Starting phenix.real_space_refine
on Wed Feb  4 02:51:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9n10_48801/02_2026/9n10_48801.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9n10_48801/02_2026/9n10_48801.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9n10_48801/02_2026/9n10_48801.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9n10_48801/02_2026/9n10_48801.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9n10_48801/02_2026/9n10_48801.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9n10_48801/02_2026/9n10_48801.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.041 sd=   1.169
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      49      5.16       5
     C    5387      2.51       5
     N    1372      2.21       5
     O    1552      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8360
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 985, 7705
          Classifications: {'peptide': 985}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 41, 'TRANS': 940}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 655
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 655
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 74}
  Time building chain proxies: 1.72, per 1000 atoms: 0.21
  Number of scatterers: 8360
  At special positions: 0
  Unit cell: (72.424, 84.769, 166.246, 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      49     16.00
     O    1552      8.00
     N    1372      7.00
     C    5387      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.44
  Conformation dependent library (CDL) restraints added in 263.9 milliseconds
  

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2008

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 5 sheets defined
      53.5% alpha, 11.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 164 through 172
    Processing helix  chain 'A' and resid 175 through 185
    Processing helix  chain 'A' and resid 186 through 189
    Processing helix  chain 'A' and resid 193 through 222
      removed outlier: 4.688A  pdb=" N   ALA A 199 " --> pdb=" O   VAL A 195 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   ILE A 200 " --> pdb=" O   GLU A 196 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ILE A 201 " --> pdb=" O   GLY A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 379
    Processing helix  chain 'A' and resid 390 through 407
    Processing helix  chain 'A' and resid 410 through 429
    Processing helix  chain 'A' and resid 435 through 444
      removed outlier: 4.002A  pdb=" N   VAL A 439 " --> pdb=" O   LYS A 435 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   GLU A 440 " --> pdb=" O   LEU A 436 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   GLY A 443 " --> pdb=" O   VAL A 439 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   CYS A 444 " --> pdb=" O   GLU A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 516
      removed outlier: 3.541A  pdb=" N   GLU A 513 " --> pdb=" O   GLU A 509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 527
    Processing helix  chain 'A' and resid 538 through 554
      removed outlier: 3.745A  pdb=" N   ASN A 554 " --> pdb=" O   ALA A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 586
      removed outlier: 3.849A  pdb=" N   VAL A 581 " --> pdb=" O   GLU A 577 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LYS A 586 " --> pdb=" O   VAL A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 603
    Processing helix  chain 'A' and resid 607 through 611
    Processing helix  chain 'A' and resid 655 through 662
      removed outlier: 5.262A  pdb=" N   LEU A 659 " --> pdb=" O   ASP A 656 " (cutoff:3.500A)
      removed outlier: 5.551A  pdb=" N   ASP A 660 " --> pdb=" O   ARG A 657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 683 through 699
      removed outlier: 3.546A  pdb=" N   LEU A 690 " --> pdb=" O   GLU A 686 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LYS A 693 " --> pdb=" O   VAL A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 723
    Processing helix  chain 'A' and resid 756 through 767
    Processing helix  chain 'A' and resid 778 through 790
    Processing helix  chain 'A' and resid 793 through 799
      removed outlier: 4.087A  pdb=" N   GLN A 798 " --> pdb=" O   LYS A 795 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 800 through 805
      removed outlier: 3.911A  pdb=" N   LEU A 805 " --> pdb=" O   ASP A 801 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 810 through 813
      removed outlier: 3.858A  pdb=" N   HIS A 813 " --> pdb=" O   SER A 810 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 810 through 813'
    Processing helix  chain 'A' and resid 824 through 832
      removed outlier: 4.439A  pdb=" N   GLU A 830 " --> pdb=" O   ASP A 826 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 842 through 844
      No H-bonds generated for 'chain 'A' and resid 842 through 844'
    Processing helix  chain 'A' and resid 845 through 857
      removed outlier: 3.693A  pdb=" N   ILE A 849 " --> pdb=" O   ASP A 845 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 869 through 876
    Processing helix  chain 'A' and resid 887 through 894
    Processing helix  chain 'A' and resid 903 through 944
      removed outlier: 3.824A  pdb=" N   VAL A 907 " --> pdb=" O   PHE A 903 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ILE A 920 " --> pdb=" O   ILE A 916 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   GLY A 933 " --> pdb=" O   GLY A 929 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   ILE A 935 " --> pdb=" O   ASN A 931 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 951 through 963
      removed outlier: 3.614A  pdb=" N   ILE A 955 " --> pdb=" O   GLU A 951 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   LEU A 956 " --> pdb=" O   ALA A 952 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 967 through 973
      removed outlier: 3.507A  pdb=" N   ARG A 972 " --> pdb=" O   ALA A 969 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLU A 973 " --> pdb=" O   LEU A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 999
    Processing helix  chain 'A' and resid 1001 through 1025
      removed outlier: 3.512A  pdb=" N   PHE A1007 " --> pdb=" O   PRO A1003 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1028 through 1035
    Processing helix  chain 'A' and resid 1107 through 1115
    Processing helix  chain 'A' and resid 1155 through 1184
      removed outlier: 3.520A  pdb=" N   ARG A1179 " --> pdb=" O   CYS A1175 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ALA A1180 " --> pdb=" O   GLU A1176 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   TYR A1181 " --> pdb=" O   MET A1177 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   THR A1182 " --> pdb=" O   LEU A1178 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   ARG A1184 " --> pdb=" O   ALA A1180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1192 through 1196
      removed outlier: 4.482A  pdb=" N   ASN A1196 " --> pdb=" O   PHE A1193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1197 through 1214
      removed outlier: 3.675A  pdb=" N   THR A1214 " --> pdb=" O   THR A1210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1216 through 1224
      removed outlier: 3.591A  pdb=" N   SER A1221 " --> pdb=" O   PRO A1217 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ILE A1222 " --> pdb=" O   GLY A1218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1229 through 1242
      removed outlier: 3.541A  pdb=" N   TRP A1239 " --> pdb=" O   LEU A1235 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ALA A1240 " --> pdb=" O   ALA A1236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1244 through 1249
      removed outlier: 3.539A  pdb=" N   GLU A1248 " --> pdb=" O   LEU A1244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1251 through 1260
    Processing helix  chain 'B' and resid 107 through 117
    Processing helix  chain 'B' and resid 120 through 131
      removed outlier: 4.311A  pdb=" N   GLY B 124 " --> pdb=" O   PHE B 120 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   CYS B 125 " --> pdb=" O   PRO B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 134
      No H-bonds generated for 'chain 'B' and resid 132 through 134'
    Processing helix  chain 'B' and resid 138 through 170
    Processing sheet with id=AA1, first strand: chain 'A' and resid 432 through 433
      removed outlier: 6.896A  pdb=" N   VAL A 860 " --> pdb=" O   ILE A 878 " (cutoff:3.500A)
      removed outlier: 7.508A  pdb=" N   VAL A 880 " --> pdb=" O   VAL A 860 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   MET A 862 " --> pdb=" O   VAL A 880 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   ASP A 451 " --> pdb=" O   THR A 863 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   ILE A 448 " --> pdb=" O   ILE A 772 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   ILE A 774 " --> pdb=" O   ILE A 448 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   SER A 450 " --> pdb=" O   ILE A 774 " (cutoff:3.500A)
      removed outlier: 8.121A  pdb=" N   TYR A 838 " --> pdb=" O   VAL A 771 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   MET A 773 " --> pdb=" O   TYR A 838 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ILE A 807 " --> pdb=" O   SER A 839 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 499 through 502
      removed outlier: 6.217A  pdb=" N   ILE A 464 " --> pdb=" O   PHE A 488 " (cutoff:3.500A)
      removed outlier: 5.651A  pdb=" N   ALA A 463 " --> pdb=" O   PHE A 750 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   PHE A 750 " --> pdb=" O   ALA A 463 " (cutoff:3.500A)
      removed outlier: 5.567A  pdb=" N   MET A 744 " --> pdb=" O   ILE A 469 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   ILE A 707 " --> pdb=" O   MET A 744 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   TYR A 746 " --> pdb=" O   LEU A 705 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   LEU A 705 " --> pdb=" O   TYR A 746 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   ALA A 748 " --> pdb=" O   ARG A 703 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ARG A 703 " --> pdb=" O   ALA A 748 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 559 through 562
      removed outlier: 3.559A  pdb=" N   THR A 559 " --> pdb=" O   HIS A 572 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 632 through 633
      removed outlier: 3.746A  pdb=" N   LYS A 673 " --> pdb=" O   THR A 669 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1036 through 1042
      removed outlier: 7.284A  pdb=" N   LYS A1037 " --> pdb=" O   TYR A1055 " (cutoff:3.500A)
      removed outlier: 9.666A  pdb=" N   TYR A1055 " --> pdb=" O   TRP A1078 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   TRP A1078 " --> pdb=" O   TYR A1055 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   TRP A1071 " --> pdb=" O   ALA A1092 " (cutoff:3.500A)
      removed outlier: 7.530A  pdb=" N   ALA A1092 " --> pdb=" O   TRP A1071 " (cutoff:3.500A)
      removed outlier: 6.113A  pdb=" N   THR A1073 " --> pdb=" O   GLY A1090 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLY A1090 " --> pdb=" O   THR A1073 " (cutoff:3.500A)
      removed outlier: 8.875A  pdb=" N   ILE B 178 " --> pdb=" O   ALA A1085 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   ASN A1087 " --> pdb=" O   ILE B 178 " (cutoff:3.500A)

    423 hydrogen bonds defined for protein.
    1203 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.19

  Time building geometry restraints manager: 0.65 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2647
        1.34 -     1.46: 1681
        1.46 -     1.58: 4133
        1.58 -     1.70: 0
        1.70 -     1.81: 72
  Bond restraints: 8533
  Sorted by residual:
  bond pdb=" C   LEU A 436 "
       pdb=" N   PRO A 437 "
    ideal  model  delta    sigma   weight residual
    1.335  1.352 -0.018 1.19e-02 7.06e+03 2.18e+00
  bond pdb=" CA  GLU A 495 "
       pdb=" CB  GLU A 495 "
    ideal  model  delta    sigma   weight residual
    1.522  1.548 -0.025 1.75e-02 3.27e+03 2.12e+00
  bond pdb=" CA  LEU A 823 "
       pdb=" CB  LEU A 823 "
    ideal  model  delta    sigma   weight residual
    1.534  1.550 -0.017 1.57e-02 4.06e+03 1.15e+00
  bond pdb=" CB  GLU A 495 "
       pdb=" CG  GLU A 495 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.08e+00
  bond pdb=" CB  GLU A1126 "
       pdb=" CG  GLU A1126 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.05e+00
  ... (remaining 8528 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 11400
        2.09 -     4.18: 151
        4.18 -     6.27: 28
        6.27 -     8.36: 7
        8.36 -    10.45: 1
  Bond angle restraints: 11587
  Sorted by residual:
  angle pdb=" N   VAL A 587 "
        pdb=" CA  VAL A 587 "
        pdb=" C   VAL A 587 "
      ideal   model   delta    sigma   weight residual
     113.10  109.04    4.06 9.70e-01 1.06e+00 1.75e+01
  angle pdb=" N   ILE A1222 "
        pdb=" CA  ILE A1222 "
        pdb=" C   ILE A1222 "
      ideal   model   delta    sigma   weight residual
     112.96  109.07    3.89 1.00e+00 1.00e+00 1.51e+01
  angle pdb=" C   GLU A 495 "
        pdb=" CA  GLU A 495 "
        pdb=" CB  GLU A 495 "
      ideal   model   delta    sigma   weight residual
     109.08  114.66   -5.58 1.49e+00 4.50e-01 1.40e+01
  angle pdb=" CA  GLN B 109 "
        pdb=" CB  GLN B 109 "
        pdb=" CG  GLN B 109 "
      ideal   model   delta    sigma   weight residual
     114.10  121.16   -7.06 2.00e+00 2.50e-01 1.25e+01
  angle pdb=" CA  GLU A 495 "
        pdb=" CB  GLU A 495 "
        pdb=" CG  GLU A 495 "
      ideal   model   delta    sigma   weight residual
     114.10  121.16   -7.06 2.00e+00 2.50e-01 1.25e+01
  ... (remaining 11582 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 4683
       17.97 -    35.95: 371
       35.95 -    53.92: 74
       53.92 -    71.90: 16
       71.90 -    89.87: 10
  Dihedral angle restraints: 5154
    sinusoidal: 2040
      harmonic: 3114
  Sorted by residual:
  dihedral pdb=" CA  ASP A 963 "
           pdb=" C   ASP A 963 "
           pdb=" N   GLY A 964 "
           pdb=" CA  GLY A 964 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.59  -18.41     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  THR A 962 "
           pdb=" C   THR A 962 "
           pdb=" N   ASP A 963 "
           pdb=" CA  ASP A 963 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.28   16.72     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CA  ASP A 777 "
           pdb=" CB  ASP A 777 "
           pdb=" CG  ASP A 777 "
           pdb=" OD1 ASP A 777 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.45   57.45     1      2.00e+01 2.50e-03 1.11e+01
  ... (remaining 5151 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 825
       0.032 -    0.065: 356
       0.065 -    0.097: 111
       0.097 -    0.129: 50
       0.129 -    0.162: 6
  Chirality restraints: 1348
  Sorted by residual:
  chirality pdb=" CA  GLN B 109 "
            pdb=" N   GLN B 109 "
            pdb=" C   GLN B 109 "
            pdb=" CB  GLN B 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.55e-01
  chirality pdb=" CB  ILE A 789 "
            pdb=" CA  ILE A 789 "
            pdb=" CG1 ILE A 789 "
            pdb=" CG2 ILE A 789 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.37e-01
  chirality pdb=" CA  THR A 962 "
            pdb=" N   THR A 962 "
            pdb=" C   THR A 962 "
            pdb=" CB  THR A 962 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.14 2.00e-01 2.50e+01 5.24e-01
  ... (remaining 1345 not shown)

  Planarity restraints: 1458
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 937 "   -0.015 2.00e-02 2.50e+03   1.17e-02 2.75e+00
        pdb=" CG  TYR A 937 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 937 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 937 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 937 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 937 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 937 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 937 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A1250 "    0.027 5.00e-02 4.00e+02   4.10e-02 2.69e+00
        pdb=" N   PRO A1251 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A1251 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A1251 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 742 "    0.026 5.00e-02 4.00e+02   3.99e-02 2.55e+00
        pdb=" N   PRO A 743 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 743 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 743 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1455 not shown)

  Histogram of nonbonded interaction distances:
        2.52 -     3.00: 4470
        3.00 -     3.47: 9016
        3.47 -     3.95: 13667
        3.95 -     4.42: 15807
        4.42 -     4.90: 25092
  Nonbonded interactions: 68052
  Sorted by model distance:
  nonbonded pdb=" N   ASP A 865 "
            pdb=" OD1 ASP A 865 "
     model   vdw
     2.523 3.120
  nonbonded pdb=" O   LEU A 958 "
            pdb=" OG1 THR A 962 "
     model   vdw
     2.541 3.040
  nonbonded pdb=" O   ASN A 868 "
            pdb=" OD1 ASN A 868 "
     model   vdw
     2.542 3.040
  nonbonded pdb=" N   GLU A1126 "
            pdb=" OE1 GLU A1126 "
     model   vdw
     2.555 3.120
  nonbonded pdb=" C   SER A1213 "
            pdb=" OG  SER A1213 "
     model   vdw
     2.583 2.616
  ... (remaining 68047 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.770
  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:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.480
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8533  Z= 0.151
  Angle     :  0.659  10.452  11587  Z= 0.369
  Chirality :  0.043   0.162   1348
  Planarity :  0.004   0.041   1458
  Dihedral  : 14.211  89.874   3146
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 11.24 %
    Favored  : 87.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.26), residues: 1058
  helix:  1.00 (0.24), residues: 489
  sheet:  0.13 (0.45), residues: 126
  loop :  0.00 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1179 
 TYR   0.029   0.001   TYR A 937 
 PHE   0.010   0.001   PHE A 948 
 TRP   0.009   0.001   TRP A1089 
 HIS   0.006   0.001   HIS A1004 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 8533)
  covalent geometry    : angle       0.65899 (11587)
  hydrogen bonds       : bond        0.15132 (  423)
  hydrogen bonds       : angle       6.42907 ( 1203)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 160
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 MET cc_start: 0.8119 (mmt) cc_final: 0.7905 (mmt)
REVERT: A  428 LYS cc_start: 0.8584 (tttp) cc_final: 0.8092 (ttmm)
REVERT: A  692 LYS cc_start: 0.8107 (pttm) cc_final: 0.7850 (pttm)
REVERT: A 1078 TRP cc_start: 0.8907 (t-100) cc_final: 0.8283 (t-100)
REVERT: A 1181 TYR cc_start: 0.9125 (m-80) cc_final: 0.8523 (m-80)
REVERT: A 1235 LEU cc_start: 0.8934 (tp) cc_final: 0.8636 (tt)
REVERT: B  143 TYR cc_start: 0.7949 (OUTLIER) cc_final: 0.7513 (t80)
  outliers start: 8
  outliers final: 3
  residues processed: 164
  average time/residue: 0.0716
  time to fit residues: 16.3178
Evaluate side-chains
  147 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 143
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  703 ARG
Chi-restraints excluded: chain A residue 1213 SER
Chi-restraints excluded: chain B residue  143 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.3980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    0.2980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    1.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 480 ASN
A 815 ASN
A1243 ASN
** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 GLN ** 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 = 0.4289 r_free = 0.4289 target = 0.211491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.153650 restraints weight = 9689.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.151298 restraints weight = 13063.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.154274 restraints weight = 11833.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.153849 restraints weight = 7160.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.155012 restraints weight = 6491.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.1203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8533  Z= 0.137
  Angle     :  0.579   9.253  11587  Z= 0.295
  Chirality :  0.043   0.149   1348
  Planarity :  0.004   0.055   1458
  Dihedral  :  5.513  82.930   1149
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 12.85 %
    Favored  : 85.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.27), residues: 1058
  helix:  1.27 (0.24), residues: 499
  sheet:  0.37 (0.47), residues: 120
  loop :  0.00 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1179 
 TYR   0.026   0.001   TYR A 937 
 PHE   0.016   0.001   PHE A 948 
 TRP   0.007   0.001   TRP A1078 
 HIS   0.006   0.001   HIS A1004 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8533)
  covalent geometry    : angle       0.57927 (11587)
  hydrogen bonds       : bond        0.03930 (  423)
  hydrogen bonds       : angle       4.88873 ( 1203)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 157
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 MET cc_start: 0.8098 (mmt) cc_final: 0.7883 (mmt)
REVERT: A  220 ASP cc_start: 0.5880 (t0) cc_final: 0.5637 (t0)
REVERT: A  428 LYS cc_start: 0.8637 (tttp) cc_final: 0.8098 (ttmm)
REVERT: A  486 PHE cc_start: 0.8252 (m-80) cc_final: 0.8041 (m-80)
REVERT: A  488 PHE cc_start: 0.8025 (m-80) cc_final: 0.7711 (m-80)
REVERT: A  688 ASN cc_start: 0.8979 (t0) cc_final: 0.8734 (t0)
REVERT: A  692 LYS cc_start: 0.8489 (pttm) cc_final: 0.8161 (pttm)
REVERT: A  900 ASP cc_start: 0.8266 (t0) cc_final: 0.7940 (t0)
REVERT: A 1051 HIS cc_start: 0.7408 (m170) cc_final: 0.7154 (m170)
REVERT: A 1078 TRP cc_start: 0.8941 (t-100) cc_final: 0.8379 (t-100)
REVERT: A 1107 HIS cc_start: 0.8518 (t-90) cc_final: 0.8216 (t-90)
REVERT: A 1136 LYS cc_start: 0.8015 (mmtm) cc_final: 0.7624 (mmtt)
REVERT: A 1181 TYR cc_start: 0.9205 (m-80) cc_final: 0.8586 (m-80)
REVERT: A 1203 CYS cc_start: 0.7387 (OUTLIER) cc_final: 0.7111 (t)
REVERT: B  143 TYR cc_start: 0.7971 (OUTLIER) cc_final: 0.7582 (t80)
  outliers start: 14
  outliers final: 8
  residues processed: 166
  average time/residue: 0.0683
  time to fit residues: 16.2200
Evaluate side-chains
  156 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 146
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  948 PHE
Chi-restraints excluded: chain A residue 1084 GLU
Chi-restraints excluded: chain A residue 1183 VAL
Chi-restraints excluded: chain A residue 1194 ASN
Chi-restraints excluded: chain A residue 1203 CYS
Chi-restraints excluded: chain A residue 1234 LEU
Chi-restraints excluded: chain B residue  115 ILE
Chi-restraints excluded: chain B residue  143 TYR
Chi-restraints excluded: chain B residue  159 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 40 optimal weight:   20.0000
   chunk 11 optimal weight:    0.0770
   chunk 12 optimal weight:    0.8980
   chunk 98 optimal weight:    7.9990
   chunk 19 optimal weight:    5.9990
   chunk 82 optimal weight:    2.9990
   chunk 28 optimal weight:    9.9990
   chunk 63 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.7742

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

Flipped N/Q/H residues before XYZ refinement:
A1115 GLN
** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.210419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.149958 restraints weight = 9591.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.143673 restraints weight = 12544.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.146739 restraints weight = 11385.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.147575 restraints weight = 6592.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.148330 restraints weight = 5883.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.1436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8533  Z= 0.148
  Angle     :  0.562  10.340  11587  Z= 0.283
  Chirality :  0.043   0.153   1348
  Planarity :  0.004   0.045   1458
  Dihedral  :  5.094  80.558   1143
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.35 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.27), residues: 1058
  helix:  1.38 (0.24), residues: 500
  sheet:  0.66 (0.49), residues: 108
  loop :  0.05 (0.31), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1179 
 TYR   0.025   0.001   TYR A 937 
 PHE   0.012   0.001   PHE A 948 
 TRP   0.006   0.001   TRP A 678 
 HIS   0.006   0.001   HIS A 647 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 8533)
  covalent geometry    : angle       0.56225 (11587)
  hydrogen bonds       : bond        0.03712 (  423)
  hydrogen bonds       : angle       4.65863 ( 1203)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 151
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 MET cc_start: 0.7979 (mmt) cc_final: 0.7748 (mmt)
REVERT: A  428 LYS cc_start: 0.8630 (tttp) cc_final: 0.8096 (ttmm)
REVERT: A  688 ASN cc_start: 0.9174 (t0) cc_final: 0.8688 (t0)
REVERT: A  692 LYS cc_start: 0.8629 (pttm) cc_final: 0.7953 (pttm)
REVERT: A  900 ASP cc_start: 0.8267 (t0) cc_final: 0.7968 (t0)
REVERT: A 1051 HIS cc_start: 0.7523 (m170) cc_final: 0.7270 (m170)
REVERT: A 1058 SER cc_start: 0.9465 (t) cc_final: 0.9009 (p)
REVERT: A 1078 TRP cc_start: 0.8941 (t-100) cc_final: 0.8394 (t-100)
REVERT: A 1107 HIS cc_start: 0.8507 (t-90) cc_final: 0.8212 (t-90)
REVERT: A 1136 LYS cc_start: 0.8025 (mmtm) cc_final: 0.7607 (mmtt)
REVERT: A 1177 MET cc_start: 0.8692 (tmm) cc_final: 0.8462 (tmm)
REVERT: A 1181 TYR cc_start: 0.9224 (m-80) cc_final: 0.8738 (m-80)
REVERT: A 1203 CYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7214 (t)
REVERT: B  143 TYR cc_start: 0.8038 (OUTLIER) cc_final: 0.7682 (t80)
  outliers start: 20
  outliers final: 11
  residues processed: 162
  average time/residue: 0.0765
  time to fit residues: 17.1915
Evaluate side-chains
  156 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 143
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue 1084 GLU
Chi-restraints excluded: chain A residue 1183 VAL
Chi-restraints excluded: chain A residue 1194 ASN
Chi-restraints excluded: chain A residue 1203 CYS
Chi-restraints excluded: chain A residue 1213 SER
Chi-restraints excluded: chain A residue 1234 LEU
Chi-restraints excluded: chain A residue 1246 LEU
Chi-restraints excluded: chain B residue  143 TYR
Chi-restraints excluded: chain B residue  159 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 90 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   chunk 42 optimal weight:    0.7980
   chunk 12 optimal weight:    0.5980
   chunk 26 optimal weight:    5.9990
   chunk 79 optimal weight:    0.4980
   chunk 97 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 19 optimal weight:   20.0000
   chunk 38 optimal weight:   10.0000
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.209716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.151354 restraints weight = 9686.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.148201 restraints weight = 13220.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.151199 restraints weight = 12396.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.151575 restraints weight = 7113.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.152632 restraints weight = 6610.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8533  Z= 0.138
  Angle     :  0.549  10.696  11587  Z= 0.276
  Chirality :  0.042   0.150   1348
  Planarity :  0.003   0.045   1458
  Dihedral  :  5.077  83.483   1143
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.95 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.27), residues: 1058
  helix:  1.53 (0.24), residues: 497
  sheet:  1.10 (0.55), residues: 91
  loop : -0.07 (0.30), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1179 
 TYR   0.025   0.001   TYR A 937 
 PHE   0.015   0.001   PHE A 169 
 TRP   0.006   0.001   TRP A 678 
 HIS   0.006   0.001   HIS A1004 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 8533)
  covalent geometry    : angle       0.54946 (11587)
  hydrogen bonds       : bond        0.03476 (  423)
  hydrogen bonds       : angle       4.46360 ( 1203)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 149
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 MET cc_start: 0.8010 (mmt) cc_final: 0.7786 (mmt)
REVERT: A  428 LYS cc_start: 0.8637 (tttp) cc_final: 0.8094 (ttmm)
REVERT: A  900 ASP cc_start: 0.8299 (t0) cc_final: 0.7998 (t0)
REVERT: A 1051 HIS cc_start: 0.7425 (m170) cc_final: 0.7197 (m170)
REVERT: A 1058 SER cc_start: 0.9490 (t) cc_final: 0.9027 (p)
REVERT: A 1078 TRP cc_start: 0.8932 (t-100) cc_final: 0.8432 (t-100)
REVERT: A 1107 HIS cc_start: 0.8488 (t-90) cc_final: 0.8171 (t-90)
REVERT: A 1177 MET cc_start: 0.8635 (tmm) cc_final: 0.8316 (tmm)
REVERT: A 1181 TYR cc_start: 0.9257 (m-80) cc_final: 0.8745 (m-80)
REVERT: A 1203 CYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7206 (t)
REVERT: B  143 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.7752 (t80)
  outliers start: 21
  outliers final: 11
  residues processed: 162
  average time/residue: 0.0736
  time to fit residues: 16.6705
Evaluate side-chains
  156 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 143
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  979 ASN
Chi-restraints excluded: chain A residue 1122 LEU
Chi-restraints excluded: chain A residue 1183 VAL
Chi-restraints excluded: chain A residue 1194 ASN
Chi-restraints excluded: chain A residue 1203 CYS
Chi-restraints excluded: chain A residue 1205 ILE
Chi-restraints excluded: chain A residue 1234 LEU
Chi-restraints excluded: chain A residue 1246 LEU
Chi-restraints excluded: chain B residue  143 TYR
Chi-restraints excluded: chain B residue  159 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 29 optimal weight:    9.9990
   chunk 51 optimal weight:    0.0040
   chunk 44 optimal weight:    8.9990
   chunk 91 optimal weight:    2.9990
   chunk 101 optimal weight:    0.1980
   chunk 99 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 84 optimal weight:    6.9990
   chunk 52 optimal weight:    0.0870
   chunk 71 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.4370

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

Flipped N/Q/H residues before XYZ refinement:
** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.211908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.154297 restraints weight = 9619.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.150065 restraints weight = 12996.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.153208 restraints weight = 10706.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.153182 restraints weight = 6504.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.154212 restraints weight = 6069.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.1896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8533  Z= 0.114
  Angle     :  0.552  10.757  11587  Z= 0.275
  Chirality :  0.042   0.141   1348
  Planarity :  0.003   0.047   1458
  Dihedral  :  4.959  81.927   1143
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.24 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.27), residues: 1058
  helix:  1.61 (0.24), residues: 501
  sheet:  1.14 (0.55), residues: 91
  loop : -0.06 (0.30), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1179 
 TYR   0.024   0.001   TYR A 937 
 PHE   0.010   0.001   PHE A 917 
 TRP   0.006   0.001   TRP A1078 
 HIS   0.006   0.001   HIS A 647 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8533)
  covalent geometry    : angle       0.55232 (11587)
  hydrogen bonds       : bond        0.03279 (  423)
  hydrogen bonds       : angle       4.33439 ( 1203)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 147
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  428 LYS cc_start: 0.8638 (tttp) cc_final: 0.8084 (ttmm)
REVERT: A  556 TYR cc_start: 0.7716 (p90) cc_final: 0.7413 (p90)
REVERT: A  692 LYS cc_start: 0.8483 (pttm) cc_final: 0.8211 (pttm)
REVERT: A  900 ASP cc_start: 0.8268 (t0) cc_final: 0.7989 (t0)
REVERT: A 1051 HIS cc_start: 0.7492 (m170) cc_final: 0.7244 (m170)
REVERT: A 1058 SER cc_start: 0.9505 (t) cc_final: 0.9000 (p)
REVERT: A 1078 TRP cc_start: 0.8875 (t-100) cc_final: 0.8388 (t-100)
REVERT: A 1107 HIS cc_start: 0.8523 (t-90) cc_final: 0.8152 (t-90)
REVERT: A 1177 MET cc_start: 0.8483 (tmm) cc_final: 0.8282 (tmm)
REVERT: A 1181 TYR cc_start: 0.9267 (m-80) cc_final: 0.8766 (m-80)
REVERT: A 1203 CYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7194 (t)
REVERT: A 1260 MET cc_start: 0.8029 (mmt) cc_final: 0.7727 (mmt)
REVERT: B  143 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.7781 (t80)
  outliers start: 17
  outliers final: 8
  residues processed: 156
  average time/residue: 0.0795
  time to fit residues: 17.2250
Evaluate side-chains
  151 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 141
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  707 ILE
Chi-restraints excluded: chain A residue 1194 ASN
Chi-restraints excluded: chain A residue 1203 CYS
Chi-restraints excluded: chain A residue 1213 SER
Chi-restraints excluded: chain A residue 1234 LEU
Chi-restraints excluded: chain A residue 1246 LEU
Chi-restraints excluded: chain B residue  143 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 95 optimal weight:    0.5980
   chunk 19 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 81 optimal weight:    0.0370
   chunk 3 optimal weight:    0.6980
   chunk 32 optimal weight:    9.9990
   chunk 40 optimal weight:    2.9990
   chunk 38 optimal weight:    6.9990
   chunk 78 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0470
   overall best weight:    0.4356

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

Flipped N/Q/H residues before XYZ refinement:
** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.211932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.153083 restraints weight = 9587.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.147685 restraints weight = 13135.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.150849 restraints weight = 11250.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.151347 restraints weight = 6565.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.151943 restraints weight = 6086.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8533  Z= 0.114
  Angle     :  0.554  10.794  11587  Z= 0.274
  Chirality :  0.042   0.144   1348
  Planarity :  0.003   0.047   1458
  Dihedral  :  4.903  80.265   1143
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.88 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.27), residues: 1058
  helix:  1.60 (0.24), residues: 507
  sheet:  1.13 (0.53), residues: 98
  loop : -0.00 (0.31), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1179 
 TYR   0.024   0.001   TYR A 937 
 PHE   0.010   0.001   PHE A 917 
 TRP   0.006   0.001   TRP A 678 
 HIS   0.005   0.001   HIS A1004 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 8533)
  covalent geometry    : angle       0.55391 (11587)
  hydrogen bonds       : bond        0.03217 (  423)
  hydrogen bonds       : angle       4.26331 ( 1203)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 139
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  428 LYS cc_start: 0.8638 (tttp) cc_final: 0.8096 (ttmm)
REVERT: A  556 TYR cc_start: 0.7700 (p90) cc_final: 0.7418 (p90)
REVERT: A  692 LYS cc_start: 0.8461 (pttm) cc_final: 0.8176 (pttm)
REVERT: A  900 ASP cc_start: 0.8219 (t0) cc_final: 0.7928 (t0)
REVERT: A  979 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.8157 (p0)
REVERT: A 1051 HIS cc_start: 0.7423 (m170) cc_final: 0.7195 (m170)
REVERT: A 1078 TRP cc_start: 0.8897 (t-100) cc_final: 0.8383 (t-100)
REVERT: A 1107 HIS cc_start: 0.8420 (t-90) cc_final: 0.8031 (t-90)
REVERT: A 1181 TYR cc_start: 0.9297 (m-80) cc_final: 0.8807 (m-80)
REVERT: A 1203 CYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7209 (t)
REVERT: B  143 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.7775 (t80)
  outliers start: 17
  outliers final: 8
  residues processed: 148
  average time/residue: 0.0806
  time to fit residues: 16.5644
Evaluate side-chains
  146 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 135
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  707 ILE
Chi-restraints excluded: chain A residue  979 ASN
Chi-restraints excluded: chain A residue 1183 VAL
Chi-restraints excluded: chain A residue 1203 CYS
Chi-restraints excluded: chain A residue 1213 SER
Chi-restraints excluded: chain A residue 1234 LEU
Chi-restraints excluded: chain A residue 1246 LEU
Chi-restraints excluded: chain B residue  143 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 24 optimal weight:   10.0000
   chunk 47 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9990
   chunk 76 optimal weight:    8.9990
   chunk 50 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 84 optimal weight:    0.0470
   chunk 104 optimal weight:    0.8980
   chunk 88 optimal weight:    0.8980
   overall best weight:    0.7478

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

Flipped N/Q/H residues before XYZ refinement:
A 815 ASN
** A1243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.209752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.150868 restraints weight = 9652.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.143118 restraints weight = 11906.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.146123 restraints weight = 11216.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.147115 restraints weight = 6590.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.147898 restraints weight = 5867.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   8533  Z= 0.145
  Angle     :  0.578  10.714  11587  Z= 0.286
  Chirality :  0.043   0.152   1348
  Planarity :  0.003   0.048   1458
  Dihedral  :  4.894  78.030   1143
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.67 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.27), residues: 1058
  helix:  1.56 (0.24), residues: 508
  sheet:  1.09 (0.54), residues: 98
  loop :  0.02 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1179 
 TYR   0.024   0.001   TYR A 937 
 PHE   0.011   0.001   PHE A1169 
 TRP   0.012   0.001   TRP A1129 
 HIS   0.006   0.001   HIS A1004 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 8533)
  covalent geometry    : angle       0.57810 (11587)
  hydrogen bonds       : bond        0.03332 (  423)
  hydrogen bonds       : angle       4.30158 ( 1203)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 141
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  428 LYS cc_start: 0.8643 (tttp) cc_final: 0.8051 (ttmm)
REVERT: A  556 TYR cc_start: 0.7787 (p90) cc_final: 0.7519 (p90)
REVERT: A  692 LYS cc_start: 0.8545 (pttm) cc_final: 0.8208 (pttm)
REVERT: A  699 GLN cc_start: 0.8419 (mt0) cc_final: 0.8072 (mp10)
REVERT: A  900 ASP cc_start: 0.8192 (t0) cc_final: 0.7927 (t0)
REVERT: A 1051 HIS cc_start: 0.7482 (m170) cc_final: 0.7262 (m170)
REVERT: A 1058 SER cc_start: 0.9479 (t) cc_final: 0.9147 (p)
REVERT: A 1078 TRP cc_start: 0.8905 (t-100) cc_final: 0.8389 (t-100)
REVERT: A 1107 HIS cc_start: 0.8413 (t-90) cc_final: 0.7988 (t-90)
REVERT: A 1136 LYS cc_start: 0.7848 (mmtt) cc_final: 0.7262 (tppt)
REVERT: A 1177 MET cc_start: 0.8750 (tmm) cc_final: 0.8486 (tmm)
REVERT: A 1181 TYR cc_start: 0.9299 (m-80) cc_final: 0.8809 (m-80)
REVERT: A 1203 CYS cc_start: 0.7341 (OUTLIER) cc_final: 0.7058 (t)
REVERT: A 1260 MET cc_start: 0.8014 (mmt) cc_final: 0.7706 (mmt)
REVERT: B  143 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.7803 (t80)
  outliers start: 17
  outliers final: 10
  residues processed: 152
  average time/residue: 0.0720
  time to fit residues: 15.2264
Evaluate side-chains
  148 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 136
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  707 ILE
Chi-restraints excluded: chain A residue  916 ILE
Chi-restraints excluded: chain A residue  979 ASN
Chi-restraints excluded: chain A residue 1183 VAL
Chi-restraints excluded: chain A residue 1203 CYS
Chi-restraints excluded: chain A residue 1213 SER
Chi-restraints excluded: chain A residue 1234 LEU
Chi-restraints excluded: chain A residue 1246 LEU
Chi-restraints excluded: chain B residue  143 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 87 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0980
   chunk 71 optimal weight:    0.9980
   chunk 104 optimal weight:    0.8980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A1243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.209397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.150628 restraints weight = 9574.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.147158 restraints weight = 14280.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.150133 restraints weight = 11710.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.150534 restraints weight = 7080.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.151326 restraints weight = 6521.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.2245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8533  Z= 0.151
  Angle     :  0.590  10.576  11587  Z= 0.294
  Chirality :  0.043   0.153   1348
  Planarity :  0.003   0.051   1458
  Dihedral  :  4.903  74.495   1143
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 18.09 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.27), residues: 1058
  helix:  1.50 (0.24), residues: 508
  sheet:  1.22 (0.54), residues: 96
  loop :  0.05 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1179 
 TYR   0.024   0.001   TYR A 937 
 PHE   0.011   0.001   PHE A1169 
 TRP   0.008   0.001   TRP A1129 
 HIS   0.006   0.001   HIS A1004 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 8533)
  covalent geometry    : angle       0.59036 (11587)
  hydrogen bonds       : bond        0.03376 (  423)
  hydrogen bonds       : angle       4.33095 ( 1203)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 139
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  428 LYS cc_start: 0.8655 (tttp) cc_final: 0.8074 (ttmm)
REVERT: A  556 TYR cc_start: 0.7652 (p90) cc_final: 0.7417 (p90)
REVERT: A  692 LYS cc_start: 0.8450 (pttm) cc_final: 0.8146 (pttm)
REVERT: A  699 GLN cc_start: 0.8378 (mt0) cc_final: 0.8092 (mp10)
REVERT: A  900 ASP cc_start: 0.8218 (t0) cc_final: 0.7973 (t0)
REVERT: A 1058 SER cc_start: 0.9490 (t) cc_final: 0.9120 (p)
REVERT: A 1078 TRP cc_start: 0.8938 (t-100) cc_final: 0.8438 (t-100)
REVERT: A 1107 HIS cc_start: 0.8457 (t-90) cc_final: 0.8051 (t-90)
REVERT: A 1136 LYS cc_start: 0.7679 (mmtt) cc_final: 0.7335 (tppt)
REVERT: A 1181 TYR cc_start: 0.9290 (m-80) cc_final: 0.8810 (m-80)
REVERT: A 1203 CYS cc_start: 0.7447 (OUTLIER) cc_final: 0.7188 (t)
REVERT: A 1260 MET cc_start: 0.7980 (mmt) cc_final: 0.7678 (mmt)
  outliers start: 14
  outliers final: 9
  residues processed: 146
  average time/residue: 0.0747
  time to fit residues: 15.3197
Evaluate side-chains
  144 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 134
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  707 ILE
Chi-restraints excluded: chain A residue  916 ILE
Chi-restraints excluded: chain A residue 1183 VAL
Chi-restraints excluded: chain A residue 1203 CYS
Chi-restraints excluded: chain A residue 1213 SER
Chi-restraints excluded: chain A residue 1234 LEU
Chi-restraints excluded: chain A residue 1246 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   chunk 50 optimal weight:    0.7980
   chunk 96 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** A1243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.207893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.148853 restraints weight = 9734.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.143506 restraints weight = 13959.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.146243 restraints weight = 12359.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.147186 restraints weight = 7346.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.147824 restraints weight = 6701.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   8533  Z= 0.177
  Angle     :  0.611  10.417  11587  Z= 0.304
  Chirality :  0.043   0.159   1348
  Planarity :  0.003   0.051   1458
  Dihedral  :  4.612  68.648   1141
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 18.74 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.27), residues: 1058
  helix:  1.46 (0.24), residues: 508
  sheet:  1.07 (0.53), residues: 99
  loop :  0.03 (0.31), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1179 
 TYR   0.024   0.001   TYR A 937 
 PHE   0.019   0.001   PHE A 488 
 TRP   0.007   0.001   TRP A1129 
 HIS   0.006   0.001   HIS A1004 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 8533)
  covalent geometry    : angle       0.61061 (11587)
  hydrogen bonds       : bond        0.03519 (  423)
  hydrogen bonds       : angle       4.41401 ( 1203)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 139
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  428 LYS cc_start: 0.8679 (tttp) cc_final: 0.8070 (ttmm)
REVERT: A  556 TYR cc_start: 0.7817 (p90) cc_final: 0.7574 (p90)
REVERT: A  762 GLN cc_start: 0.8104 (tp-100) cc_final: 0.7898 (tp-100)
REVERT: A  900 ASP cc_start: 0.8291 (t0) cc_final: 0.7997 (t0)
REVERT: A 1058 SER cc_start: 0.9505 (t) cc_final: 0.9114 (p)
REVERT: A 1078 TRP cc_start: 0.8983 (t-100) cc_final: 0.8458 (t-100)
REVERT: A 1107 HIS cc_start: 0.8562 (t-90) cc_final: 0.8062 (t-90)
REVERT: A 1136 LYS cc_start: 0.7810 (mmtt) cc_final: 0.7560 (tppt)
REVERT: A 1181 TYR cc_start: 0.9274 (m-80) cc_final: 0.8783 (m-80)
REVERT: A 1203 CYS cc_start: 0.7355 (OUTLIER) cc_final: 0.7038 (t)
REVERT: A 1260 MET cc_start: 0.7960 (mmt) cc_final: 0.7666 (mmt)
  outliers start: 12
  outliers final: 10
  residues processed: 144
  average time/residue: 0.0757
  time to fit residues: 15.4821
Evaluate side-chains
  148 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 137
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  707 ILE
Chi-restraints excluded: chain A residue  916 ILE
Chi-restraints excluded: chain A residue 1183 VAL
Chi-restraints excluded: chain A residue 1203 CYS
Chi-restraints excluded: chain A residue 1213 SER
Chi-restraints excluded: chain A residue 1234 LEU
Chi-restraints excluded: chain A residue 1246 LEU
Chi-restraints excluded: chain B residue  159 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   chunk 32 optimal weight:   10.0000
   chunk 28 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 104 optimal weight:    0.3980
   chunk 92 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 93 optimal weight:    0.4980
   chunk 89 optimal weight:    0.0970
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 113 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 = 0.4288 r_free = 0.4288 target = 0.211214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.150656 restraints weight = 9611.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.147052 restraints weight = 13546.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.150454 restraints weight = 10491.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.150283 restraints weight = 6522.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.150977 restraints weight = 6287.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8533  Z= 0.123
  Angle     :  0.599  10.619  11587  Z= 0.298
  Chirality :  0.042   0.163   1348
  Planarity :  0.004   0.052   1458
  Dihedral  :  4.449  62.445   1141
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 19.06 %
    Favored  : 79.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.27), residues: 1058
  helix:  1.56 (0.24), residues: 508
  sheet:  1.24 (0.53), residues: 98
  loop :  0.07 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 687 
 TYR   0.025   0.001   TYR A 937 
 PHE   0.025   0.001   PHE A 488 
 TRP   0.010   0.001   TRP A1129 
 HIS   0.007   0.001   HIS A 647 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 8533)
  covalent geometry    : angle       0.59887 (11587)
  hydrogen bonds       : bond        0.03300 (  423)
  hydrogen bonds       : angle       4.28643 ( 1203)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 137
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  428 LYS cc_start: 0.8671 (tttp) cc_final: 0.8064 (ttmm)
REVERT: A  556 TYR cc_start: 0.7745 (p90) cc_final: 0.7516 (p90)
REVERT: A  762 GLN cc_start: 0.8024 (tp-100) cc_final: 0.7817 (tp-100)
REVERT: A  900 ASP cc_start: 0.8224 (t0) cc_final: 0.7935 (t0)
REVERT: A  988 LYS cc_start: 0.7829 (mmmt) cc_final: 0.7222 (tppt)
REVERT: A 1058 SER cc_start: 0.9486 (t) cc_final: 0.9077 (p)
REVERT: A 1078 TRP cc_start: 0.8931 (t-100) cc_final: 0.8440 (t-100)
REVERT: A 1107 HIS cc_start: 0.8509 (t-90) cc_final: 0.8007 (t-90)
REVERT: A 1136 LYS cc_start: 0.7672 (mmtt) cc_final: 0.7416 (tppt)
REVERT: A 1181 TYR cc_start: 0.9269 (m-80) cc_final: 0.8767 (m-80)
REVERT: A 1203 CYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6862 (t)
REVERT: A 1260 MET cc_start: 0.7981 (mmt) cc_final: 0.7686 (mmt)
  outliers start: 12
  outliers final: 9
  residues processed: 142
  average time/residue: 0.0722
  time to fit residues: 14.5725
Evaluate side-chains
  145 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 135
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  707 ILE
Chi-restraints excluded: chain A residue  916 ILE
Chi-restraints excluded: chain A residue 1183 VAL
Chi-restraints excluded: chain A residue 1203 CYS
Chi-restraints excluded: chain A residue 1213 SER
Chi-restraints excluded: chain A residue 1234 LEU
Chi-restraints excluded: chain A residue 1246 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 93 optimal weight:    0.5980
   chunk 102 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 71 optimal weight:    0.2980
   chunk 56 optimal weight:    0.0980
   chunk 68 optimal weight:    0.8980
   chunk 39 optimal weight:   10.0000
   chunk 48 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 96 optimal weight:    0.3980
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.209971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.151132 restraints weight = 9581.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.148564 restraints weight = 11460.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.150986 restraints weight = 10954.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.151663 restraints weight = 6440.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.152441 restraints weight = 5808.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.2553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8533  Z= 0.116
  Angle     :  0.587  10.613  11587  Z= 0.291
  Chirality :  0.042   0.156   1348
  Planarity :  0.003   0.052   1458
  Dihedral  :  4.312  54.426   1141
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 19.16 %
    Favored  : 79.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.34 (0.27), residues: 1058
  helix:  1.55 (0.24), residues: 513
  sheet:  1.26 (0.53), residues: 98
  loop :  0.11 (0.32), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 111 
 TYR   0.024   0.001   TYR A 937 
 PHE   0.010   0.001   PHE A 917 
 TRP   0.012   0.001   TRP A1129 
 HIS   0.006   0.001   HIS A 647 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8533)
  covalent geometry    : angle       0.58715 (11587)
  hydrogen bonds       : bond        0.03188 (  423)
  hydrogen bonds       : angle       4.23437 ( 1203)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1203.06 seconds
wall clock time: 21 minutes 36.12 seconds (1296.12 seconds total)