008 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04988 (  379)
  hydrogen bonds       : angle       5.20856 ( 1056)
  SS BOND              : bond        0.00201 (    1)
  SS BOND              : angle       1.47307 (    2)
  covalent geometry    : bond        0.00462 ( 9690)
  covalent geometry    : angle       0.68146 (13164)

*********************** 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  : 0.894 
Fit side-chains
REVERT: A   99 ARG cc_start: 0.6028 (tpt170) cc_final: 0.5777 (tpt170)
REVERT: A  153 GLN cc_start: 0.5915 (pp30) cc_final: 0.5290 (pm20)
REVERT: A  427 MET cc_start: 0.4315 (tpp) cc_final: 0.3783 (tpp)
REVERT: A  463 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7226 (tmm)
REVERT: A  569 GLN cc_start: 0.6600 (tt0) cc_final: 0.6323 (tp40)
REVERT: A  993 PHE cc_start: 0.6128 (OUTLIER) cc_final: 0.5579 (m-10)
  outliers start: 27
  outliers final: 17
  residues processed: 104
  average time/residue: 0.2585
  time to fit residues: 36.7456
Evaluate side-chains
  100 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 81
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
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  568 VAL
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 109 optimal weight:    9.9990
   chunk 103 optimal weight:    0.7980
   chunk 17 optimal weight:    7.9990
   chunk 55 optimal weight:    0.5980
   chunk 80 optimal weight:    0.9980
   chunk 94 optimal weight:    9.9990
   chunk 14 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 38 optimal weight:    9.9990
   overall best weight:    1.8784

-------------------------------------------------------------------------------
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 = 0.4779 r_free = 0.4779 target = 0.270724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.246753 restraints weight = 9754.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.4580 rms_B_bonded: 1.06
r_work: 0.4324 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.4324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6625
moved from start:          0.1642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9691  Z= 0.149
  Angle     :  0.609   8.941  13166  Z= 0.309
  Chirality :  0.044   0.141   1416
  Planarity :  0.005   0.049   1736
  Dihedral  :  4.577  21.774   1326
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 16.55 %
    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: -0.98 (0.24), residues: 1209
  helix:  1.17 (0.27), residues: 371
  sheet: -1.30 (0.38), residues: 183
  loop : -1.58 (0.24), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 953 
 HIS   0.005   0.001   HIS B  94 
 PHE   0.039   0.002   PHE A 924 
 TYR   0.011   0.001   TYR A 853 
 ARG   0.009   0.000   ARG A1008 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04398 (  379)
  hydrogen bonds       : angle       5.08534 ( 1056)
  SS BOND              : bond        0.00314 (    1)
  SS BOND              : angle       1.22656 (    2)
  covalent geometry    : bond        0.00341 ( 9690)
  covalent geometry    : angle       0.60906 (13164)

*********************** 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
  113 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 87
  time to evaluate  : 0.944 
Fit side-chains
REVERT: A  153 GLN cc_start: 0.5887 (pp30) cc_final: 0.5238 (pm20)
REVERT: A  427 MET cc_start: 0.4271 (tpp) cc_final: 0.3745 (tpp)
REVERT: A  463 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7230 (tmm)
REVERT: A  569 GLN cc_start: 0.6489 (tt0) cc_final: 0.6244 (tp40)
REVERT: A  650 MET cc_start: 0.8588 (tpp) cc_final: 0.8219 (tpp)
REVERT: A  993 PHE cc_start: 0.6014 (OUTLIER) cc_final: 0.5492 (m-10)
REVERT: B  203 LEU cc_start: 0.7086 (tp) cc_final: 0.6448 (tt)
  outliers start: 26
  outliers final: 21
  residues processed: 106
  average time/residue: 0.2473
  time to fit residues: 36.0451
Evaluate side-chains
  104 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 81
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
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  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   54 ILE
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  245 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:    2.9990
   chunk 82 optimal weight:    7.9990
   chunk 100 optimal weight:    3.9990
   chunk 90 optimal weight:    7.9990
   chunk 119 optimal weight:    0.9980
   chunk 94 optimal weight:    9.9990
   chunk 81 optimal weight:    0.6980
   chunk 92 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 89 optimal weight:    0.0970
   chunk 8 optimal weight:    9.9990
   overall best weight:    0.6778

-------------------------------------------------------------------------------
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 = 0.4807 r_free = 0.4807 target = 0.274673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4629 r_free = 0.4629 target = 0.252281 restraints weight = 9859.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.4626 rms_B_bonded: 1.10
r_work: 0.4377 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.4377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6522
moved from start:          0.1781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9691  Z= 0.106
  Angle     :  0.564   7.941  13166  Z= 0.285
  Chirality :  0.042   0.155   1416
  Planarity :  0.004   0.049   1736
  Dihedral  :  4.207  19.279   1326
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 17.37 %
    Favored  : 80.27 %
  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: -0.80 (0.24), residues: 1209
  helix:  1.43 (0.27), residues: 371
  sheet: -1.30 (0.37), residues: 195
  loop : -1.49 (0.24), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 953 
 HIS   0.006   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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03609 (  379)
  hydrogen bonds       : angle       4.90851 ( 1056)
  SS BOND              : bond        0.00477 (    1)
  SS BOND              : angle       0.90161 (    2)
  covalent geometry    : bond        0.00234 ( 9690)
  covalent geometry    : angle       0.56385 (13164)

*********************** 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: 23
    poor density    : 88
  time to evaluate  : 1.005 
Fit side-chains
REVERT: A  427 MET cc_start: 0.4103 (tpp) cc_final: 0.3615 (tpp)
REVERT: A  463 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.6988 (tmm)
REVERT: A  468 VAL cc_start: 0.7125 (m) cc_final: 0.6855 (t)
REVERT: A  636 LYS cc_start: 0.6320 (ptpp) cc_final: 0.6051 (ptpp)
REVERT: A  993 PHE cc_start: 0.5902 (OUTLIER) cc_final: 0.5287 (m-10)
REVERT: B   65 GLU cc_start: 0.7975 (tp30) cc_final: 0.7751 (mm-30)
REVERT: B  203 LEU cc_start: 0.7016 (tp) cc_final: 0.6351 (tt)
REVERT: B  340 GLN cc_start: 0.8259 (tt0) cc_final: 0.8036 (tt0)
  outliers start: 23
  outliers final: 19
  residues processed: 102
  average time/residue: 0.2466
  time to fit residues: 35.1411
Evaluate side-chains
  104 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
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  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  245 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 32 optimal weight:   20.0000
   chunk 80 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9990
   chunk 22 optimal weight:   30.0000
   chunk 74 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 50 optimal weight:    6.9990
   chunk 18 optimal weight:    0.2980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4812 r_free = 0.4812 target = 0.275257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.251948 restraints weight = 9793.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.4622 rms_B_bonded: 1.10
r_work: 0.4378 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.4378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6516
moved from start:          0.1878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9691  Z= 0.104
  Angle     :  0.549   8.054  13166  Z= 0.277
  Chirality :  0.042   0.146   1416
  Planarity :  0.004   0.047   1736
  Dihedral  :  4.122  19.916   1326
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.57 %
    Favored  : 80.27 %
  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: -0.68 (0.24), residues: 1209
  helix:  1.53 (0.27), residues: 371
  sheet: -1.25 (0.37), residues: 195
  loop : -1.42 (0.24), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 953 
 HIS   0.006   0.001   HIS A 223 
 PHE   0.034   0.001   PHE A 924 
 TYR   0.010   0.001   TYR A 853 
 ARG   0.010   0.000   ARG A1008 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03520 (  379)
  hydrogen bonds       : angle       4.84533 ( 1056)
  SS BOND              : bond        0.00520 (    1)
  SS BOND              : angle       0.88039 (    2)
  covalent geometry    : bond        0.00231 ( 9690)
  covalent geometry    : angle       0.54941 (13164)

*********************** 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
  110 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 89
  time to evaluate  : 0.920 
Fit side-chains
REVERT: A  153 GLN cc_start: 0.5699 (pp30) cc_final: 0.5145 (pm20)
REVERT: A  427 MET cc_start: 0.4103 (tpp) cc_final: 0.3639 (tpp)
REVERT: A  463 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.7002 (tmm)
REVERT: A  468 VAL cc_start: 0.7140 (m) cc_final: 0.6871 (t)
REVERT: A  569 GLN cc_start: 0.6506 (tp40) cc_final: 0.6275 (tp40)
REVERT: A  993 PHE cc_start: 0.5904 (OUTLIER) cc_final: 0.5237 (m-10)
REVERT: B  203 LEU cc_start: 0.6970 (tp) cc_final: 0.6306 (tt)
REVERT: B  340 GLN cc_start: 0.8247 (tt0) cc_final: 0.7967 (tt0)
  outliers start: 21
  outliers final: 17
  residues processed: 103
  average time/residue: 0.2420
  time to fit residues: 34.6096
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  : 1.009 
-------------------------------------------------------------------------------
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  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  296 ILE
Chi-restraints excluded: chain B residue  360 LEU
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:    0.0570
   chunk 106 optimal weight:    0.4980
   chunk 35 optimal weight:   20.0000
   chunk 3 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 97 optimal weight:    8.9990
   chunk 90 optimal weight:    0.1980
   chunk 49 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.7500

-------------------------------------------------------------------------------
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 = 0.4813 r_free = 0.4813 target = 0.275465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4624 r_free = 0.4624 target = 0.251950 restraints weight = 9926.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.4624 rms_B_bonded: 1.08
r_work: 0.4367 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.4367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6531
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9691  Z= 0.105
  Angle     :  0.559   8.650  13166  Z= 0.282
  Chirality :  0.042   0.148   1416
  Planarity :  0.004   0.047   1736
  Dihedral  :  4.077  20.300   1326
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.88 %
    Favored  : 79.96 %
  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:  1.56 (0.27), residues: 370
  sheet: -1.31 (0.36), residues: 200
  loop : -1.43 (0.24), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 115 
 HIS   0.005   0.001   HIS A 223 
 PHE   0.035   0.001   PHE A 924 
 TYR   0.010   0.001   TYR A 853 
 ARG   0.010   0.000   ARG A1008 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03457 (  379)
  hydrogen bonds       : angle       4.77101 ( 1056)
  SS BOND              : bond        0.00464 (    1)
  SS BOND              : angle       0.84100 (    2)
  covalent geometry    : bond        0.00234 ( 9690)
  covalent geometry    : angle       0.55945 (13164)

********************** 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
  112 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 1.083 
Fit side-chains
REVERT: A  153 GLN cc_start: 0.5731 (pp30) cc_final: 0.5126 (pm20)
REVERT: A  421 TRP cc_start: 0.5081 (t60) cc_final: 0.4875 (t60)
REVERT: A  427 MET cc_start: 0.4022 (tpp) cc_final: 0.3539 (tpp)
REVERT: A  463 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.6988 (tmm)
REVERT: A  468 VAL cc_start: 0.7141 (m) cc_final: 0.6883 (t)
REVERT: A  993 PHE cc_start: 0.5919 (OUTLIER) cc_final: 0.5256 (m-10)
REVERT: B  203 LEU cc_start: 0.6945 (tp) cc_final: 0.6280 (tt)
REVERT: B  340 GLN cc_start: 0.8245 (tt0) cc_final: 0.7963 (tt0)
  outliers start: 21
  outliers final: 18
  residues processed: 104
  average time/residue: 0.2703
  time to fit residues: 39.9196
Evaluate side-chains
  111 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
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  252 PHE
Chi-restraints excluded: chain B residue  296 ILE
Chi-restraints excluded: chain B residue  360 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 19 optimal weight:    0.3980
   chunk 53 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 12 optimal weight:    6.9990
   chunk 89 optimal weight:    9.9990
   chunk 110 optimal weight:    0.9990
   chunk 92 optimal weight:    1.9990
   chunk 111 optimal weight:    8.9990
   chunk 2 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 13 optimal weight:   10.0000
   overall best weight:    1.2788

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
** A 223 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 = 0.4803 r_free = 0.4803 target = 0.273751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.250807 restraints weight = 9767.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.4614 rms_B_bonded: 1.07
r_work: 0.4389 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work (final): 0.4389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6531
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9691  Z= 0.123
  Angle     :  0.575   8.583  13166  Z= 0.290
  Chirality :  0.042   0.143   1416
  Planarity :  0.004   0.047   1736
  Dihedral  :  4.238  25.512   1326
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 18.19 %
    Favored  : 79.75 %
  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: -0.70 (0.24), residues: 1209
  helix:  1.48 (0.27), residues: 371
  sheet: -1.29 (0.37), residues: 193
  loop : -1.40 (0.24), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 115 
 HIS   0.006   0.001   HIS A 223 
 PHE   0.037   0.001   PHE A 924 
 TYR   0.010   0.001   TYR A 853 
 ARG   0.010   0.000   ARG A1008 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03732 (  379)
  hydrogen bonds       : angle       4.79488 ( 1056)
  SS BOND              : bond        0.00395 (    1)
  SS BOND              : angle       0.92811 (    2)
  covalent geometry    : bond        0.00280 ( 9690)
  covalent geometry    : angle       0.57465 (13164)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4276.85 seconds
wall clock time: 74 minutes 27.36 seconds (4467.36 seconds total)