Starting phenix.real_space_refine
on Sat Aug 23 13:31:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j8a_36065/08_2025/8j8a_36065.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j8a_36065/08_2025/8j8a_36065.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j8a_36065/08_2025/8j8a_36065.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j8a_36065/08_2025/8j8a_36065.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j8a_36065/08_2025/8j8a_36065.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j8a_36065/08_2025/8j8a_36065.cif"
  }
  resolution = 2.51
  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=   0.000 sd=   0.009
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      50      5.16       5
     C    7855      2.51       5
     N    2097      2.21       5
     O    2220      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12222
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 751, 6105
          Classifications: {'peptide': 751}
          Link IDs: {'PTRANS': 30, 'TRANS': 720}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 6117
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 751, 6105
          Classifications: {'peptide': 751}
          Link IDs: {'PTRANS': 30, 'TRANS': 720}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 751, 6105
          Classifications: {'peptide': 751}
          Link IDs: {'PTRANS': 30, 'TRANS': 720}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 6237
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR B1029 " occ=0.50
      ... (22 atoms not shown)
      pdb=" OH BTYR B1029 " occ=0.50
  Time building chain proxies: 4.43, per 1000 atoms: 0.36
  Number of scatterers: 12222
  At special positions: 0
  Unit cell: (117.03, 105.41, 111.22, 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      50     16.00
     O    2220      8.00
     N    2097      7.00
     C    7855      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: 1.03
  Conformation dependent library (CDL) restraints added in 775.1 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2826

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 14 sheets defined
      52.3% alpha, 10.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 439 through 451
    Processing helix  chain 'A' and resid 452 through 456
    Processing helix  chain 'A' and resid 502 through 513
    Processing helix  chain 'A' and resid 522 through 528
      removed outlier: 3.871A  pdb=" N   LYS A 528 " --> pdb=" O   GLU A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 560
    Processing helix  chain 'A' and resid 560 through 566
      removed outlier: 4.283A  pdb=" N   ILE A 564 " --> pdb=" O   TRP A 560 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ILE A 565 " --> pdb=" O   PRO A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 604
      removed outlier: 3.505A  pdb=" N   THR A 604 " --> pdb=" O   ALA A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 620
      removed outlier: 3.783A  pdb=" N   HIS A 620 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 631
      removed outlier: 3.655A  pdb=" N   HIS A 631 " --> pdb=" O   SER A 627 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 634
      No H-bonds generated for 'chain 'A' and resid 632 through 634'
    Processing helix  chain 'A' and resid 642 through 653
      removed outlier: 4.066A  pdb=" N   LYS A 646 " --> pdb=" O   ASP A 642 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   GLU A 647 " --> pdb=" O   ASP A 643 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 665
    Processing helix  chain 'A' and resid 672 through 682
    Processing helix  chain 'A' and resid 687 through 707
      removed outlier: 4.797A  pdb=" N   LYS A 696 " --> pdb=" O   GLN A 692 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   GLN A 706 " --> pdb=" O   ALA A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 732
      removed outlier: 4.376A  pdb=" N   SER A 731 " --> pdb=" O   LYS A 727 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   ASN A 732 " --> pdb=" O   CYS A 728 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 738 through 750
    Processing helix  chain 'A' and resid 754 through 767
    Processing helix  chain 'A' and resid 806 through 814
      removed outlier: 3.626A  pdb=" N   THR A 812 " --> pdb=" O   GLU A 808 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 842 through 847
    Processing helix  chain 'A' and resid 854 through 858
    Processing helix  chain 'A' and resid 867 through 877
    Processing helix  chain 'A' and resid 882 through 891
      removed outlier: 3.989A  pdb=" N   LYS A 891 " --> pdb=" O   HIS A 887 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 942 through 953
    Processing helix  chain 'A' and resid 953 through 958
    Processing helix  chain 'A' and resid 984 through 990
    Processing helix  chain 'A' and resid 997 through 1003
    Processing helix  chain 'A' and resid 1027 through 1070
      removed outlier: 3.702A  pdb=" N   ILE A1031 " --> pdb=" O   SER A1027 " (cutoff:3.500A)
      Proline residue:  A1037  - end of helix
    Processing helix  chain 'A' and resid 1075 through 1079
      removed outlier: 4.023A  pdb=" N   HIS A1078 " --> pdb=" O   ASN A1075 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1081 through 1092
    Processing helix  chain 'A' and resid 1098 through 1104
    Processing helix  chain 'A' and resid 1109 through 1118
      removed outlier: 4.189A  pdb=" N   LEU A1118 " --> pdb=" O   ASN A1114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1122 through 1127
    Processing helix  chain 'A' and resid 1129 through 1133
    Processing helix  chain 'A' and resid 1134 through 1160
      removed outlier: 3.585A  pdb=" N   GLN A1160 " --> pdb=" O   GLU A1156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1166 through 1187
    Processing helix  chain 'B' and resid 439 through 451
    Processing helix  chain 'B' and resid 452 through 456
    Processing helix  chain 'B' and resid 502 through 513
    Processing helix  chain 'B' and resid 522 through 528
      removed outlier: 3.889A  pdb=" N   LYS B 528 " --> pdb=" O   GLU B 524 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 547 through 560
      removed outlier: 3.562A  pdb=" N   PHE B 559 " --> pdb=" O   TYR B 555 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 566
      removed outlier: 3.965A  pdb=" N   ILE B 564 " --> pdb=" O   TRP B 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 592 through 604
      removed outlier: 3.505A  pdb=" N   THR B 604 " --> pdb=" O   ALA B 600 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 616 through 620
      removed outlier: 3.801A  pdb=" N   HIS B 620 " --> pdb=" O   LEU B 617 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 621 through 631
      removed outlier: 3.661A  pdb=" N   HIS B 631 " --> pdb=" O   SER B 627 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 632 through 634
      No H-bonds generated for 'chain 'B' and resid 632 through 634'
    Processing helix  chain 'B' and resid 642 through 653
      removed outlier: 3.926A  pdb=" N   LYS B 646 " --> pdb=" O   ASP B 642 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   GLU B 647 " --> pdb=" O   ASP B 643 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 659 through 665
      removed outlier: 3.613A  pdb=" N   GLU B 663 " --> pdb=" O   LEU B 659 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 672 through 682
    Processing helix  chain 'B' and resid 687 through 707
      removed outlier: 4.756A  pdb=" N   LYS B 696 " --> pdb=" O   GLN B 692 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   GLN B 706 " --> pdb=" O   ALA B 702 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 715 through 732
      removed outlier: 4.355A  pdb=" N   SER B 731 " --> pdb=" O   LYS B 727 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   ASN B 732 " --> pdb=" O   CYS B 728 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 738 through 750
    Processing helix  chain 'B' and resid 754 through 767
    Processing helix  chain 'B' and resid 806 through 814
      removed outlier: 4.105A  pdb=" N   THR B 812 " --> pdb=" O   GLU B 808 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 842 through 847
    Processing helix  chain 'B' and resid 864 through 877
    Processing helix  chain 'B' and resid 882 through 891
      removed outlier: 3.962A  pdb=" N   LYS B 891 " --> pdb=" O   HIS B 887 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 942 through 952
    Processing helix  chain 'B' and resid 953 through 958
    Processing helix  chain 'B' and resid 982 through 991
      removed outlier: 3.609A  pdb=" N   ILE B 986 " --> pdb=" O   SER B 982 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   VAL B 987 " --> pdb=" O   LEU B 983 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LYS B 991 " --> pdb=" O   VAL B 987 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 997 through 1003
    Processing helix  chain 'B' and resid 1027 through 1070
      removed outlier: 3.831A  pdb=" N   ILE B1031 " --> pdb=" O   SER B1027 " (cutoff:3.500A)
      Proline residue:  B1037  - end of helix
    Processing helix  chain 'B' and resid 1081 through 1092
    Processing helix  chain 'B' and resid 1098 through 1104
    Processing helix  chain 'B' and resid 1109 through 1116
    Processing helix  chain 'B' and resid 1122 through 1127
    Processing helix  chain 'B' and resid 1129 through 1133
    Processing helix  chain 'B' and resid 1134 through 1160
      removed outlier: 3.527A  pdb=" N   GLN B1160 " --> pdb=" O   GLU B1156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1166 through 1187
      removed outlier: 3.699A  pdb=" N   GLU B1172 " --> pdb=" O   SER B1168 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 465 through 469
      removed outlier: 5.890A  pdb=" N   ILE A 534 " --> pdb=" O   LYS A 570 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   LEU A 572 " --> pdb=" O   ILE A 534 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   ALA A 536 " --> pdb=" O   LEU A 572 " (cutoff:3.500A)
      removed outlier: 5.757A  pdb=" N   VAL A 569 " --> pdb=" O   PHE A 639 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 588 through 590
    Processing sheet with id=AA3, first strand: chain 'A' and resid 736 through 737
    Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 827
      removed outlier: 4.373A  pdb=" N   VAL A 825 " --> pdb=" O   ALA A 832 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 909 through 913
      removed outlier: 4.300A  pdb=" N   TYR A 917 " --> pdb=" O   LEU A1009 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 922 through 926
      removed outlier: 6.059A  pdb=" N   THR A 922 " --> pdb=" O   THR A 935 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LYS A 977 " --> pdb=" O   GLU A 962 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   GLU A 962 " --> pdb=" O   LYS A 977 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1014 through 1016
    Processing sheet with id=AA8, first strand: chain 'B' and resid 465 through 469
      removed outlier: 5.955A  pdb=" N   ILE B 534 " --> pdb=" O   LYS B 570 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   LEU B 572 " --> pdb=" O   ILE B 534 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   ALA B 536 " --> pdb=" O   LEU B 572 " (cutoff:3.500A)
      removed outlier: 5.763A  pdb=" N   VAL B 569 " --> pdb=" O   PHE B 639 " (cutoff:3.500A)
      removed outlier: 7.966A  pdb=" N   ILE B 685 " --> pdb=" O   VAL B 636 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   THR B 638 " --> pdb=" O   ILE B 685 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 588 through 590
    Processing sheet with id=AB1, first strand: chain 'B' and resid 736 through 737
    Processing sheet with id=AB2, first strand: chain 'B' and resid 824 through 827
      removed outlier: 4.479A  pdb=" N   VAL B 825 " --> pdb=" O   ALA B 832 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 909 through 913
      removed outlier: 4.589A  pdb=" N   TYR B 917 " --> pdb=" O   LEU B1009 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 922 through 926
      removed outlier: 6.046A  pdb=" N   THR B 922 " --> pdb=" O   THR B 935 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   GLU B 962 " --> pdb=" O   LYS B 977 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 1014 through 1016

    583 hydrogen bonds defined for protein.
    1656 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: 2.46

  Time building geometry restraints manager: 1.39 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3943
        1.34 -     1.46: 2701
        1.46 -     1.58: 5794
        1.58 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 12516
  Sorted by residual:
  bond pdb=" CB  ILE B 801 "
       pdb=" CG2 ILE B 801 "
    ideal  model  delta    sigma   weight residual
    1.521  1.486  0.035 3.30e-02 9.18e+02 1.12e+00
  bond pdb=" CB  ILE A 801 "
       pdb=" CG2 ILE A 801 "
    ideal  model  delta    sigma   weight residual
    1.521  1.488  0.033 3.30e-02 9.18e+02 1.00e+00
  bond pdb=" CG  LEU A 549 "
       pdb=" CD1 LEU A 549 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 8.25e-01
  bond pdb=" C   PHE A 785 "
       pdb=" N   GLY A 786 "
    ideal  model  delta    sigma   weight residual
    1.331  1.318  0.012 1.46e-02 4.69e+03 7.23e-01
  bond pdb=" CB  ASP B 416 "
       pdb=" CG  ASP B 416 "
    ideal  model  delta    sigma   weight residual
    1.516  1.537 -0.021 2.50e-02 1.60e+03 7.11e-01
  ... (remaining 12511 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 16508
        1.42 -     2.83: 328
        2.83 -     4.25: 63
        4.25 -     5.66: 11
        5.66 -     7.08: 1
  Bond angle restraints: 16911
  Sorted by residual:
  angle pdb=" C   LYS B1190 "
        pdb=" N   PHE B1191 "
        pdb=" CA  PHE B1191 "
      ideal   model   delta    sigma   weight residual
     121.54  128.62   -7.08 1.91e+00 2.74e-01 1.37e+01
  angle pdb=" N   VAL A 415 "
        pdb=" CA  VAL A 415 "
        pdb=" C   VAL A 415 "
      ideal   model   delta    sigma   weight residual
     109.46  105.00    4.46 1.38e+00 5.25e-01 1.04e+01
  angle pdb=" N   ILE A 845 "
        pdb=" CA  ILE A 845 "
        pdb=" C   ILE A 845 "
      ideal   model   delta    sigma   weight residual
     113.39  108.97    4.42 1.47e+00 4.63e-01 9.02e+00
  angle pdb=" CA  ILE A 845 "
        pdb=" C   ILE A 845 "
        pdb=" N   MET A 846 "
      ideal   model   delta    sigma   weight residual
     118.55  116.15    2.40 8.60e-01 1.35e+00 7.79e+00
  angle pdb=" N   GLU B1173 "
        pdb=" CA  GLU B1173 "
        pdb=" C   GLU B1173 "
      ideal   model   delta    sigma   weight residual
     111.36  108.37    2.99 1.09e+00 8.42e-01 7.54e+00
  ... (remaining 16906 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.29: 6848
       17.29 -    34.58: 550
       34.58 -    51.87: 86
       51.87 -    69.16: 19
       69.16 -    86.45: 10
  Dihedral angle restraints: 7513
    sinusoidal: 3102
      harmonic: 4411
  Sorted by residual:
  dihedral pdb=" CA  GLU B1073 "
           pdb=" C   GLU B1073 "
           pdb=" N   LEU B1074 "
           pdb=" CA  LEU B1074 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.87   23.13     0      5.00e+00 4.00e-02 2.14e+01
  dihedral pdb=" CA  GLU A1073 "
           pdb=" C   GLU A1073 "
           pdb=" N   LEU A1074 "
           pdb=" CA  LEU A1074 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.34   22.66     0      5.00e+00 4.00e-02 2.05e+01
  dihedral pdb=" CA  PRO B 938 "
           pdb=" C   PRO B 938 "
           pdb=" N   LEU B 939 "
           pdb=" CA  LEU B 939 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.89  -17.11     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 7510 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1201
       0.034 -    0.067: 455
       0.067 -    0.100: 116
       0.100 -    0.134: 54
       0.134 -    0.167: 1
  Chirality restraints: 1827
  Sorted by residual:
  chirality pdb=" CA  VAL A 415 "
            pdb=" N   VAL A 415 "
            pdb=" C   VAL A 415 "
            pdb=" CB  VAL A 415 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.01e-01
  chirality pdb=" CA  PRO B 980 "
            pdb=" N   PRO B 980 "
            pdb=" C   PRO B 980 "
            pdb=" CB  PRO B 980 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.22e-01
  chirality pdb=" CA  LYS B 991 "
            pdb=" N   LYS B 991 "
            pdb=" C   LYS B 991 "
            pdb=" CB  LYS B 991 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.17e-01
  ... (remaining 1824 not shown)

  Planarity restraints: 2157
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 937 "    0.030 5.00e-02 4.00e+02   4.55e-02 3.31e+00
        pdb=" N   PRO B 938 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B 938 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 938 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 937 "   -0.030 5.00e-02 4.00e+02   4.54e-02 3.30e+00
        pdb=" N   PRO A 938 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 938 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 938 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 979 "    0.028 5.00e-02 4.00e+02   4.30e-02 2.96e+00
        pdb=" N   PRO A 980 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 980 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 980 "    0.024 5.00e-02 4.00e+02
  ... (remaining 2154 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 765
        2.74 -     3.28: 12320
        3.28 -     3.82: 20341
        3.82 -     4.36: 25397
        4.36 -     4.90: 43225
  Nonbonded interactions: 102048
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 919 "
            pdb=" OD1 ASN A1007 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   GLY B 781 "
            pdb=" NZ  LYS B1190 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" OH  TYR B 923 "
            pdb=" OD2 ASP B 997 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OH  TYR A 923 "
            pdb=" OD2 ASP A 997 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" NH2 ARG B1049 "
            pdb=" O   GLU B1106 "
     model   vdw
     2.279 3.120
  ... (remaining 102043 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 414 through 1028 or resid 1030 through 1192))
  selection = (chain 'B' and (resid 414 through 1028 or resid 1030 through 1192))
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.060
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
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  12516  Z= 0.116
  Angle     :  0.499   7.078  16911  Z= 0.271
  Chirality :  0.041   0.167   1827
  Planarity :  0.004   0.048   2157
  Dihedral  : 12.916  86.447   4687
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.38 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.21), residues: 1497
  helix:  1.81 (0.20), residues: 645
  sheet: -0.07 (0.38), residues: 196
  loop : -0.14 (0.23), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 526 
 TYR   0.015   0.001   TYR B 858 
 PHE   0.013   0.001   PHE A1107 
 TRP   0.016   0.002   TRP A 820 
 HIS   0.004   0.001   HIS B 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (12516)
  covalent geometry    : angle       0.49906 (16911)
  hydrogen bonds       : bond        0.21221 (  583)
  hydrogen bonds       : angle       6.61479 ( 1656)

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

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

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.527 
Fit side-chains
REVERT: A  433 MET cc_start: 0.8026 (ptp) cc_final: 0.7823 (ptp)
REVERT: A  970 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7867 (mt-10)
REVERT: A  999 ILE cc_start: 0.8550 (mm) cc_final: 0.8274 (mm)
REVERT: B  433 MET cc_start: 0.7978 (ptp) cc_final: 0.7758 (ptp)
REVERT: B  503 LYS cc_start: 0.9235 (tttm) cc_final: 0.8994 (tptp)
REVERT: B  916 TYR cc_start: 0.7797 (m-80) cc_final: 0.7315 (m-80)
REVERT: B  973 GLU cc_start: 0.8215 (tm-30) cc_final: 0.8006 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 127
  average time/residue: 0.6968
  time to fit residues: 95.6756
Evaluate side-chains
  84 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:   10.0000
   chunk 149 optimal weight:    1.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 523 GLN
A 851 ASN
A 864 GLN
B 523 GLN
B 733 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.097562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.070784 restraints weight = 31078.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 3.05
r_work: 0.2893 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2957
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2957
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.1429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  12516  Z= 0.202
  Angle     :  0.580   6.375  16911  Z= 0.311
  Chirality :  0.044   0.171   1827
  Planarity :  0.005   0.050   2157
  Dihedral  :  4.288  22.167   1671
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  5.46 %
    Favored  : 93.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.22), residues: 1497
  helix:  1.73 (0.20), residues: 677
  sheet: -0.20 (0.37), residues: 218
  loop : -0.13 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 929 
 TYR   0.017   0.002   TYR A 920 
 PHE   0.017   0.002   PHE A 559 
 TRP   0.012   0.002   TRP A1170 
 HIS   0.004   0.001   HIS B 752 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 (12516)
  covalent geometry    : angle       0.57966 (16911)
  hydrogen bonds       : bond        0.05407 (  583)
  hydrogen bonds       : angle       4.58798 ( 1656)

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

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

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.547 
Fit side-chains
REVERT: A  433 MET cc_start: 0.7829 (ptp) cc_final: 0.7575 (ptp)
REVERT: A  610 THR cc_start: 0.8646 (m) cc_final: 0.8431 (t)
REVERT: A  916 TYR cc_start: 0.8355 (m-80) cc_final: 0.7612 (m-80)
REVERT: A  957 MET cc_start: 0.8870 (tpt) cc_final: 0.8521 (tpt)
REVERT: A  970 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8283 (mt-10)
REVERT: A  985 ARG cc_start: 0.7902 (tpp80) cc_final: 0.7485 (tpp80)
REVERT: A  988 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7503 (pm20)
REVERT: B  433 MET cc_start: 0.7720 (ptp) cc_final: 0.7445 (ptp)
REVERT: B  503 LYS cc_start: 0.9160 (tttm) cc_final: 0.8859 (tptp)
REVERT: B  684 ARG cc_start: 0.6025 (mtp85) cc_final: 0.5762 (mtp180)
REVERT: B  916 TYR cc_start: 0.7772 (m-80) cc_final: 0.7290 (m-80)
REVERT: B  973 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8044 (tm-30)
  outliers start: 18
  outliers final: 5
  residues processed: 97
  average time/residue: 0.7156
  time to fit residues: 75.1278
Evaluate side-chains
  90 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain A residue  988 GLU
Chi-restraints excluded: chain A residue 1153 ASP
Chi-restraints excluded: chain B residue  522 THR
Chi-restraints excluded: chain B residue 1153 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 45 optimal weight:    4.9990
   chunk 117 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   chunk 126 optimal weight:    0.9980
   chunk 106 optimal weight:    0.0370
   chunk 138 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0980
   chunk 4 optimal weight:    3.9990
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
A 733 ASN
A 864 GLN
A 930 ASN
B 981 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.099376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.072666 restraints weight = 37644.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 3.32
r_work: 0.2924 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2968
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2968 r_free = 0.2968    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2968 r_free = 0.2968    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2968
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.1741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12516  Z= 0.116
  Angle     :  0.493   6.938  16911  Z= 0.263
  Chirality :  0.041   0.166   1827
  Planarity :  0.004   0.047   2157
  Dihedral  :  4.046  19.705   1671
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  7.51 %
    Favored  : 91.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.22), residues: 1497
  helix:  1.72 (0.20), residues: 677
  sheet: -0.26 (0.37), residues: 218
  loop : -0.26 (0.24), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 929 
 TYR   0.014   0.001   TYR B 888 
 PHE   0.011   0.001   PHE A 649 
 TRP   0.008   0.001   TRP A 820 
 HIS   0.003   0.001   HIS B 887 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (12516)
  covalent geometry    : angle       0.49305 (16911)
  hydrogen bonds       : bond        0.04369 (  583)
  hydrogen bonds       : angle       4.29329 ( 1656)

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

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

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
REVERT: A  433 MET cc_start: 0.7733 (ptp) cc_final: 0.7515 (ptp)
REVERT: A  610 THR cc_start: 0.8672 (m) cc_final: 0.8456 (t)
REVERT: A  684 ARG cc_start: 0.5957 (mtp85) cc_final: 0.5524 (mtp180)
REVERT: A  916 TYR cc_start: 0.8273 (m-80) cc_final: 0.8003 (m-80)
REVERT: A  957 MET cc_start: 0.8924 (tpt) cc_final: 0.8703 (tpt)
REVERT: A  985 ARG cc_start: 0.7954 (tpp80) cc_final: 0.7521 (tpp80)
REVERT: A  988 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7468 (pm20)
REVERT: B  433 MET cc_start: 0.7587 (ptp) cc_final: 0.7335 (ptp)
REVERT: B  503 LYS cc_start: 0.9124 (tttm) cc_final: 0.8808 (tptp)
REVERT: B  684 ARG cc_start: 0.5972 (mtp85) cc_final: 0.5713 (mtp180)
REVERT: B  916 TYR cc_start: 0.7811 (m-80) cc_final: 0.7306 (m-80)
REVERT: B  929 ARG cc_start: 0.8428 (ttp-110) cc_final: 0.8157 (mtp180)
REVERT: B  973 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8042 (tm-30)
  outliers start: 16
  outliers final: 8
  residues processed: 94
  average time/residue: 0.7380
  time to fit residues: 74.7381
Evaluate side-chains
  88 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  756 MET
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  988 GLU
Chi-restraints excluded: chain A residue 1153 ASP
Chi-restraints excluded: chain B residue  964 ILE
Chi-restraints excluded: chain B residue 1024 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 140 optimal weight:    0.0170
   chunk 67 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 131 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9980
   chunk 139 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0870
   overall best weight:    0.8200

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

Flipped N/Q/H residues before XYZ refinement:
B 981 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.096987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.069904 restraints weight = 40471.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 3.41
r_work: 0.2860 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2889
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2889 r_free = 0.2889    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2889 r_free = 0.2889    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2889
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12516  Z= 0.152
  Angle     :  0.507   6.488  16911  Z= 0.270
  Chirality :  0.042   0.168   1827
  Planarity :  0.004   0.048   2157
  Dihedral  :  4.094  21.356   1671
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  8.34 %
    Favored  : 90.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.22), residues: 1497
  helix:  1.72 (0.20), residues: 675
  sheet: -0.41 (0.37), residues: 218
  loop : -0.26 (0.24), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 929 
 TYR   0.017   0.001   TYR B 858 
 PHE   0.012   0.001   PHE A 990 
 TRP   0.008   0.001   TRP B1170 
 HIS   0.004   0.001   HIS A 752 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (12516)
  covalent geometry    : angle       0.50675 (16911)
  hydrogen bonds       : bond        0.04432 (  583)
  hydrogen bonds       : angle       4.21514 ( 1656)

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

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

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
REVERT: A  433 MET cc_start: 0.7763 (ptp) cc_final: 0.7524 (ptp)
REVERT: A  454 LYS cc_start: 0.9275 (mmmt) cc_final: 0.8872 (mmmt)
REVERT: A  610 THR cc_start: 0.8678 (m) cc_final: 0.8442 (t)
REVERT: A  916 TYR cc_start: 0.8266 (m-80) cc_final: 0.8025 (m-80)
REVERT: A  957 MET cc_start: 0.8964 (tpt) cc_final: 0.8697 (tpt)
REVERT: A  985 ARG cc_start: 0.8022 (tpp80) cc_final: 0.7456 (tpp80)
REVERT: A  988 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7590 (pm20)
REVERT: B  433 MET cc_start: 0.7663 (ptp) cc_final: 0.7431 (ptp)
REVERT: B  503 LYS cc_start: 0.9122 (tttm) cc_final: 0.8790 (tptp)
REVERT: B  684 ARG cc_start: 0.6189 (mtp85) cc_final: 0.5954 (mtp180)
REVERT: B  916 TYR cc_start: 0.7837 (m-80) cc_final: 0.7128 (m-80)
REVERT: B  973 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8059 (tm-30)
  outliers start: 20
  outliers final: 11
  residues processed: 92
  average time/residue: 0.6654
  time to fit residues: 66.2587
Evaluate side-chains
  93 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  931 ILE
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  988 GLU
Chi-restraints excluded: chain A residue 1153 ASP
Chi-restraints excluded: chain B residue  678 SER
Chi-restraints excluded: chain B residue  801 ILE
Chi-restraints excluded: chain B residue  964 ILE
Chi-restraints excluded: chain B residue 1024 GLU
Chi-restraints excluded: chain B residue 1153 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 145 optimal weight:    0.7980
   chunk 72 optimal weight:    0.6980
   chunk 98 optimal weight:    2.9990
   chunk 125 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 63 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9990
   chunk 124 optimal weight:    1.9990
   chunk 46 optimal weight:    0.4980
   chunk 132 optimal weight:    1.9990
   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 981 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.096948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.069611 restraints weight = 48303.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.2991 rms_B_bonded: 3.68
r_work: 0.2846 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2880
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2880
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12516  Z= 0.136
  Angle     :  0.496   7.892  16911  Z= 0.262
  Chirality :  0.041   0.164   1827
  Planarity :  0.004   0.047   2157
  Dihedral  :  4.051  20.821   1671
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  :  9.10 %
    Favored  : 89.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.22), residues: 1497
  helix:  1.73 (0.20), residues: 675
  sheet: -0.49 (0.37), residues: 218
  loop : -0.30 (0.24), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 929 
 TYR   0.016   0.001   TYR B 858 
 PHE   0.013   0.001   PHE A 559 
 TRP   0.007   0.001   TRP B1170 
 HIS   0.003   0.001   HIS B 887 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (12516)
  covalent geometry    : angle       0.49561 (16911)
  hydrogen bonds       : bond        0.04250 (  583)
  hydrogen bonds       : angle       4.15852 ( 1656)

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

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

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.528 
Fit side-chains
REVERT: A  433 MET cc_start: 0.7757 (ptp) cc_final: 0.7512 (ptp)
REVERT: A  610 THR cc_start: 0.8692 (m) cc_final: 0.8449 (t)
REVERT: A  684 ARG cc_start: 0.5948 (mtp85) cc_final: 0.5612 (mtp180)
REVERT: A  916 TYR cc_start: 0.8263 (m-80) cc_final: 0.8019 (m-80)
REVERT: A  957 MET cc_start: 0.8964 (tpt) cc_final: 0.8705 (tpt)
REVERT: A  973 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7929 (tm-30)
REVERT: A  985 ARG cc_start: 0.8030 (tpp80) cc_final: 0.7448 (tpp80)
REVERT: B  433 MET cc_start: 0.7617 (ptp) cc_final: 0.7347 (ptp)
REVERT: B  454 LYS cc_start: 0.9324 (mmmt) cc_final: 0.8861 (mmmm)
REVERT: B  503 LYS cc_start: 0.9107 (tttm) cc_final: 0.8778 (tptp)
REVERT: B  684 ARG cc_start: 0.6016 (mtp85) cc_final: 0.5786 (mtp180)
REVERT: B  916 TYR cc_start: 0.7851 (m-80) cc_final: 0.7057 (m-80)
REVERT: B  973 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8031 (tm-30)
REVERT: B 1040 ARG cc_start: 0.8520 (ttp80) cc_final: 0.8087 (ttm-80)
  outliers start: 21
  outliers final: 11
  residues processed: 99
  average time/residue: 0.6319
  time to fit residues: 67.7130
Evaluate side-chains
  96 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  931 ILE
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue 1153 ASP
Chi-restraints excluded: chain B residue  505 LEU
Chi-restraints excluded: chain B residue  522 THR
Chi-restraints excluded: chain B residue  964 ILE
Chi-restraints excluded: chain B residue 1153 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 76 optimal weight:    8.9990
   chunk 45 optimal weight:    0.1980
   chunk 37 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 90 optimal weight:    0.8980
   chunk 80 optimal weight:    0.4980
   chunk 148 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 142 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 981 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.096783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.070032 restraints weight = 38006.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 3.33
r_work: 0.2867 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2896
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2896
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.2257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12516  Z= 0.130
  Angle     :  0.499   9.264  16911  Z= 0.262
  Chirality :  0.041   0.162   1827
  Planarity :  0.004   0.054   2157
  Dihedral  :  4.017  20.737   1671
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  9.93 %
    Favored  : 88.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.22), residues: 1497
  helix:  1.78 (0.20), residues: 675
  sheet: -0.49 (0.37), residues: 218
  loop : -0.32 (0.24), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 929 
 TYR   0.016   0.001   TYR B 858 
 PHE   0.014   0.001   PHE A 559 
 TRP   0.007   0.001   TRP A1189 
 HIS   0.003   0.001   HIS B 887 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (12516)
  covalent geometry    : angle       0.49853 (16911)
  hydrogen bonds       : bond        0.04167 (  583)
  hydrogen bonds       : angle       4.11493 ( 1656)

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

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

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 89
  time to evaluate  : 0.403 
Fit side-chains
REVERT: A  433 MET cc_start: 0.7773 (ptp) cc_final: 0.7528 (ptp)
REVERT: A  454 LYS cc_start: 0.9204 (mmmm) cc_final: 0.8861 (mmmm)
REVERT: A  610 THR cc_start: 0.8703 (m) cc_final: 0.8462 (t)
REVERT: A  916 TYR cc_start: 0.8255 (m-80) cc_final: 0.8016 (m-80)
REVERT: A  929 ARG cc_start: 0.8559 (ttp-110) cc_final: 0.8290 (mtp180)
REVERT: A  957 MET cc_start: 0.8970 (tpt) cc_final: 0.8616 (tpt)
REVERT: A  973 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7770 (tm-30)
REVERT: A 1040 ARG cc_start: 0.8509 (ttp80) cc_final: 0.8077 (ttm-80)
REVERT: B  433 MET cc_start: 0.7602 (ptp) cc_final: 0.7326 (ptp)
REVERT: B  454 LYS cc_start: 0.9324 (mmmt) cc_final: 0.8918 (mmtt)
REVERT: B  503 LYS cc_start: 0.9109 (tttm) cc_final: 0.8784 (tptp)
REVERT: B  684 ARG cc_start: 0.6033 (mtp85) cc_final: 0.5809 (mtp180)
REVERT: B  916 TYR cc_start: 0.7926 (m-80) cc_final: 0.7101 (m-80)
REVERT: B  973 GLU cc_start: 0.8455 (tm-30) cc_final: 0.7989 (tm-30)
REVERT: B 1040 ARG cc_start: 0.8484 (ttp80) cc_final: 0.8076 (ttm-80)
  outliers start: 19
  outliers final: 13
  residues processed: 99
  average time/residue: 0.6764
  time to fit residues: 72.2837
Evaluate side-chains
  97 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  931 ILE
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue 1138 LYS
Chi-restraints excluded: chain A residue 1153 ASP
Chi-restraints excluded: chain B residue  522 THR
Chi-restraints excluded: chain B residue  801 ILE
Chi-restraints excluded: chain B residue  964 ILE
Chi-restraints excluded: chain B residue 1118 LEU
Chi-restraints excluded: chain B residue 1153 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 55 optimal weight:    0.4980
   chunk 69 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 130 optimal weight:    0.9980
   chunk 139 optimal weight:    0.7980
   chunk 120 optimal weight:    0.0050
   chunk 64 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 79 optimal weight:    0.4980
   chunk 47 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
B 981 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.097747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.071216 restraints weight = 35290.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 3.18
r_work: 0.2891 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2944
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2944 r_free = 0.2944    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2944 r_free = 0.2944    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2944
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12516  Z= 0.116
  Angle     :  0.491   8.601  16911  Z= 0.257
  Chirality :  0.041   0.161   1827
  Planarity :  0.004   0.055   2157
  Dihedral  :  3.941  20.184   1671
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 10.39 %
    Favored  : 88.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.22), residues: 1497
  helix:  1.82 (0.20), residues: 675
  sheet: -0.49 (0.38), residues: 218
  loop : -0.30 (0.24), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B 929 
 TYR   0.015   0.001   TYR B 858 
 PHE   0.015   0.001   PHE A 559 
 TRP   0.007   0.001   TRP A1189 
 HIS   0.003   0.001   HIS B 887 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (12516)
  covalent geometry    : angle       0.49150 (16911)
  hydrogen bonds       : bond        0.03976 (  583)
  hydrogen bonds       : angle       4.04921 ( 1656)

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

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

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.451 
Fit side-chains
REVERT: A  433 MET cc_start: 0.7588 (ptp) cc_final: 0.7356 (ptp)
REVERT: A  454 LYS cc_start: 0.9181 (mmmm) cc_final: 0.8930 (mmmt)
REVERT: A  523 GLN cc_start: 0.7724 (tm-30) cc_final: 0.7439 (mm-40)
REVERT: A  610 THR cc_start: 0.8645 (m) cc_final: 0.8403 (t)
REVERT: A  684 ARG cc_start: 0.5972 (mtp85) cc_final: 0.5633 (mtp180)
REVERT: A  916 TYR cc_start: 0.8198 (m-80) cc_final: 0.7956 (m-80)
REVERT: A  957 MET cc_start: 0.8908 (tpt) cc_final: 0.8575 (tpt)
REVERT: A  973 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7711 (tm-30)
REVERT: A 1040 ARG cc_start: 0.8388 (ttp80) cc_final: 0.7956 (ttm-80)
REVERT: B  433 MET cc_start: 0.7495 (ptp) cc_final: 0.7209 (ptp)
REVERT: B  503 LYS cc_start: 0.9104 (tttm) cc_final: 0.8771 (tptp)
REVERT: B  684 ARG cc_start: 0.5891 (mtp85) cc_final: 0.5673 (mtp180)
REVERT: B  916 TYR cc_start: 0.7938 (m-80) cc_final: 0.7491 (m-80)
REVERT: B  973 GLU cc_start: 0.8411 (tm-30) cc_final: 0.7929 (tm-30)
REVERT: B 1040 ARG cc_start: 0.8389 (ttp80) cc_final: 0.7976 (ttm-80)
  outliers start: 18
  outliers final: 10
  residues processed: 94
  average time/residue: 0.6463
  time to fit residues: 65.7602
Evaluate side-chains
  92 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain A residue  756 MET
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue 1153 ASP
Chi-restraints excluded: chain B residue  522 THR
Chi-restraints excluded: chain B residue  964 ILE
Chi-restraints excluded: chain B residue 1153 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 12 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9990
   chunk 108 optimal weight:    0.0670
   chunk 121 optimal weight:    0.0670
   chunk 25 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 128 optimal weight:    0.9990
   chunk 98 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 5 optimal weight:    4.9990
   chunk 115 optimal weight:    0.3980
   overall best weight:    0.3056

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.099093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.072961 restraints weight = 30432.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 3.01
r_work: 0.2921 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2989
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2989 r_free = 0.2989    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2989 r_free = 0.2989    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2989
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.2454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  12516  Z= 0.102
  Angle     :  0.481   9.000  16911  Z= 0.250
  Chirality :  0.040   0.158   1827
  Planarity :  0.004   0.057   2157
  Dihedral  :  3.788  18.969   1671
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 10.69 %
    Favored  : 87.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.22), residues: 1497
  helix:  1.88 (0.20), residues: 675
  sheet: -0.36 (0.39), residues: 214
  loop : -0.22 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B 929 
 TYR   0.013   0.001   TYR A 920 
 PHE   0.009   0.001   PHE A 990 
 TRP   0.007   0.001   TRP A1189 
 HIS   0.002   0.000   HIS B 887 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 (12516)
  covalent geometry    : angle       0.48140 (16911)
  hydrogen bonds       : bond        0.03712 (  583)
  hydrogen bonds       : angle       3.99667 ( 1656)

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

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

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.458 
Fit side-chains
REVERT: A  433 MET cc_start: 0.7437 (ptp) cc_final: 0.7197 (ptp)
REVERT: A  454 LYS cc_start: 0.9166 (mmmm) cc_final: 0.8926 (mmmm)
REVERT: A  610 THR cc_start: 0.8576 (m) cc_final: 0.8353 (t)
REVERT: A  673 GLU cc_start: 0.7162 (pm20) cc_final: 0.6960 (pm20)
REVERT: A  684 ARG cc_start: 0.5970 (mtp85) cc_final: 0.5625 (mtp180)
REVERT: A  916 TYR cc_start: 0.8152 (m-80) cc_final: 0.7923 (m-80)
REVERT: A  929 ARG cc_start: 0.8492 (ttp-110) cc_final: 0.8172 (mtp180)
REVERT: A  957 MET cc_start: 0.8908 (tpt) cc_final: 0.8693 (tpt)
REVERT: A 1040 ARG cc_start: 0.8283 (ttp80) cc_final: 0.7851 (ttm-80)
REVERT: B  433 MET cc_start: 0.7346 (ptp) cc_final: 0.7125 (ptp)
REVERT: B  454 LYS cc_start: 0.9347 (mmmt) cc_final: 0.8859 (mmmm)
REVERT: B  503 LYS cc_start: 0.9101 (tttm) cc_final: 0.8778 (tptp)
REVERT: B  684 ARG cc_start: 0.5769 (mtp85) cc_final: 0.5562 (mtp180)
REVERT: B  916 TYR cc_start: 0.7904 (m-80) cc_final: 0.7410 (m-80)
REVERT: B  973 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7882 (tm-30)
REVERT: B 1040 ARG cc_start: 0.8279 (ttp80) cc_final: 0.7834 (ttm-80)
  outliers start: 19
  outliers final: 12
  residues processed: 92
  average time/residue: 0.6937
  time to fit residues: 69.0535
Evaluate side-chains
  92 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain A residue  756 MET
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  931 ILE
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue 1153 ASP
Chi-restraints excluded: chain B residue  505 LEU
Chi-restraints excluded: chain B residue  648 LEU
Chi-restraints excluded: chain B residue  701 ASP
Chi-restraints excluded: chain B residue  964 ILE
Chi-restraints excluded: chain B residue 1153 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 127 optimal weight:    5.9990
   chunk 43 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 148 optimal weight:    0.7980
   chunk 133 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 67 optimal weight:    0.0870
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.6358

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.097440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.070387 restraints weight = 45918.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 3.61
r_work: 0.2854 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2926
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2926 r_free = 0.2926    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2926 r_free = 0.2926    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2926
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12516  Z= 0.127
  Angle     :  0.502   9.083  16911  Z= 0.261
  Chirality :  0.041   0.222   1827
  Planarity :  0.004   0.052   2157
  Dihedral  :  3.877  19.710   1671
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 11.37 %
    Favored  : 87.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.22), residues: 1497
  helix:  1.88 (0.20), residues: 673
  sheet: -0.37 (0.38), residues: 216
  loop : -0.21 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG B 929 
 TYR   0.015   0.001   TYR B 858 
 PHE   0.012   0.001   PHE A 559 
 TRP   0.006   0.001   TRP A1189 
 HIS   0.003   0.001   HIS B 887 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (12516)
  covalent geometry    : angle       0.50206 (16911)
  hydrogen bonds       : bond        0.03939 (  583)
  hydrogen bonds       : angle       4.00848 ( 1656)

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

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

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.456 
Fit side-chains
REVERT: A  433 MET cc_start: 0.7512 (ptp) cc_final: 0.7287 (ptp)
REVERT: A  454 LYS cc_start: 0.9177 (mmmm) cc_final: 0.8942 (mmmm)
REVERT: A  523 GLN cc_start: 0.7771 (tm-30) cc_final: 0.7513 (mm-40)
REVERT: A  610 THR cc_start: 0.8585 (m) cc_final: 0.8354 (t)
REVERT: A  684 ARG cc_start: 0.5992 (mtp85) cc_final: 0.5686 (mtp180)
REVERT: A  916 TYR cc_start: 0.8168 (m-80) cc_final: 0.7959 (m-80)
REVERT: A  957 MET cc_start: 0.8907 (tpt) cc_final: 0.8591 (tpt)
REVERT: A 1040 ARG cc_start: 0.8350 (ttp80) cc_final: 0.7887 (ttm-80)
REVERT: B  433 MET cc_start: 0.7431 (ptp) cc_final: 0.7145 (ptp)
REVERT: B  454 LYS cc_start: 0.9373 (mmmt) cc_final: 0.8919 (mmtp)
REVERT: B  503 LYS cc_start: 0.9089 (tttm) cc_final: 0.8796 (tptp)
REVERT: B  684 ARG cc_start: 0.5942 (mtp85) cc_final: 0.5728 (mtp180)
REVERT: B  916 TYR cc_start: 0.7923 (m-80) cc_final: 0.7475 (m-80)
REVERT: B  973 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7912 (tm-30)
REVERT: B 1040 ARG cc_start: 0.8362 (ttp80) cc_final: 0.7897 (ttm-80)
  outliers start: 17
  outliers final: 13
  residues processed: 90
  average time/residue: 0.6917
  time to fit residues: 67.3482
Evaluate side-chains
  94 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  931 ILE
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue 1153 ASP
Chi-restraints excluded: chain B residue  522 THR
Chi-restraints excluded: chain B residue  648 LEU
Chi-restraints excluded: chain B residue  678 SER
Chi-restraints excluded: chain B residue  701 ASP
Chi-restraints excluded: chain B residue  803 VAL
Chi-restraints excluded: chain B residue  964 ILE
Chi-restraints excluded: chain B residue 1153 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 144 optimal weight:    0.9980
   chunk 88 optimal weight:    0.8980
   chunk 112 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0570
   chunk 134 optimal weight:    0.5980
   chunk 96 optimal weight:    0.5980
   chunk 2 optimal weight:    4.9990
   chunk 64 optimal weight:    0.7980
   chunk 102 optimal weight:    0.3980
   chunk 103 optimal weight:    0.7980
   chunk 107 optimal weight:    0.5980
   overall best weight:    0.4498

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.098144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.071559 restraints weight = 39940.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 3.38
r_work: 0.2882 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2950
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2950 r_free = 0.2950    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2950 r_free = 0.2950    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2950
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12516  Z= 0.110
  Angle     :  0.493   8.766  16911  Z= 0.255
  Chirality :  0.040   0.205   1827
  Planarity :  0.004   0.057   2157
  Dihedral  :  3.835  19.282   1671
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 11.52 %
    Favored  : 87.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.22), residues: 1497
  helix:  1.87 (0.20), residues: 675
  sheet: -0.32 (0.38), residues: 216
  loop : -0.18 (0.25), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 929 
 TYR   0.014   0.001   TYR B 858 
 PHE   0.011   0.001   PHE A 559 
 TRP   0.006   0.001   TRP A1189 
 HIS   0.003   0.000   HIS B 887 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (12516)
  covalent geometry    : angle       0.49254 (16911)
  hydrogen bonds       : bond        0.03806 (  583)
  hydrogen bonds       : angle       3.99507 ( 1656)

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

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

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A  433 MET cc_start: 0.7508 (ptp) cc_final: 0.7302 (ptp)
REVERT: A  454 LYS cc_start: 0.9162 (mmmm) cc_final: 0.8941 (mmmm)
REVERT: A  523 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7522 (mm-40)
REVERT: A  610 THR cc_start: 0.8589 (m) cc_final: 0.8362 (t)
REVERT: A  684 ARG cc_start: 0.6025 (mtp85) cc_final: 0.5731 (mtp180)
REVERT: A  916 TYR cc_start: 0.8151 (m-80) cc_final: 0.7918 (m-80)
REVERT: A  957 MET cc_start: 0.8909 (tpt) cc_final: 0.8595 (tpt)
REVERT: A 1040 ARG cc_start: 0.8331 (ttp80) cc_final: 0.7890 (ttm-80)
REVERT: B  433 MET cc_start: 0.7401 (ptp) cc_final: 0.7101 (ptp)
REVERT: B  454 LYS cc_start: 0.9368 (mmmt) cc_final: 0.8916 (mmtp)
REVERT: B  503 LYS cc_start: 0.9108 (tttm) cc_final: 0.8816 (tptp)
REVERT: B  684 ARG cc_start: 0.5889 (mtp85) cc_final: 0.5668 (mtp180)
REVERT: B  916 TYR cc_start: 0.7920 (m-80) cc_final: 0.7477 (m-80)
REVERT: B  973 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7887 (tm-30)
REVERT: B 1040 ARG cc_start: 0.8328 (ttp80) cc_final: 0.7880 (ttm-80)
  outliers start: 13
  outliers final: 13
  residues processed: 89
  average time/residue: 0.5831
  time to fit residues: 56.1989
Evaluate side-chains
  91 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  931 ILE
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue 1153 ASP
Chi-restraints excluded: chain B residue  522 THR
Chi-restraints excluded: chain B residue  648 LEU
Chi-restraints excluded: chain B residue  678 SER
Chi-restraints excluded: chain B residue  701 ASP
Chi-restraints excluded: chain B residue  803 VAL
Chi-restraints excluded: chain B residue  964 ILE
Chi-restraints excluded: chain B residue 1153 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 100 optimal weight:    0.6980
   chunk 139 optimal weight:    3.9990
   chunk 109 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0040
   chunk 148 optimal weight:    0.6980
   chunk 136 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9980
   chunk 130 optimal weight:    0.9980
   chunk 132 optimal weight:    1.9990
   overall best weight:    0.5792

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.097463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.071478 restraints weight = 29440.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 2.93
r_work: 0.2900 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2957
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2957
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.2550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12516  Z= 0.122
  Angle     :  0.496   8.622  16911  Z= 0.258
  Chirality :  0.041   0.236   1827
  Planarity :  0.004   0.060   2157
  Dihedral  :  3.865  19.573   1671
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 11.14 %
    Favored  : 87.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.22), residues: 1497
  helix:  1.89 (0.20), residues: 673
  sheet: -0.34 (0.38), residues: 216
  loop : -0.20 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG A 929 
 TYR   0.015   0.001   TYR B 858 
 PHE   0.011   0.001   PHE A 990 
 TRP   0.006   0.001   TRP A1189 
 HIS   0.003   0.001   HIS B 887 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (12516)
  covalent geometry    : angle       0.49608 (16911)
  hydrogen bonds       : bond        0.03898 (  583)
  hydrogen bonds       : angle       3.99761 ( 1656)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4471.22 seconds
wall clock time: 77 minutes 7.35 seconds (4627.35 seconds total)