Starting phenix.real_space_refine
on Wed Jul 30 12:49:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j8a_36065/07_2025/8j8a_36065.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j8a_36065/07_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_36065/07_2025/8j8a_36065.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j8a_36065/07_2025/8j8a_36065.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j8a_36065/07_2025/8j8a_36065.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j8a_36065/07_2025/8j8a_36065.cif"
  }
  resolution = 2.51
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.009
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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 10.52, per 1000 atoms: 0.86
  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: 2.74
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  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: 1.50
  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: 3.95

  Time building geometry restraints manager: 3.29 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:             4.640
  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:          0.500
  Check model and map are aligned:         0.100
  Set scattering table:                    0.110
  Process input model:                     33.520
  Find NCS groups from input model:        0.460
  Set up NCS constraints:                  0.060
  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:12.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.410
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.21), 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
 TRP   0.016   0.002   TRP A 820 
 HIS   0.004   0.001   HIS B 566 
 PHE   0.013   0.001   PHE A1107 
 TYR   0.015   0.001   TYR B 858 
 ARG   0.009   0.001   ARG B 526 

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

*********************** 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  : 1.452 
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: 1.2826
  time to fit residues: 177.5152
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  : 1.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    0.4980
   chunk 113 optimal weight:    0.0030
   chunk 63 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 76 optimal weight:    7.9990
   chunk 60 optimal weight:    1.9990
   chunk 117 optimal weight:    0.5980
   chunk 45 optimal weight:    0.5980
   chunk 71 optimal weight:    0.7980
   chunk 87 optimal weight:    3.9990
   chunk 136 optimal weight:    2.9990
   overall best weight:    0.4990

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 523 GLN
B 733 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.100834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.074756 restraints weight = 26534.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 2.83
r_work: 0.2967 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3020
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3020 r_free = 0.3020    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3020 r_free = 0.3020    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3020
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.1227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  12516  Z= 0.136
  Angle     :  0.535   6.586  16911  Z= 0.289
  Chirality :  0.042   0.175   1827
  Planarity :  0.004   0.046   2157
  Dihedral  :  4.055  21.316   1671
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  5.69 %
    Favored  : 93.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.22), residues: 1497
  helix:  1.84 (0.20), residues: 677
  sheet:  0.01 (0.37), residues: 214
  loop : -0.14 (0.24), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1170 
 HIS   0.003   0.001   HIS B1051 
 PHE   0.018   0.001   PHE A 559 
 TYR   0.015   0.001   TYR A 920 
 ARG   0.011   0.001   ARG B 929 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05106 (  583)
  hydrogen bonds       : angle       4.63234 ( 1656)
  covalent geometry    : bond        0.00301 (12516)
  covalent geometry    : angle       0.53469 (16911)

*********************** 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
  107 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 1.629 
Fit side-chains
REVERT: A  433 MET cc_start: 0.7713 (ptp) cc_final: 0.7480 (ptp)
REVERT: A  916 TYR cc_start: 0.8297 (m-80) cc_final: 0.7822 (m-80)
REVERT: A  957 MET cc_start: 0.8802 (tpt) cc_final: 0.8503 (tpt)
REVERT: B  433 MET cc_start: 0.7676 (ptp) cc_final: 0.7460 (ptp)
REVERT: B  503 LYS cc_start: 0.9158 (tttm) cc_final: 0.8865 (tptp)
REVERT: B  916 TYR cc_start: 0.7744 (m-80) cc_final: 0.7227 (m-80)
REVERT: B  973 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8052 (tm-30)
  outliers start: 14
  outliers final: 4
  residues processed: 98
  average time/residue: 1.3550
  time to fit residues: 144.5229
Evaluate side-chains
  87 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 1.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue 1153 ASP
Chi-restraints excluded: chain B residue  647 GLU
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 108 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 124 optimal weight:    1.9990
   chunk 119 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 127 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 145 optimal weight:    0.5980
   chunk 24 optimal weight:    6.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 733 ASN
** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.098529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.072129 restraints weight = 30293.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 3.01
r_work: 0.2912 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2966
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2966 r_free = 0.2966    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2966 r_free = 0.2966    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2966
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.1732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12516  Z= 0.142
  Angle     :  0.509   6.469  16911  Z= 0.271
  Chirality :  0.042   0.169   1827
  Planarity :  0.004   0.046   2157
  Dihedral  :  4.082  20.738   1671
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  7.20 %
    Favored  : 91.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.22), residues: 1497
  helix:  1.75 (0.20), residues: 677
  sheet: -0.38 (0.38), residues: 198
  loop : -0.17 (0.24), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B1170 
 HIS   0.003   0.001   HIS A 752 
 PHE   0.014   0.001   PHE B 990 
 TYR   0.016   0.001   TYR B 858 
 ARG   0.010   0.001   ARG B 929 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04581 (  583)
  hydrogen bonds       : angle       4.24447 ( 1656)
  covalent geometry    : bond        0.00333 (12516)
  covalent geometry    : angle       0.50924 (16911)

*********************** 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
  103 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 1.587 
Fit side-chains
   revert: symmetry clash
REVERT: A  433 MET cc_start: 0.7708 (ptp) cc_final: 0.7448 (ptp)
REVERT: A  957 MET cc_start: 0.8907 (tpt) cc_final: 0.8681 (tpt)
REVERT: A  985 ARG cc_start: 0.7865 (tpp80) cc_final: 0.7204 (tpp80)
REVERT: B  433 MET cc_start: 0.7594 (ptp) cc_final: 0.7309 (ptp)
REVERT: B  503 LYS cc_start: 0.9116 (tttm) cc_final: 0.8676 (tppt)
REVERT: B  684 ARG cc_start: 0.6001 (mtp85) cc_final: 0.5721 (mtp180)
REVERT: B  916 TYR cc_start: 0.7774 (m-80) cc_final: 0.7292 (m-80)
REVERT: B  973 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8005 (tm-30)
REVERT: B  988 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8361 (mm-30)
  outliers start: 18
  outliers final: 7
  residues processed: 93
  average time/residue: 1.4766
  time to fit residues: 148.9614
Evaluate side-chains
  88 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 1.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue 1153 ASP
Chi-restraints excluded: chain B residue  415 VAL
Chi-restraints excluded: chain B residue  964 ILE
Chi-restraints excluded: chain B residue  988 GLU
Chi-restraints excluded: chain B residue 1024 GLU
Chi-restraints excluded: chain B residue 1153 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 140 optimal weight:    0.1980
   chunk 109 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 114 optimal weight:    0.5980
   chunk 113 optimal weight:    0.2980
   chunk 100 optimal weight:    4.9990
   chunk 98 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9990
   chunk 144 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 105 optimal weight:    0.9990
   overall best weight:    0.5382

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

Flipped N/Q/H residues before XYZ refinement:
A 851 ASN
B 981 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.098786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.071913 restraints weight = 40136.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.3046 rms_B_bonded: 3.41
r_work: 0.2910 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2930
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    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 = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2930
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.1979

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= 0.120
  Angle     :  0.485   7.099  16911  Z= 0.257
  Chirality :  0.041   0.167   1827
  Planarity :  0.004   0.045   2157
  Dihedral  :  3.955  19.097   1671
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  8.34 %
    Favored  : 89.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.22), residues: 1497
  helix:  1.78 (0.20), residues: 675
  sheet: -0.30 (0.37), residues: 218
  loop : -0.23 (0.24), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B1170 
 HIS   0.003   0.001   HIS B 887 
 PHE   0.009   0.001   PHE A 990 
 TYR   0.014   0.001   TYR B 858 
 ARG   0.010   0.000   ARG B 929 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04157 (  583)
  hydrogen bonds       : angle       4.14407 ( 1656)
  covalent geometry    : bond        0.00277 (12516)
  covalent geometry    : angle       0.48511 (16911)

*********************** 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
  107 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 1.545 
Fit side-chains
REVERT: A  433 MET cc_start: 0.7715 (ptp) cc_final: 0.7487 (ptp)
REVERT: A  454 LYS cc_start: 0.9259 (mmmt) cc_final: 0.8828 (mmmm)
REVERT: A  957 MET cc_start: 0.8959 (tpt) cc_final: 0.8719 (tpt)
REVERT: A 1040 ARG cc_start: 0.8487 (ttp80) cc_final: 0.8049 (ttm-80)
REVERT: B  433 MET cc_start: 0.7604 (ptp) cc_final: 0.7332 (ptp)
REVERT: B  503 LYS cc_start: 0.9119 (tttm) cc_final: 0.8785 (tptp)
REVERT: B  684 ARG cc_start: 0.5930 (mtp85) cc_final: 0.5626 (mtp180)
REVERT: B  916 TYR cc_start: 0.7853 (m-80) cc_final: 0.7406 (m-80)
REVERT: B  973 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8069 (tm-30)
REVERT: B 1040 ARG cc_start: 0.8448 (ttp80) cc_final: 0.8035 (ttm-80)
  outliers start: 22
  outliers final: 13
  residues processed: 95
  average time/residue: 1.5379
  time to fit residues: 162.4490
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  : 1.499 
-------------------------------------------------------------------------------
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  931 ILE
Chi-restraints excluded: chain A residue 1153 ASP
Chi-restraints excluded: chain B residue  415 VAL
Chi-restraints excluded: chain B residue  505 LEU
Chi-restraints excluded: chain B residue  522 THR
Chi-restraints excluded: chain B residue  678 SER
Chi-restraints excluded: chain B residue  964 ILE
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 90 optimal weight:    0.9980
   chunk 84 optimal weight:    5.9990
   chunk 146 optimal weight:    2.9990
   chunk 10 optimal weight:    0.4980
   chunk 38 optimal weight:    0.0000
   chunk 0 optimal weight:    6.9990
   chunk 96 optimal weight:    6.9990
   chunk 13 optimal weight:    4.9990
   chunk 86 optimal weight:    3.9990
   chunk 104 optimal weight:    0.6980
   chunk 47 optimal weight:    0.6980
   overall best weight:    0.5784

-------------------------------------------------------------------------------
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 = 0.3507 r_free = 0.3507 target = 0.098293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.071276 restraints weight = 39397.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 3.37
r_work: 0.2930 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2930
-------------------------------------------------------------------------------
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 = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2944
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2125

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= 0.122
  Angle     :  0.479   8.188  16911  Z= 0.254
  Chirality :  0.041   0.168   1827
  Planarity :  0.004   0.045   2157
  Dihedral  :  3.923  19.643   1671
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  8.64 %
    Favored  : 89.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.22), residues: 1497
  helix:  1.80 (0.20), residues: 675
  sheet: -0.37 (0.37), residues: 218
  loop : -0.26 (0.24), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B1170 
 HIS   0.003   0.001   HIS B 887 
 PHE   0.010   0.001   PHE A 990 
 TYR   0.015   0.001   TYR B 858 
 ARG   0.011   0.000   ARG B 929 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04088 (  583)
  hydrogen bonds       : angle       4.07212 ( 1656)
  covalent geometry    : bond        0.00281 (12516)
  covalent geometry    : angle       0.47891 (16911)

*********************** 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
  106 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 82
  time to evaluate  : 1.519 
Fit side-chains
REVERT: A  433 MET cc_start: 0.7658 (ptp) cc_final: 0.7423 (ptp)
REVERT: A  916 TYR cc_start: 0.8030 (m-80) cc_final: 0.7316 (m-80)
REVERT: A  957 MET cc_start: 0.8921 (tpt) cc_final: 0.8675 (tpt)
REVERT: A  985 ARG cc_start: 0.7380 (tpp80) cc_final: 0.6952 (mtm-85)
REVERT: A 1040 ARG cc_start: 0.8436 (ttp80) cc_final: 0.7992 (ttm-80)
REVERT: B  433 MET cc_start: 0.7507 (ptp) cc_final: 0.7226 (ptp)
REVERT: B  503 LYS cc_start: 0.9107 (tttm) cc_final: 0.8760 (tptp)
REVERT: B  673 GLU cc_start: 0.7212 (pm20) cc_final: 0.7010 (pm20)
REVERT: B  684 ARG cc_start: 0.5888 (mtp85) cc_final: 0.5611 (mtp180)
REVERT: B  916 TYR cc_start: 0.7811 (m-80) cc_final: 0.7020 (m-80)
REVERT: B  973 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7954 (tm-30)
REVERT: B 1040 ARG cc_start: 0.8407 (ttp80) cc_final: 0.7976 (ttm-80)
  outliers start: 24
  outliers final: 14
  residues processed: 96
  average time/residue: 1.4469
  time to fit residues: 151.2771
Evaluate side-chains
  96 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 1.502 
-------------------------------------------------------------------------------
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  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  415 VAL
Chi-restraints excluded: chain B residue  522 THR
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 1153 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 129 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0170
   chunk 20 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 101 optimal weight:    0.7980
   chunk 112 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 96 optimal weight:    0.8980
   chunk 75 optimal weight:    5.9990
   chunk 106 optimal weight:    0.7980
   overall best weight:    0.7018

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

Flipped N/Q/H residues before XYZ refinement:
A1010 HIS
B 981 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.097483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.070450 restraints weight = 40218.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 3.40
r_work: 0.2909 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2928
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2928 r_free = 0.2928    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2928 r_free = 0.2928    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2928
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.2265

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= 0.135
  Angle     :  0.501   9.343  16911  Z= 0.262
  Chirality :  0.041   0.163   1827
  Planarity :  0.004   0.046   2157
  Dihedral  :  3.957  20.168   1671
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 10.08 %
    Favored  : 88.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.22), residues: 1497
  helix:  1.80 (0.20), residues: 675
  sheet: -0.41 (0.38), residues: 218
  loop : -0.28 (0.24), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B1170 
 HIS   0.003   0.001   HIS B 887 
 PHE   0.013   0.001   PHE A 559 
 TYR   0.016   0.001   TYR B 858 
 ARG   0.013   0.001   ARG A 929 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04122 (  583)
  hydrogen bonds       : angle       4.07444 ( 1656)
  covalent geometry    : bond        0.00318 (12516)
  covalent geometry    : angle       0.50097 (16911)

*********************** 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
  106 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 1.480 
Fit side-chains
REVERT: A  433 MET cc_start: 0.7709 (ptp) cc_final: 0.7464 (ptp)
REVERT: A  454 LYS cc_start: 0.9208 (mmmm) cc_final: 0.8867 (mmmm)
REVERT: A  684 ARG cc_start: 0.5916 (mtp85) cc_final: 0.5569 (mtp180)
REVERT: A  916 TYR cc_start: 0.8016 (m-80) cc_final: 0.7247 (m-80)
REVERT: A  929 ARG cc_start: 0.8538 (ttp-110) cc_final: 0.8235 (mtp180)
REVERT: A  957 MET cc_start: 0.8923 (tpt) cc_final: 0.8660 (tpt)
REVERT: A  973 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7850 (tm-30)
REVERT: A  985 ARG cc_start: 0.7465 (tpp80) cc_final: 0.7041 (mtm-85)
REVERT: A 1040 ARG cc_start: 0.8448 (ttp80) cc_final: 0.8004 (ttm-80)
REVERT: B  433 MET cc_start: 0.7592 (ptp) cc_final: 0.7328 (ptp)
REVERT: B  454 LYS cc_start: 0.9307 (mmmt) cc_final: 0.8770 (mmmm)
REVERT: B  503 LYS cc_start: 0.9105 (tttm) cc_final: 0.8762 (tptp)
REVERT: B  673 GLU cc_start: 0.7260 (pm20) cc_final: 0.7027 (pm20)
REVERT: B  684 ARG cc_start: 0.5889 (mtp85) cc_final: 0.5673 (mtp180)
REVERT: B  801 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8286 (tp)
REVERT: B  916 TYR cc_start: 0.7896 (m-80) cc_final: 0.7088 (m-80)
REVERT: B  973 GLU cc_start: 0.8459 (tm-30) cc_final: 0.7986 (tm-30)
REVERT: B 1040 ARG cc_start: 0.8425 (ttp80) cc_final: 0.8005 (ttm-80)
  outliers start: 20
  outliers final: 14
  residues processed: 97
  average time/residue: 1.4532
  time to fit residues: 153.1184
Evaluate side-chains
  99 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 1.454 
-------------------------------------------------------------------------------
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  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  415 VAL
Chi-restraints excluded: chain B residue  505 LEU
Chi-restraints excluded: chain B residue  522 THR
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 1153 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 130 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 66 optimal weight:    0.0370
   chunk 131 optimal weight:    2.9990
   chunk 54 optimal weight:    0.4980
   chunk 10 optimal weight:    0.2980
   chunk 76 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.5658

-------------------------------------------------------------------------------
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 = 0.097745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.070508 restraints weight = 47582.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 3.67
r_work: 0.2909 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2921
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2921
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.2338

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= 0.121
  Angle     :  0.495   8.478  16911  Z= 0.257
  Chirality :  0.041   0.161   1827
  Planarity :  0.004   0.050   2157
  Dihedral  :  3.921  19.849   1671
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 10.61 %
    Favored  : 87.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.22), residues: 1497
  helix:  1.83 (0.20), residues: 675
  sheet: -0.43 (0.38), residues: 218
  loop : -0.28 (0.24), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1189 
 HIS   0.003   0.001   HIS B 887 
 PHE   0.011   0.001   PHE A 559 
 TYR   0.015   0.001   TYR B 858 
 ARG   0.012   0.000   ARG B 929 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04001 (  583)
  hydrogen bonds       : angle       4.04073 ( 1656)
  covalent geometry    : bond        0.00283 (12516)
  covalent geometry    : angle       0.49451 (16911)

*********************** 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
  105 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 1.642 
Fit side-chains
REVERT: A  433 MET cc_start: 0.7632 (ptp) cc_final: 0.7393 (ptp)
REVERT: A  454 LYS cc_start: 0.9192 (mmmm) cc_final: 0.8911 (mmmm)
REVERT: A  523 GLN cc_start: 0.7734 (tm-30) cc_final: 0.7445 (mm-40)
REVERT: A  684 ARG cc_start: 0.5978 (mtp85) cc_final: 0.5698 (mtp180)
REVERT: A  957 MET cc_start: 0.8882 (tpt) cc_final: 0.8533 (tpt)
REVERT: A  973 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7828 (tm-30)
REVERT: A  985 ARG cc_start: 0.7489 (tpp80) cc_final: 0.7075 (mtm-85)
REVERT: A 1040 ARG cc_start: 0.8399 (ttp80) cc_final: 0.7945 (ttm-80)
REVERT: B  433 MET cc_start: 0.7553 (ptp) cc_final: 0.7272 (ptp)
REVERT: B  454 LYS cc_start: 0.9332 (mmmt) cc_final: 0.8863 (mmtt)
REVERT: B  503 LYS cc_start: 0.9102 (tttm) cc_final: 0.8761 (tptp)
REVERT: B  673 GLU cc_start: 0.7235 (pm20) cc_final: 0.7003 (pm20)
REVERT: B  684 ARG cc_start: 0.5865 (mtp85) cc_final: 0.5654 (mtp180)
REVERT: B  801 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8254 (tp)
REVERT: B  916 TYR cc_start: 0.7889 (m-80) cc_final: 0.7065 (m-80)
REVERT: B  973 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7939 (tm-30)
REVERT: B 1040 ARG cc_start: 0.8381 (ttp80) cc_final: 0.7957 (ttm-80)
  outliers start: 19
  outliers final: 12
  residues processed: 96
  average time/residue: 1.4336
  time to fit residues: 149.5257
Evaluate side-chains
  96 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 1.480 
-------------------------------------------------------------------------------
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  415 VAL
Chi-restraints excluded: chain B residue  505 LEU
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 1153 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 134 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9980
   chunk 64 optimal weight:    0.8980
   chunk 129 optimal weight:    0.0010
   chunk 106 optimal weight:    0.5980
   chunk 118 optimal weight:    0.8980
   chunk 23 optimal weight:    9.9990
   chunk 21 optimal weight:    0.6980
   chunk 76 optimal weight:    0.7980
   overall best weight:    0.5786

-------------------------------------------------------------------------------
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 = 0.3495 r_free = 0.3495 target = 0.097583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.071310 restraints weight = 30308.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 2.98
r_work: 0.2903 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2959
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2959
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.2423

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     :  0.491   8.590  16911  Z= 0.255
  Chirality :  0.041   0.161   1827
  Planarity :  0.004   0.053   2157
  Dihedral  :  3.914  19.921   1671
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 10.54 %
    Favored  : 87.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.22), residues: 1497
  helix:  1.82 (0.20), residues: 677
  sheet: -0.42 (0.38), residues: 218
  loop : -0.25 (0.24), residues: 602

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03978 (  583)
  hydrogen bonds       : angle       4.03796 ( 1656)
  covalent geometry    : bond        0.00284 (12516)
  covalent geometry    : angle       0.49079 (16911)

*********************** 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
  105 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 1.680 
Fit side-chains
REVERT: A  433 MET cc_start: 0.7591 (ptp) cc_final: 0.7343 (ptp)
REVERT: A  454 LYS cc_start: 0.9183 (mmmm) cc_final: 0.8947 (mmmt)
REVERT: A  673 GLU cc_start: 0.7216 (pm20) cc_final: 0.7007 (pm20)
REVERT: A  684 ARG cc_start: 0.6026 (mtp85) cc_final: 0.5732 (mtp180)
REVERT: A  916 TYR cc_start: 0.7915 (m-80) cc_final: 0.7592 (m-80)
REVERT: A  957 MET cc_start: 0.8897 (tpt) cc_final: 0.8553 (tpt)
REVERT: A  973 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7848 (tm-30)
REVERT: A  985 ARG cc_start: 0.7511 (tpp80) cc_final: 0.7113 (mtm-85)
REVERT: A 1040 ARG cc_start: 0.8393 (ttp80) cc_final: 0.7951 (ttm-80)
REVERT: B  433 MET cc_start: 0.7527 (ptp) cc_final: 0.7243 (ptp)
REVERT: B  503 LYS cc_start: 0.9117 (tttm) cc_final: 0.8792 (tptp)
REVERT: B  673 GLU cc_start: 0.7220 (pm20) cc_final: 0.6987 (pm20)
REVERT: B  684 ARG cc_start: 0.5877 (mtp85) cc_final: 0.5665 (mtp180)
REVERT: B  801 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8223 (tp)
REVERT: B  916 TYR cc_start: 0.7942 (m-80) cc_final: 0.7459 (m-80)
REVERT: B  973 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7926 (tm-30)
REVERT: B 1040 ARG cc_start: 0.8383 (ttp80) cc_final: 0.7933 (ttm-80)
  outliers start: 22
  outliers final: 15
  residues processed: 93
  average time/residue: 1.8496
  time to fit residues: 187.8581
Evaluate side-chains
  97 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 1.457 
-------------------------------------------------------------------------------
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  931 ILE
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue 1153 ASP
Chi-restraints excluded: chain B residue  415 VAL
Chi-restraints excluded: chain B residue  505 LEU
Chi-restraints excluded: chain B residue  522 THR
Chi-restraints excluded: chain B residue  678 SER
Chi-restraints excluded: chain B residue  801 ILE
Chi-restraints excluded: chain B residue  807 SER
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 7 optimal weight:    4.9990
   chunk 44 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0000
   chunk 135 optimal weight:    0.9980
   chunk 75 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0000
   chunk 129 optimal weight:    0.0000
   chunk 93 optimal weight:    0.9980
   overall best weight:    0.2792

-------------------------------------------------------------------------------
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 = 0.3519 r_free = 0.3519 target = 0.099006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.072376 restraints weight = 39835.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 3.38
r_work: 0.2901 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2970
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2970 r_free = 0.2970    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2970 r_free = 0.2970    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2970
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.2487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  12516  Z= 0.101
  Angle     :  0.479   8.924  16911  Z= 0.248
  Chirality :  0.040   0.159   1827
  Planarity :  0.004   0.058   2157
  Dihedral  :  3.793  18.997   1671
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 11.37 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.22), residues: 1497
  helix:  1.89 (0.20), residues: 677
  sheet: -0.35 (0.38), residues: 218
  loop : -0.24 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1189 
 HIS   0.002   0.000   HIS B 887 
 PHE   0.011   0.001   PHE A 559 
 TYR   0.013   0.001   TYR B 858 
 ARG   0.013   0.000   ARG B 929 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03706 (  583)
  hydrogen bonds       : angle       3.98952 ( 1656)
  covalent geometry    : bond        0.00226 (12516)
  covalent geometry    : angle       0.47883 (16911)

*********************** 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
  97 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 1.308 
Fit side-chains
REVERT: A  433 MET cc_start: 0.7466 (ptp) cc_final: 0.7211 (ptp)
REVERT: A  454 LYS cc_start: 0.9190 (mmmm) cc_final: 0.8978 (mmmt)
REVERT: A  523 GLN cc_start: 0.7738 (tm-30) cc_final: 0.7466 (mm-40)
REVERT: A  673 GLU cc_start: 0.7216 (pm20) cc_final: 0.7015 (pm20)
REVERT: A  916 TYR cc_start: 0.7897 (m-80) cc_final: 0.7573 (m-80)
REVERT: A  957 MET cc_start: 0.8870 (tpt) cc_final: 0.8555 (tpt)
REVERT: A  973 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7659 (tm-30)
REVERT: A  985 ARG cc_start: 0.7478 (tpp80) cc_final: 0.7074 (mtm-85)
REVERT: A 1040 ARG cc_start: 0.8321 (ttp80) cc_final: 0.7883 (ttm-80)
REVERT: B  433 MET cc_start: 0.7393 (ptp) cc_final: 0.7160 (ptp)
REVERT: B  454 LYS cc_start: 0.9355 (mmmt) cc_final: 0.8904 (mmtp)
REVERT: B  503 LYS cc_start: 0.9103 (tttm) cc_final: 0.8789 (tptp)
REVERT: B  673 GLU cc_start: 0.7200 (pm20) cc_final: 0.6990 (pm20)
REVERT: B  684 ARG cc_start: 0.5732 (mtp85) cc_final: 0.5530 (mtp180)
REVERT: B  916 TYR cc_start: 0.7915 (m-80) cc_final: 0.7437 (m-80)
REVERT: B  973 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7880 (tm-30)
REVERT: B 1040 ARG cc_start: 0.8306 (ttp80) cc_final: 0.7862 (ttm-80)
  outliers start: 14
  outliers final: 12
  residues processed: 91
  average time/residue: 1.5213
  time to fit residues: 149.6321
Evaluate side-chains
  90 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 1.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  756 MET
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  648 LEU
Chi-restraints excluded: chain B residue  678 SER
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 46 optimal weight:    0.0770
   chunk 89 optimal weight:    0.0570
   chunk 137 optimal weight:    0.8980
   chunk 81 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 126 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0970
   chunk 103 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.3654

-------------------------------------------------------------------------------
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 = 0.3535 r_free = 0.3535 target = 0.099249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.073060 restraints weight = 33150.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 3.16
r_work: 0.2976 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3005
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3005 r_free = 0.3005    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3005 r_free = 0.3005    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3005
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  12516  Z= 0.104
  Angle     :  0.477   8.734  16911  Z= 0.248
  Chirality :  0.040   0.236   1827
  Planarity :  0.004   0.059   2157
  Dihedral  :  3.766  18.983   1671
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 11.14 %
    Favored  : 87.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.22), residues: 1497
  helix:  1.88 (0.20), residues: 677
  sheet: -0.35 (0.38), residues: 218
  loop : -0.22 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1189 
 HIS   0.002   0.000   HIS B 887 
 PHE   0.010   0.001   PHE A 559 
 TYR   0.013   0.001   TYR B 858 
 ARG   0.014   0.000   ARG A 929 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03706 (  583)
  hydrogen bonds       : angle       3.95974 ( 1656)
  covalent geometry    : bond        0.00236 (12516)
  covalent geometry    : angle       0.47735 (16911)

********************** 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
  99 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 1.592 
Fit side-chains
REVERT: A  433 MET cc_start: 0.7535 (ptp) cc_final: 0.7296 (ptp)
REVERT: A  454 LYS cc_start: 0.9161 (mmmm) cc_final: 0.8933 (mmmm)
REVERT: A  523 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7505 (mm-40)
REVERT: A  673 GLU cc_start: 0.7240 (pm20) cc_final: 0.7025 (pm20)
REVERT: A  684 ARG cc_start: 0.5942 (mtp85) cc_final: 0.5607 (mtp180)
REVERT: A  916 TYR cc_start: 0.7908 (m-80) cc_final: 0.7587 (m-80)
REVERT: A  957 MET cc_start: 0.8877 (tpt) cc_final: 0.8573 (tpt)
REVERT: A  973 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7799 (tm-30)
REVERT: A  985 ARG cc_start: 0.7487 (tpp80) cc_final: 0.7109 (mtm-85)
REVERT: A 1040 ARG cc_start: 0.8314 (ttp80) cc_final: 0.7876 (ttm-80)
REVERT: B  433 MET cc_start: 0.7406 (ptp) cc_final: 0.7188 (ptp)
REVERT: B  454 LYS cc_start: 0.9352 (mmmt) cc_final: 0.8896 (mmtp)
REVERT: B  503 LYS cc_start: 0.9123 (tttm) cc_final: 0.8838 (tptp)
REVERT: B  673 GLU cc_start: 0.7198 (pm20) cc_final: 0.6981 (pm20)
REVERT: B  916 TYR cc_start: 0.7962 (m-80) cc_final: 0.7495 (m-80)
REVERT: B  973 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7933 (tm-30)
REVERT: B 1040 ARG cc_start: 0.8295 (ttp80) cc_final: 0.7848 (ttm-80)
  outliers start: 16
  outliers final: 12
  residues processed: 93
  average time/residue: 1.5610
  time to fit residues: 157.1754
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  : 1.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  756 MET
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  415 VAL
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  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 90 optimal weight:    0.6980
   chunk 143 optimal weight:    0.6980
   chunk 132 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 133 optimal weight:    0.9980
   chunk 134 optimal weight:    0.6980
   chunk 9 optimal weight:    5.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3506 r_free = 0.3506 target = 0.097416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.071137 restraints weight = 32619.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 3.12
r_work: 0.2938 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2967
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2967 r_free = 0.2967    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2967 r_free = 0.2967    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2967
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12516  Z= 0.135
  Angle     :  0.501   8.536  16911  Z= 0.261
  Chirality :  0.042   0.256   1827
  Planarity :  0.004   0.059   2157
  Dihedral  :  3.907  20.396   1671
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 11.45 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.22), residues: 1497
  helix:  1.85 (0.20), residues: 673
  sheet: -0.38 (0.38), residues: 220
  loop : -0.21 (0.25), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 820 
 HIS   0.003   0.001   HIS A 887 
 PHE   0.011   0.001   PHE A 990 
 TYR   0.015   0.001   TYR B 858 
 ARG   0.014   0.001   ARG A 929 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04017 (  583)
  hydrogen bonds       : angle       4.00583 ( 1656)
  covalent geometry    : bond        0.00321 (12516)
  covalent geometry    : angle       0.50080 (16911)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9380.87 seconds
wall clock time: 162 minutes 24.86 seconds (9744.86 seconds total)